From 51566ffd8df7175d1ee51a963ec9bb2e33f2f912 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Tue, 2 Jul 2019 16:45:53 -0400 Subject: [PATCH 01/69] Created classes for PCORnet discharge status, skilled nursing facility discharge status, adult foster home facility discharge status, assisted living facility discharge status, against medical advice discharge status, home health discharge status, hospice discharge status, nursing home discharge status, other acute inpatient discharge status, rehabilitation facility discharge status, residential facility discharge status, still in hospital discharge status, PCORnet admitting source data item, skilled nursing facility admitting source, and home health admitting source with definition, RDFS:label, and term editor annotations. --- PCORnetCDM.owl | 226 +++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 202 insertions(+), 24 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index e5c8cc0..00b38e4 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1,41 +1,41 @@ + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> + - - - - - - - - + + + + + + + Amanda Hicks + Josh Hanna William R. Hogan RDFized PCORnet CDM - Josh Hanna @@ -95,7 +95,6 @@ definition definition - definition textual definition @@ -106,7 +105,6 @@ editor note editor note - editor note @@ -8803,6 +8801,186 @@ excludes emergency department encounters + + + + + A data item that is about a patient discharge (or lack thereof) and (where applicable) the type of facility to which the patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet discharge status + + + + + + + + + A PCORnet discharge status that is about a skilled nursing facility to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet skilled nursing facility discharge status + + + + + + + + + A PCORnet discharge status that is about an adult foster home facility to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet adult foster home facility discharge status + + + + + + + + + A PCORnet discharge status that is about an assisted living facility to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet assisted living facility discharge status + + + + + + + + + A PCORnet discharge status that is about a distinct hospital facility to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet other acute inpatient hospital discharge status + + + + + + + + + A PCORnet discharge status that is about a nursing home facility to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet nursing home facility discharge status + + + + + + + + + A PCORnet discharge status that is about a rehabilitation facility to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet rehabilitation facility discharge status + + + + + + + + + A PCORnet discharge status that is about a residential facility to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet residential facility discharge status + + + + + + + + + A PCORnet discharge status that is about a hospice to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet hospice discharge status + + + + + + + + + Matthew Diller + S. Clint Dowland + PCORnet against medical advice discharge status + + + + + + + + + A PCORnet discharge status that is about a hospital facility in which a patient remains, having not been discharged. + Matthew Diller + S. Clint Dowland + PCORnet still in hospital discharge status + + + + + + + + + A PCORnet discharge status that is about a home healthcare organization and the household to which a patient was discharged. + Matthew Diller + S. Clint Dowland + PCORnet home health discharge status + + + + + + + + + A PCORnet admitting source data item that is about a household. + A data item that is about a patient admission and the type of facility from which a patient was discharged prior to admission. + Matthew Diller + S. Clint Dowland + PCORnet admitting source data item + + + + + + + + + A PCORnet data item that is about a home healthcare organization and the household from which a patient was discharged prior to admission. + Matthew Diller + S. Clint Dowland + PCORnet home health admitting source + + + + + + + + + A PCORnet data item that is about a skilled nursing facility from which a patient was discharged prior to admission. + Matthew Diller + S. Clint Dowland + PCORnet skilled nursing facility admitting source + + + + @@ -10212,5 +10390,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + From 8c138c77b550aa8043344909af320a393428dca5 Mon Sep 17 00:00:00 2001 From: Hicks Date: Wed, 3 Jul 2019 11:20:34 -0400 Subject: [PATCH 02/69] updated develop branch with master owl file --- PCORnetCDM.owl | 115 ++++++++++++++++++++++------------------------- catalog-v001.xml | 2 +- 2 files changed, 54 insertions(+), 63 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 608825d..cde3e25 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1,32 +1,32 @@ + xmlns:xml="http://www.w3.org/XML/1998/namespace" + xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#" + xmlns:obo="http://purl.obolibrary.org/obo/" + xmlns:foaf="http://xmlns.com/foaf/0.1/" + xmlns:dc="http://purl.org/dc/elements/1.1/" + xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"> - - - - - + + + + + Amanda Hicks 2019-08-03 @@ -7283,7 +7283,6 @@ Environmental exposures include those imposed by natural environments, experimen - @@ -7620,7 +7619,6 @@ Environmental exposures include those imposed by natural environments, experimen - @@ -7930,6 +7928,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -8110,6 +8114,7 @@ Environmental exposures include those imposed by natural environments, experimen + @@ -8126,7 +8131,6 @@ Environmental exposures include those imposed by natural environments, experimen - @@ -8702,7 +8706,8 @@ excludes emergency department encounters - + + + + + + + + + + + + + + + + + + + @@ -8810,8 +8833,8 @@ excludes emergency department encounters - + rta1 @@ -8918,8 +8941,8 @@ excludes emergency department encounters - + rta2 @@ -8947,9 +8970,9 @@ excludes emergency department encounters + - John Doe's Hispanic or Latino identity datum @@ -8968,8 +8991,8 @@ excludes emergency department encounters - + John Doe’s PCORnet Hispanic identity datum @@ -8988,9 +9011,9 @@ excludes emergency department encounters + - Jane Doe's not Hispanic or Latino identity datum @@ -9009,8 +9032,8 @@ excludes emergency department encounters - + Jane Doe’s PCORnet not Hispanic identity datum @@ -9041,6 +9064,8 @@ excludes emergency department encounters John Doe's patient role + + @@ -9066,7 +9091,6 @@ excludes emergency department encounters - @@ -9175,39 +9199,6 @@ excludes emergency department encounters - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -9267,5 +9258,5 @@ excludes emergency department encounters - + diff --git a/catalog-v001.xml b/catalog-v001.xml index 3aeb476..454593a 100644 --- a/catalog-v001.xml +++ b/catalog-v001.xml @@ -5,6 +5,6 @@ - + From a52d186ce24c0c961b9dda39b036350df62ac6af Mon Sep 17 00:00:00 2001 From: Hicks Date: Wed, 3 Jul 2019 11:58:28 -0400 Subject: [PATCH 03/69] reviewed new classes and merge changes --- PCORnetCDM.owl | 372 ++++++++++------------------------------------- catalog-v001.xml | 2 +- 2 files changed, 80 insertions(+), 294 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index cde3e25..363a3fa 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -7077,16 +7077,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - TODO: Add homeomorphy axiom - - - - - - @@ -7150,7 +7140,7 @@ Environmental exposures include those imposed by natural environments, experimen - + International Classification of Diseases @@ -7162,35 +7152,9 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -7208,14 +7172,7 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - + @@ -7369,7 +7326,7 @@ Environmental exposures include those imposed by natural environments, experimen - + Systematized Nomenclature of Medicine @@ -7470,6 +7427,32 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + + + + + + + + Amanda Hicks + a document act in which concludes an inpatient encounter + discharge process + + + + @@ -7619,63 +7602,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, - An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. - This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. - Chris Mungall - cjm - 2017-06-05T17:55:39Z - exposure event or process - https://github.com/oborel/obo-relations/pull/173 - - - - - - - - - - - - - - Any entity that is ordered in discrete units along a linear axis. - Chris Mungall - sequentially ordered entity - - - - - - - - - Any individual unit of a collection of like units arranged in a linear order - Chris Mungall - An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. - sequence atomic unit - - - - - - - - - Any entity that can be divided into parts such that each part is an atomical unit of a sequence - Chris Mungall - Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. - sequence bearer - - - - @@ -7858,7 +7784,6 @@ Environmental exposures include those imposed by natural environments, experimen - @@ -7902,7 +7827,6 @@ Environmental exposures include those imposed by natural environments, experimen a diagnosis about some patient that occurs before or during the admission of that patient Amanda Hicks PCORnet CDM 4.1 - PCORnet diagnosis identifier admitting diagnosis @@ -7919,21 +7843,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - question text - - - - - - - - - - @@ -7954,41 +7863,10 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - - - - - - - - - - - - - - material information bearer of question text plus answer set - - - - - - - - - - Amanda Hicks PCORnet black or African American identity datum PCORnet item @@ -8000,12 +7878,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - PCORnet CDM item identifier @@ -8015,23 +7887,7 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - PCORnet item - PROMIS response data item - - - - - - - - - option as memeber of answer set @@ -8113,28 +7969,11 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - - - - - - - - - - - + - + @@ -8143,6 +7982,8 @@ Environmental exposures include those imposed by natural environments, experimen + Amanda Hicks + a social act in which a patient is registered with a health care provider for the purposes of recieving care in an inpatient encounter admission process @@ -8151,7 +7992,6 @@ Environmental exposures include those imposed by natural environments, experimen - @@ -8162,7 +8002,7 @@ Environmental exposures include those imposed by natural environments, experimen - + @@ -8185,51 +8025,15 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - - - - - a diagnosis that occurs before or simultaneously with the discharge of the patient whom the diagnosis is about - code set + Amanda Hicks + PCORnet CDM 4.1 discharge diagnosis - - - - - - - - - - - - - - - - - - - - - discharge process - - - - @@ -8251,6 +8055,8 @@ Environmental exposures include those imposed by natural environments, experimen a diagnosis about a patient that is the specified output of a diagnostic process that occurs during an outpatient encounter + Amanda Hicks + PCORnet CDM 4.1 final diagnosis @@ -8276,6 +8082,9 @@ Environmental exposures include those imposed by natural environments, experimen + a diagnosis that is the output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge + Amanda Hicks + PCORnet CDM 4.1 interim diagnosis @@ -8294,7 +8103,7 @@ Environmental exposures include those imposed by natural environments, experimen - PCORnet sexual orientationidentity datum + PCORnet sexual orientation identity datum @@ -8310,7 +8119,7 @@ Environmental exposures include those imposed by natural environments, experimen - + @@ -8318,7 +8127,7 @@ Environmental exposures include those imposed by natural environments, experimen - + @@ -8326,7 +8135,6 @@ Environmental exposures include those imposed by natural environments, experimen - An outpatient encounter that occurs in an outpatient clinic, physician office, ambulatory surgery facility, urgent care facilitu, or a hospital encounters and @@ -8346,7 +8154,6 @@ excludes emergency department encounters - A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility. Amanda Hicks PCORnet CDM 4.1 @@ -8385,12 +8192,8 @@ excludes emergency department encounters - Amanda Hicks - PCORnet CDM 4.1 - Hospital outpatient services given to help the doctor decide if the patient needs to be admitted as an inpatient or can be discharged. Observations services may be given in the emergency department or another area of the hospital.” Definition from Medicare, CMS Product No. 11435, https://www.medicare.gov/Pubs/pdf/11435.pdf. - PCORnet bisexual identity datum + PCORnet gay identity datum - observation stay @@ -8522,6 +8325,39 @@ excludes emergency department encounters + + + + + PCORnet diagnosis identifier + + + + + + + + + + + + + + + + + + + + + + + a set of non-lexical symbols with a conventionally agreed usage among a group for a particular purpose + code set + + + + @@ -8702,12 +8538,6 @@ excludes emergency department encounters - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + A PCORnet data item that is about an emergency department from which a patient was discharged prior to admission. + Matthew Diller + S. Clint Dowland + PCORnet emergency department admitting source data item + + + + + + + + + A PCORnet data item that is about another department in the same hospital from which a patient was discharged prior to admission. + Matthew Diller + S. Clint Dowland + PCORnet intra-hospital admitting source data item + + + + + + + + + A PCORnet data item that is about a patient admission that is causally upstream of an outpatient encounter. + Matthew Diller + S. Clint Dowland + PCORnet ambulatory visit admitting source data item From 73a8636a675326f039af61e57670adbc655a2c94 Mon Sep 17 00:00:00 2001 From: Matthew Diller Date: Wed, 3 Jul 2019 14:08:33 -0400 Subject: [PATCH 05/69] Update .gitignore to add .DS_Store --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 3bafc35..ac15987 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ *.properties catalog-v001.xml +.DS_Store From 03650db30828c47050fb7ae57c98b0e374eb9b6d Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 3 Jul 2019 15:51:13 -0400 Subject: [PATCH 06/69] Created classes for health care encounter identifier, facility identifier, institutional professional consult, and non-acute institutional stay, with RDFS:label definition and term editor labels. --- PCORnetCDM.owl | 100 ++++++++++++++++++++++++++++++++++++------------- 1 file changed, 74 insertions(+), 26 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 8951f8e..9b9321a 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1,38 +1,38 @@ + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> + - - - - - + + + + Amanda Hicks - 2019-08-03 + Josh Hanna William R. Hogan + 2019-08-03 RDFized PCORnet CDM - Josh Hanna @@ -8575,6 +8575,54 @@ excludes emergency department encounters + + + + + A proper name that denotes a health care encounter and has part some symbol. + Matthew Diller + S. Clint Dowland + PCORnet health care encounter identifier + + + + + + + + + A proper name that denotes a health care facility and has part some symbol. + Matthew Diller + S. Clint Dowland + PCORnet facility identifier + + + + + + + + + A health care encounter that realizes some health care provider role that inheres in some Homo sapiens. + Matthew Diller + S. Clint Dowland + institutional professional consult + + + + + + + + + A health care encounter that occurs in some hospice facility, skilled nursing facility, rehabilitation facility, nursing home facility, residential home facility, overnight non-hospital dialysis facility, adult foster home facility, or assisted living facility. + Matthew Diller + S. Clint Dowland + non-acute institutional stay + + + + - + rta1 @@ -8808,8 +8856,8 @@ excludes emergency department encounters - + rta2 @@ -8837,9 +8885,9 @@ excludes emergency department encounters - + John Doe's Hispanic or Latino identity datum @@ -8858,8 +8906,8 @@ excludes emergency department encounters - + John Doe’s PCORnet Hispanic identity datum @@ -8878,9 +8926,9 @@ excludes emergency department encounters - + Jane Doe's not Hispanic or Latino identity datum @@ -8899,8 +8947,8 @@ excludes emergency department encounters - + Jane Doe’s PCORnet not Hispanic identity datum @@ -9081,5 +9129,5 @@ excludes emergency department encounters - + From 63ab9b8b31eded67505478599221eace587a39ab Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Mon, 15 Jul 2019 13:48:51 -0400 Subject: [PATCH 07/69] Edited definitions of admitting diagnosis, discharge diagnosis, final diagnosis, and interim diagnosis. --- PCORnetCDM.owl | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 9b9321a..715df0d 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -7824,8 +7824,9 @@ Environmental exposures include those imposed by natural environments, experimen - a diagnosis about some patient that occurs before or during the admission of that patient + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or during the admission of that patient Amanda Hicks + S. Clint Dowland PCORnet CDM 4.1 admitting diagnosis @@ -8026,9 +8027,10 @@ Environmental exposures include those imposed by natural environments, experimen - a diagnosis that occurs before or simultaneously with the discharge of the patient whom the diagnosis is about - Amanda Hicks - PCORnet CDM 4.1 + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or simultaneously with the discharge of that patient + Amanda Hicks + S. Clint Dowland + PCORnet CDM 4.1 discharge diagnosis @@ -8054,9 +8056,10 @@ Environmental exposures include those imposed by natural environments, experimen - a diagnosis about a patient that is the specified output of a diagnostic process that occurs during an outpatient encounter - Amanda Hicks - PCORnet CDM 4.1 + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an outpatient encounter + Amanda Hicks + S. Clint Dowland + PCORnet CDM 4.1 final diagnosis @@ -8082,9 +8085,10 @@ Environmental exposures include those imposed by natural environments, experimen - a diagnosis that is the output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge - Amanda Hicks - PCORnet CDM 4.1 + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge of that patient + Amanda Hicks + S. Clint Dowland + PCORnet CDM 4.1 interim diagnosis From 2509595a7a3f078346e89628b434ea0bc6c39517 Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Wed, 7 Aug 2019 11:58:40 -0400 Subject: [PATCH 08/69] Created class 'observation stay' with definition, term editor, and rdfs:label; and deprecated 'emergency department encounter' and added annotations to 'ED encounter'. --- PCORnetCDM.owl | 7028 ++++++++++++++++++++++++------------------------ 1 file changed, 3534 insertions(+), 3494 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 715df0d..64942d1 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1,38 +1,59 @@ - + + + + + + + + + + + + + + + +]> + + + - - - - - - - - - - - Amanda Hicks - Josh Hanna - William R. Hogan + xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#" + xmlns:obo="http://purl.obolibrary.org/obo/" + xmlns:foaf="http://xmlns.com/foaf/0.1/" + xmlns:dc="http://purl.org/dc/elements/1.1/" + xmlns:subsets="&obo;ro/subsets#"> + 2019-08-03 + William R. Hogan + Josh Hanna + Amanda Hicks RDFized PCORnet CDM + + + + + + + + + @@ -50,7 +71,7 @@ - + BFO OWL specification label BFO OWL specification label @@ -59,7 +80,7 @@ - + BFO CLIF specification label BFO CLIF specification label @@ -68,13 +89,13 @@ - + - + example of usage example of usage @@ -83,23 +104,23 @@ - + - + + textual definition definition definition - textual definition - + editor note editor note @@ -108,37 +129,37 @@ - + - + - + - + - + - + imported from @@ -146,22 +167,22 @@ - + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. - + - + - + elucidation elucidation @@ -170,7 +191,7 @@ - + has associated axiom(nl) has associated axiom(nl) @@ -179,7 +200,7 @@ - + has associated axiom(fol) has associated axiom(fol) @@ -188,56 +209,56 @@ - + - + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - + - - tooth SubClassOf 'never in taxon' value 'Aves' + + never in taxon x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. + ?X DisjointWith RO_0002162 some ?Y Chris Mungall + tooth SubClassOf 'never in taxon' value 'Aves' + - ?X DisjointWith RO_0002162 some ?Y - never in taxon - - + + mutually spatially disjoint with + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) non-overlapping with shares no parts with + + - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) - mutually spatially disjoint with - - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - - An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + taxonomic class assertion + An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. @@ -245,73 +266,73 @@ - + - + defined by inverse - + - - An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + logical macro assertion - https://github.com/oborel/obo-relations/wiki/ShortcutRelations + https://github.com/oborel/obo-relations/wiki/ShortcutRelations + An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. - - An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + annotation property cardinality - - + An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + + - + + logical macro assertion on a class A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL - logical macro assertion on a class - + - - A logical macro assertion whose domain is an IRI for a property + logical macro assertion on a property + A logical macro assertion whose domain is an IRI for a property - - Used to annotate object properties to describe a logical meta-property or characteristic of the object property. + logical macro assertion on an object property - + Used to annotate object properties to describe a logical meta-property or characteristic of the object property. + - + logical macro assertion on an annotation property @@ -319,30 +340,30 @@ - - An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + dispositional interpretation - + An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + - + + has no connections with 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' - A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. shares no connection with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) - has no connections with - + A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. + - + inherited annotation property @@ -350,220 +371,222 @@ - - Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + curator guidance link - + Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + - - brain always_present_in_taxon 'Vertebrata' - forelimb always_present_in_taxon Euarchontoglires + + always present in taxon S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. never lost in - always present in taxon - + brain always_present_in_taxon 'Vertebrata' + forelimb always_present_in_taxon Euarchontoglires + - - This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. + temporal logical macro assertion on a class - + This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. + - + measurement property has unit - + - + has start time value - + - + has end time value - + - - Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + start, days post fertilization - + Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + - - Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + end, days post fertilization - + Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + - - Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + start, years post birth - + Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + - - Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + end, years post birth - + Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + - - Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + start, months post birth - + Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + - - Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + end, months post birth - + Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + - - Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + month of gestation - + Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + - - A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + has developmental stage marker - + A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + - - Count of number of days intervening between the start of the stage and the time of coitum. - For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + start, days post coitum - + For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + Count of number of days intervening between the start of the stage and the time of coitum. + - - Count of number of days intervening between the end of the stage and the time of coitum. + end, days post coitum - + Count of number of days intervening between the end of the stage and the time of coitum. + - + start, weeks post birth - + - + end, weeks post birth - + - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + is asymmetric relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - + https://github.com/oborel/obo-relations/wiki/InteractionRelations + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + is symmetric relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - + https://github.com/oborel/obo-relations/wiki/InteractionRelations + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + - - R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + is relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - + https://github.com/oborel/obo-relations/wiki/InteractionRelations + R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + - + + is direct form of + Chris Mungall relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: @@ -574,220 +597,218 @@ Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall - is direct form of - + - + + is indirect form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall - is indirect form of - + - + logical macro assertion on an axiom - + - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom - + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive - + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + - - An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + is relational form of a class - + An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + - - A shortcut relationship that holds between two entities based on their identity criteria + logical macro assertion involving identity - + A shortcut relationship that holds between two entities based on their identity criteria + - - A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + in approximate one to one relationship with - + A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + - - x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y - The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + is approximately equivalent to - + The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y + - + + is opposite of 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is opposite of - + - - x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is indistinguishable from - + x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + - + evidential logical macro assertion on an axiom - + - - A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom has evidence - + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom + - - A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom contradicted by evidence - + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom + - - In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. - this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. - If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion + is representative IRI for equivalence set OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member - + In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. + If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion + this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. + - - Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" - cjm - 2018-03-13T23:59:29Z + is directional form of - + 2018-03-13T23:59:29Z + cjm + Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" + - - cjm - 2018-03-14T00:03:16Z + is positive form of - + 2018-03-14T00:03:16Z + cjm + - - cjm - 2018-03-14T00:03:24Z + is negative form of - + 2018-03-14T00:03:24Z + cjm + - - part-of is homeomorphic for independent continuants. + + is homeomorphic for + 2018-10-21T19:46:34Z + cjm R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. - cjm - 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. - is homeomorphic for + part-of is homeomorphic for independent continuants. + - - - external_ontology_notes + + external_ontology_notes - + PCORnet CDM Comments @@ -795,122 +816,122 @@ Where we have an annotation assertion - + eco subset - + - + - + - + - - subset_property + + subset_property - + - + - - database_cross_reference + + database_cross_reference - - has_exact_synonym + + has_exact_synonym - - has_narrow_synonym + + has_narrow_synonym - - has_obo_namespace + + has_obo_namespace - - has_related_synonym + + has_related_synonym - + - - in_subset + + in_subset - + is defined by - - - is defined by This is an experimental annotation + is defined by + + - + label @@ -918,21 +939,21 @@ Where we have an annotation assertion - - see also + + see also - + - + @@ -949,327 +970,327 @@ Where we have an annotation assertion - - - - - - - - - + + + + + + + + + - - + + - - + + - - - + + + - - - - - exists-at - existsAt + + exists at BFO2 Reference: entity BFO2 Reference: temporal region b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) - - exists at + existsAt + exists-at + + + + - - - - - - - o-has-part - hasOccurrentPart + + + has occurrent part + http://purl.obolibrary.org/obo/vo.owl + [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. + [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. + o-has-part + (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] + [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent + hasOccurrentPart [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) - [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent - http://purl.obolibrary.org/obo/vo.owl - [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) - (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] - - has occurrent part + + + + + - - - - - - + + + has proper occurrent part + http://purl.obolibrary.org/obo/vo.owl o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 - http://purl.obolibrary.org/obo/vo.owl - - has proper occurrent part + + + + + - - - - - - - has-t-part + + + has temporal part + http://purl.obolibrary.org/obo/vo.owl [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life. - [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) - http://purl.obolibrary.org/obo/vo.owl - - has temporal part + [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating + has-t-part + + + + + - - - - - - o-part-of + + + part of occurrent + http://purl.obolibrary.org/obo/vo.owl + BFO2 Reference: occurrent occurrentPartOf - Mary’s 5th birthday occurrent_part_of Mary’s life - The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. - the first set of the tennis match occurrent_part_of the tennis match. + o-part-of + (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] + (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) + (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] + (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] + (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - BFO2 Reference: occurrent - http://purl.obolibrary.org/obo/vo.owl + Mary’s 5th birthday occurrent_part_of Mary’s life + The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) - (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] - (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] - (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] - (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] - (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] - - part of occurrent + the first set of the tennis match occurrent_part_of the tennis match. + + + + - - - - - - o-ppart-of - properOccurrentPartOf + + + proper part of occurrent [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) + properOccurrentPartOf + o-ppart-of (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] - - proper part of occurrent + + + + - - - - - - t-part-of + + + temporal part of + http://purl.obolibrary.org/obo/vo.owl + (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] + (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] temporalPartOf - the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life - the process boundary which separates the 3rd and 4th years of your life. - your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating + t-part-of + (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) - http://purl.obolibrary.org/obo/vo.owl if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) - (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] - (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] - (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] - - temporal part of + the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life + the process boundary which separates the 3rd and 4th years of your life. + your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating + + + + - - - - - + + occupies temporal region spans occupiesTemporalRegion p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) - - occupies temporal region + + + + + - - - - + + has temporal occupant span-of - spanOf [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) - - has temporal occupant + spanOf + + + + - - - - during-which-exists + + during which exists [copied from inverse property 'exists at'] BFO2 Reference: entity + during-which-exists [copied from inverse property 'exists at'] BFO2 Reference: temporal region [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) - - during which exists + + + - + - + - + - - - - is_specified_input_of - some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - + + is_specified_input_of + PERSON:Bjoern Peters A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters - is_specified_input_of + is_specified_input_of + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + + + - + - + - - + + - + - + - + - - - + + + - - + + @@ -1277,129 +1298,130 @@ Where we have an annotation assertion - + - - - - - - - - - contained in + + contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) + contained in contained_in - - - contained in + + + + + + + + + - - contains - - + contains + contains + + - - - - - penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is allergic trigger for + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) + + + - - - - - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is autoimmune trigger for + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + + + - - - - penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has allergic trigger + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + + - - - - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has autoimmune trigger + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + + - - + + - - + David Osumi-Sutherland + - - - - - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - David Osumi-Sutherland + tracheates + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + David Osumi-Sutherland + + + - - - + + bounding layer of + David Osumi-Sutherland + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y @@ -1409,267 +1431,268 @@ range: spatial region or site (immaterial continuant) has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - - A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. - bounding layer of + + + - - - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. - Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland - - Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + coincident with + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + David Osumi-Sutherland + Note from NCEAS meeting: consider changing primary label + + - - - - - x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland + regulates in other organism + David Osumi-Sutherland + x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + - + + regulates transport of + David Osumi-Sutherland + A relationship that holds between a process that regulates a transport process and the entity transported by that process. + - - + + - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - David Osumi-Sutherland - - regulates transport of - - - - - - A part of relation that applies only between occurents. + occurent part of + A part of relation that applies only between occurents. + + + + - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z + has regulatory component activity + 2017-05-24T09:30:46Z + dos + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + + - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + 2017-05-24T09:31:01Z + dos + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + + - - - + + has positive regulatory component activity + 2017-05-24T09:31:17Z + dos A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - has positive regulatory component activity + + - - - - dos - 2017-05-24T09:36:08Z - A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + 2017-05-24T09:36:08Z + dos + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + + - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + 2017-05-24T09:44:33Z + dos + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z + has component process + 2017-05-24T09:49:21Z + dos + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + + + - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos - 2017-07-19T17:30:36Z + has ligand + 2017-07-19T17:30:36Z + dos + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + - - - Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos - 2017-07-20T17:11:08Z + transports + 2017-07-20T17:11:08Z + dos + Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. + - - - A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos - 2017-07-20T17:19:37Z + occurs across + 2017-07-20T17:19:37Z + dos + A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. + - - - - dos - 2017-09-17T13:52:24Z - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + 2017-09-17T13:52:24Z + dos + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + - - - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos - 2017-09-17T13:52:38Z + directly negatively regulated by + 2017-09-17T13:52:38Z + dos + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + + - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + + - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos - 2017-09-17T13:52:47Z + directly positively regulated by + 2017-09-17T13:52:47Z + dos + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + + - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + + - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + + has effector activity + 2017-09-22T14:14:36Z + dos + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + + - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos + + - - + + in register with + 2017-12-07T12:58:06Z + dos A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; @@ -1678,13 +1701,9 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - 2017-12-07T12:58:06Z - in register with - dos + - - A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; @@ -1694,93 +1713,77 @@ A and B are aligned in C according to a shared co-ordinate framework so that com Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. GOC:dos + + - - + + - - + + - - - - - David Osumi-Sutherland - di - Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + di + David Osumi-Sutherland + + - - + + - + + David Osumi-Sutherland + + - - + + - David Osumi-Sutherland - - - - + + - - - - - - - - - - - - - - - - - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - David Osumi-Sutherland - fasciculates with - (forall (?x ?y) + + fasciculates with + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -1800,81 +1803,83 @@ Examples include: the relationship between two channels collected simultaneously ) (overlaps ?nps ?npbss) )))))) - + fasciculates with + David Osumi-Sutherland + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + + + + + - fasciculates with + + + + + + + + + + + - - - - - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - + + has plasma membrane part + Lindsay Cowell + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) + Chris Mungall Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl - Chris Mungall - Lindsay Cowell + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] + + + + + - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - - has plasma membrane part - - - - - - has neurotransmitter + releases neurotransmitter + has neurotransmitter + + + + - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - + overlaps + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + x overlaps y if and only if there exists some z such that x has part z and z part of y + + + + - - - - - - - - - - - - - - - - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland - has fasciculating component - (forall (?x ?y) + + has fasciculating neuron projection + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1897,445 +1902,461 @@ Examples include: the relationship between two channels collected simultaneously - + David Osumi-Sutherland + The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + has fasciculating component + + + + - has fasciculating neuron projection + + + + + + + + + + + - - - - - - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + + continuous with + X continuous_with Y if and only if X and Y share a fiat boundary. connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - continuous with FMA:85972 + David Osumi-Sutherland + + + + + - - - - x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x - We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + + partially overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x))))) - - - partially overlaps + proper overlaps + x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom + + + + - - - + + spatially disjoint from + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy + BFO_0000051 exactly 0 (BFO_0000050 some ?Y) A is spatially_disjoint_from B if and only if they have no parts in common - There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall + There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. + + + + - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy - BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - - - spatially disjoint from - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - + + connected to + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + + - - + + - - + + - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - connected to - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - + + connects + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + The M8 connects Glasgow and Edinburgh + + + - - + + - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - connects - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) + attached to part of + attached to part of (anatomical structure to anatomical structure) + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + + + - - - Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + + supplies Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + - supplies - - + + drains Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure + - drains - - - + + has component + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - has component + + + + - - - + + has phenotype + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + Chris Mungall + + + + - - - + + + - - A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall - - has phenotype - - - - - inverse of has phenotype - Chris Mungall - - + + phenotype of + Chris Mungall + inverse of has phenotype + + + + - - - - - - - + + + develops from + Melissa Haendel x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + This is the transitive form of the develops from relation Chris Mungall David Osumi-Sutherland - Melissa Haendel Terry Meehan - This is the transitive form of the develops from relation - develops from + + + + + - - - - - - - inverse of develops from + + + develops into Chris Mungall + inverse of develops from David Osumi-Sutherland Terry Meehan - - develops into + + + + + - - - - every HOTAIR lncRNA is the gene product of some HOXC gene + + has gene product every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene - x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y Chris Mungall - has gene product + every HOTAIR lncRNA is the gene product of some HOXC gene + + + - - - - + + directly develops from + TODO - add child relations from DOS + FBbt + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. + Chris Mungall + has developmental precursor + David Osumi-Sutherland + + + + + - - + + - - + + - - + + - - - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor - FBbt - - TODO - add child relations from DOS - directly develops from + - - - - A parasite that kills or sterilizes its host + parasitoid of + A parasite that kills or sterilizes its host + + - - - inverse of parasitoid of - + has parasitoid + inverse of parasitoid of + + - - - - inverse of directly develops from - developmental precursor of - + directly develops into + developmental precursor of + inverse of directly develops from + + + - - - - - - - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit - Chris Mungall + + + regulates + false David Hill Tanya Berardini - - GO Regulation precludes parthood; the regulatory process may not be within the regulated process. + Chris Mungall regulates (processual) - false - regulates + GO + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + + + + + + - - - - - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + + negatively regulates Chris Mungall - + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. negatively regulates (process to process) - - negatively regulates + + + + + - - - - - - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + + + positively regulates Chris Mungall - positively regulates (process to process) - - positively regulates + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + + + + + - + + has prototype + This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. + heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') + 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) + Chris Mungall + x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + TODO: add homeomorphy axiom + Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + - - + + - 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) - heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') - - x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. - Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) - TODO: add homeomorphy axiom - This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - Chris Mungall - has prototype - - - - + + capable of + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + RO_0000053 some (RO_0000054 only ?Y) + + + + - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) - - capable of - - - + + capable of part of + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + has function in c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall - has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) - capable of part of + + @@ -2343,69 +2364,69 @@ Examples include: the relationship between two channels collected simultaneously - - - - x actively participates in y if and only if x participates in y and x realizes some active role + + actively participates in Chris Mungall agent in - actively participates in + x actively participates in y if and only if x participates in y and x realizes some active role + + - - + + obsolete has active participant + true 'heart development' has active participant some Shh protein - - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall has agent - - obsolete has active participant - true + Chris Mungall + This may be obsoleted and replaced by the original 'has agent' relation + x has participant y if and only if x realizes some active role that inheres in y + + + - - - - + + surrounded by x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x Chris Mungall - - surrounded by + + + + - - - - + + adjacent to + x adjacent to y if and only if x and y share a boundary. A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall - - adjacent to + The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. + The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. + + + + + - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + + @@ -2413,419 +2434,419 @@ Examples include: the relationship between two channels collected simultaneously - - - - inverse of surrounded by - Chris Mungall - - + surrounds + Chris Mungall + inverse of surrounded by + + + + - + + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - + - - + Chris Mungall - + + - - + Chris Mungall - + + - - - - - - - + + develops from part of x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall - develops from part of + + + + + + - - - - - - - - - x develops_in y if x is located in y whilst x is developing + + develops in Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 - develops in + x develops_in y if x is located in y whilst x is developing + + + + + + + - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. + obligate parasite of + A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. + - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. + facultative parasite of + A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. + - - + Chris Mungall - + + - - + Chris Mungall - + + - - - - - - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall - starts with process that occurs in - + has start location + starts with process that occurs in + Chris Mungall + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + + + + + - - - - - - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + + has end location Chris Mungall ends with process that occurs in - - has end location + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + + + + + - - - - - - + + has input p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes - - has input + + + + + + - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + + has output Chris Mungall + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. produces - - has output + + + + - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) + stem parasite of + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) + - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) + root parasite of + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) + - - - A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. + hemiparasite of + A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. + - - + + has exposure receptor A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. ExO:0000001 - has exposure receptor + - - - A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. - ExO:0000000 + has exposure stressor + ExO:0000000 + A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. + - - + + has exposure route A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 - has exposure route + - - - A broad relationship between an exposure event or process and the course takes from the source to the target. - http://purl.obolibrary.org/obo/ExO_0000004 + has exposure transport path + http://purl.obolibrary.org/obo/ExO_0000004 + A broad relationship between an exposure event or process and the course takes from the source to the target. + - - + + related via exposure to Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. - related via exposure to + - - - - - - Any portion of roundup 'has active ingredient' some glyphosate + + has active ingredient A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. + Any portion of roundup 'has active ingredient' some glyphosate has active substance has active pharmaceutical ingredient - has active ingredient + + + + - - - inverse of has active ingredient - + active ingredient in' + inverse of has active ingredient + + - - - - b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. + connecting branch of + b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. + + - - - inverse of connecting branch of - + has connecting branch + inverse of connecting branch of + + - - - - - - - - - + + has developmental contribution from + Chris Mungall Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall - has developmental contribution from + + + + + + + + + - - - - - - - - + + developmentally contributes to inverse of has developmental contribution from Chris Mungall - - developmentally contributes to + + + + + + + + - - - - - - - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T - Chris Mungall + + developmentally induced by + GO:0001759 + We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] David Osumi-Sutherland - Melissa Haendel + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T induced by - + Melissa Haendel + Chris Mungall Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - developmentally induced by + + + + + + - - - - - Inverse of developmentally induced by - Chris Mungall + developmentally induces + Chris Mungall + Inverse of developmentally induced by + + + - - - - - + + developmentally preceded by + false Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p - false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by + + + + - - - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. - c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + @@ -2833,12 +2854,12 @@ Examples include: the relationship between two channels collected simultaneously - - - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + + acts upstream of or within c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects - acts upstream of or within + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + @@ -2846,56 +2867,56 @@ Examples include: the relationship between two channels collected simultaneously - - - + + developmentally replaces + replaces x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall - replaces - developmentally replaces + + - - - + + developmentally succeeded by Inverse of developmentally preceded by Chris Mungall - developmentally succeeded by + + - - - - - - + + part of developmental precursor of 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall - part of developmental precursor of + + + + + + - - - + + results in developmental progression of + results_in_developmental_progression_of + Chris Mungall p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall - results_in_developmental_progression_of - results in developmental progression of + + @@ -2903,250 +2924,246 @@ Examples include: the relationship between two channels collected simultaneously - - - - every flower development (GO:0009908) results in development of some flower (PO:0009046) - + + results in development of + http://www.geneontology.org/GO.doc.development.shtml + results_in_development_of p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml - results_in_development_of - results in development of + every flower development (GO:0009908) results in development of some flower (PO:0009046) + + + - - - - + + results in formation of + results_in_formation_of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - Chris Mungall GOC:mtg_berkeley_2013 - results_in_formation_of - results in formation of + Chris Mungall + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + + + - - - - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - + + results in morphogenesis of + results_in_morphogenesis_of + GOC:mtg_berkeley_2013 The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. Chris Mungall - GOC:mtg_berkeley_2013 - results_in_morphogenesis_of - results in morphogenesis of + tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) + + + - - - - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + + results in maturation of + results_in_maturation_of Chris Mungall + The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process GOC:mtg_berkeley_2013 - results_in_maturation_of - results in maturation of + bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) + + + - - - foramen ovale closure SubClassOf results in disappearance of foramen ovale - - Chris Mungall - May be merged into parent relation - results_in_disappearance_of + results in disappearance of + results_in_disappearance_of + May be merged into parent relation + Chris Mungall + foramen ovale closure SubClassOf results in disappearance of foramen ovale + + - - + + results in developmental regression of every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - Chris Mungall May be merged into parent relation - results in developmental regression of + + - - - - Inverse of 'is substance that treats' - cjm - + is treated by substance + cjm + Inverse of 'is substance that treats' + + + - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + + + - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + + - - + + has exposure stimulus + 2017-06-05T17:35:04Z + cjm + Chris Mungall A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. Austin Meier - Chris Mungall Marie Angelique Laporte - cjm - 2017-06-05T17:35:04Z - has exposure stimulus + - - - + + transports or maintains localization of + regulates localization of Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall - regulates localization of - transports or maintains localization of + + - - - - - - - - - - + + inheres in part of q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. - Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + + - - inheres in part of + + + + + + + + - - + true + + - - + + - true - - - - - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + + results in acquisition of features of + results_in_acquisition_of_features_of The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall GOC:mtg_berkeley_2013 - results_in_acquisition_of_features_of - results in acquisition of features of + Chris Mungall + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + + + - + + mereotopologically related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - - mereotopologically related to + - - - - + + colocalizes with Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. + Gene Ontology Consortium Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium - colocalizes with + + + - - - - ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. - Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. - eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex + + contributes to We would like to say if and only if @@ -3158,66 +3175,70 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. + ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Chris Mungall - http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to + Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. - contributes to + http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to + eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex + + - - - + + enables + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. a particular instances of akt-2 enables some instance of protein kinase activity + has + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + is executing Chris Mungall - catalyzes executes - has + catalyzes is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. - enables + + - + + functionally related to A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function - functionally related to - - + + part of structure that is capable of + false this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall - false - part of structure that is capable of + - - - - c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + + involved in actively involved in + c involved_in p if and only if c enables some process p', and p' is part of p enables part of - involved in + Chris Mungall + + @@ -3225,716 +3246,718 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid - p regulates levels of c if p regulates some amount (PATO:0000070) of c + + regulates levels of Chris Mungall - + p regulates levels of c if p regulates some amount (PATO:0000070) of c regulates levels of (process to entity) - regulates levels of + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid + + + + - - - + + enabled by inverse of enables Chris Mungall - enabled by + + - - - - - + + + regulated by inverse of regulates Chris Mungall regulated by (processual) - - regulated by + + + + - - - inverse of negatively regulates - Chris Mungall - + negatively regulated by + Chris Mungall + inverse of negatively regulates + + - - + + positively regulated by inverse of positively regulates Chris Mungall - - positively regulated by + + - - - - A relationship that holds via some process of localization + + related via localization to Chris Mungall + A relationship that holds via some process of localization Do not use this relation directly. It is a grouping relation. - related via localization to + + - - + + has target start location This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. Chris Mungall - has target start location + - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall + has target end location + Chris Mungall + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. + - - + + imports Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. Chris Mungall - imports + - - - Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall + results in transport along + Chris Mungall + Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l + - - - - Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall + results in transport across + Chris Mungall + Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. + + - - - - 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall + results in growth of + Chris Mungall + 'pollen tube growth' results_in growth_of some 'pollen tube' + + - - + + results in transport to from or in 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) Chris Mungall - results in transport to from or in + - - - Chris Mungall + exports + Chris Mungall + - - - + + results in commitment to + http://www.geneontology.org/GO.doc.development.shtml#fate + Chris Mungall an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in commitment to + + - - - - p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate + results in determination of + http://www.geneontology.org/GO.doc.development.shtml#fate + Chris Mungall + p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. + + - + - + - - - - inverse of has input - Chris Mungall - - + input of + Chris Mungall + inverse of has input + + + + - - - + + output of inverse of has output Chris Mungall - - - output of + + + + - - - Chris Mungall + formed as result of + Chris Mungall + - - - + + results in structural organization of A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall - results in structural organization of + + - - - - The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate + results in specification of + http://www.geneontology.org/GO.doc.development.shtml#fate + Chris Mungall + The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. + + - - + + results in developmental induction of p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. Chris Mungall - results in developmental induction of + - - - Chris Mungall - http://neurolex.org/wiki/Property:DendriteLocation + has dendrite location + http://neurolex.org/wiki/Property:DendriteLocation + Chris Mungall + - - - - + + + attached to a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) - - attached to + + + - - - - m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + + has muscle origin Chris Mungall Wikipedia:Insertion_(anatomy) - has muscle origin + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + + - - - We need to import uberon muscle to create a stricter domain constraint + + + - - - - m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + + has muscle insertion Chris Mungall Wikipedia:Insertion_(anatomy) - has muscle insertion + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + + - - - We need to import uberon muscle into RO to use as a stricter domain constraint + + + - - - - - - - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + in branching relationship with - - https://github.com/obophenotype/uberon/issues/170 + https://github.com/obophenotype/uberon/issues/170 + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships + Chris Mungall + A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. + + + + + + - - + + tributary of + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) + http://en.wikipedia.org/wiki/Tributary + tributary channel of + Chris Mungall + http://www.medindia.net/glossary/venous_tributary.htm + drains to + drains into Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall - drains into - drains to - tributary channel of http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - - tributary of - http://en.wikipedia.org/wiki/Tributary + + + - - - Deschutes River distributary_of Little Lava Lake - + + distributary of x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes + http://en.wikipedia.org/wiki/Distributary + Deschutes River distributary_of Little Lava Lake branch of + Chris Mungall distributary channel of - http://en.wikipedia.org/wiki/Distributary - - This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes - distributary of + + + - - + + anabranch of + x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + anastomoses with + Chris Mungall + + + + + - + - - - - x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall - anastomoses with - - anabranch of - - + + spatially coextensive with + x spatially_coextensive_with y if and inly if x and y have the same location + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + A lump of clay and a statue + Chris Mungall + - + - + - A lump of clay and a statue - x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios - spatially coextensive with - - - - - + + branching part of x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y Chris Mungall - - branching part of FMA:85994 + + + + + - - - + + main stem of x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. Chris Mungall - - main stem of + + + - - - - x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall - + proper distributary of + Chris Mungall + x proper_distributary_of y iff x distributary_of y and x does not flow back into y + + + - - - - x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall - + proper tributary of + Chris Mungall + x proper_tributary_of y iff x tributary_of y and x does not originate from y + + + - - - - - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + has developmental potential involving + Chris Mungall + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + + + - - - - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + has potential to developmentally contribute to + Chris Mungall + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + + - - - - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall + has potential to developmentally induce + Chris Mungall + x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + + - - - - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + has potential to develop into + Chris Mungall + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + + - - - - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + has potential to directly develop into + Chris Mungall + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + + - - + + has direct input 'protein catabolic process' SubClassOf has_direct_input some protein - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' - has direct input + Chris Mungall + + - - - Chris Mungall + + obsolete has indirect input + true Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect input - true + Chris Mungall + - - translation SubClassOf has_direct_output some protein - + + obsolete has direct output + true p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + translation SubClassOf has_direct_output some protein Chris Mungall directly produces - obsolete has direct output - true + - - - - - - + + obsolete has indirect output + true Chris Mungall Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true + + + + + - - - - - + + causally downstream of inverse of upstream of Chris Mungall - causally downstream of + + + + - - - - - - Chris Mungall + immediately causally downstream of + Chris Mungall + + + + - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall + + directly activates directly positively regulates - + p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q directly activates (process to process) - directly activates + Chris Mungall + + + - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - indirectly positively regulates - + + indirectly activates + indirectly positively regulates + Chris Mungall + p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q + + - - - Chris Mungall + + directly inhibits directly negatively regulates - directly inhibits (process to process) - directly inhibits + Chris Mungall + + - - - - - Chris Mungall - indirectly negatively regulates - + + indirectly inhibits + indirectly negatively regulates + Chris Mungall + + + - - + + causally related to This relation groups causal relations between material entities and causal relations between processes + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: @@ -3950,1925 +3973,1923 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causally related to + - - - - - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain - Chris Mungall + + causally upstream of + Chris Mungall + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + + + - - - - + + immediately causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall - - immediately causally upstream of + + + + - - - - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit + + directly provides input for Chris Mungall - directly provides input for (process to process) - directly provides input for + p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit + + + + - - - - - - - transitive form of directly_provides_input_for + + + transitively provides input for Chris Mungall + transitive form of directly_provides_input_for This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) - transitively provides input for + + + + - - - - + + + causally upstream of or within + influences (processual) + Chris Mungall p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall - influences (processual) affects - causally upstream of or within + + - - false - Chris Mungall - This is an exploratory relation + differs in - https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions + false + https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions + This is an exploratory relation + Chris Mungall - - + + differs in attribute of + Chris Mungall + - - + + - Chris Mungall - differs in attribute of - - - - Chris Mungall + differs in attribute + Chris Mungall + + - - - - inverse of causally upstream of or within - Chris Mungall - - + + causally downstream of or within + Chris Mungall + inverse of causally upstream of or within + + + - - - + + involved in regulation of c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall - involved in regulation of + + - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall - + involved in positive regulation of + Chris Mungall + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + + - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall - + involved in negative regulation of + Chris Mungall + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + + - - - - + + involved in or involved in regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + involved in or reguates OWL does not allow defining object properties via a Union Chris Mungall - involved in or reguates - involved in or involved in regulation of + + + - - - + + is active in A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall - executes activity in - enables activity in + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - is active in + enables activity in + executes activity in + + - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos + + - - + + contributes to morphology of p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall - contributes to morphology of + - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - Considering relabeling as 'pairwise interacts with' - This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + + + interacts with + Considering relabeling as 'pairwise interacts with' + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with - - interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + + + - - - - - + + + biotically interacts with An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. + http://eol.org/schema/terms/interactsWith Chris Mungall interacts with on organism level - - biotically interacts with - http://eol.org/schema/terms/interactsWith + + + + - - + + trophically interacts with An interaction relationship in which the partners are related via a feeding relationship. Chris Mungall - - trophically interacts with + + - - - - A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] - Baleen whale preys on krill - An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen + + preys on Katja Shulz is subject of predation interaction with + Chris Mungall + An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members + A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] preys upon - - preys on - http://eol.org/schema/terms/preysUpon http://www.inaturalist.org/observations/2942824 + Baleen whale preys on krill + http://eol.org/schema/terms/preysUpon + Jorrit Poelen + + + - - - + + + symbiotically interacts with + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + A biotic interaction in which the two organisms live together in more or less intimate association. + We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + Chris Mungall + + - - + + - + - A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - - symbiotically interacts with - - + + commensually interacts with + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + Chris Mungall + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + + - - + + - + - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - commensually interacts with - - + + mutualistically interacts with + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + Chris Mungall + + - - + + - + - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - mutualistically interacts with - - + + interacts with via parasite-host interaction + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + This relation groups a pair of inverse relations, parasite of and parasitized by + Chris Mungall + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + + - - + + - + - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - This relation groups a pair of inverse relations, parasite of and parasitized by - - interacts with via parasite-host interaction - - - - + + parasite of + direct parasite of + http://eol.org/schema/terms/parasitizes + parasitizes + Chris Mungall + Pediculus humanus capitis parasite of human + + + + - - + + - + - Pediculus humanus capitis parasite of human - Chris Mungall - parasitizes - direct parasite of - - parasite of - http://eol.org/schema/terms/parasitizes - - - + + parasitized by Chris Mungall - has parasite - parasitised by directly parasitized by - - parasitized by + has parasite http://eol.org/schema/terms/hasParasite + parasitised by + + + - - + + participates in a abiotic-biotic interaction with + semibiotically interacts with + Chris Mungall Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall - semibiotically interacts with - - participates in a abiotic-biotic interaction with + + - - - Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + + activity directly regulates activity of Chris Mungall molecularly controls - activity directly regulates activity of + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + - - - Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall + + activity directly negatively regulates activity of inhibits + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. molecularly decreases activity of - activity directly negatively regulates activity of + Chris Mungall + - - + + activity directly positively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall activates + Chris Mungall molecularly increases activity of - activity directly positively regulates activity of + - - - + + has symptom A relation that holds between a disease or an organism and a phenotype Chris Mungall - has symptom + + - - - Chris Mungall - The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) - + host of + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + Chris Mungall + + - - - Chris Mungall - + has host http://eol.org/schema/terms/hasHost + Chris Mungall + + - - - - Bees pollinate Flowers + + pollinates This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. + http://eol.org/schema/terms/pollinates Chris Mungall + Bees pollinate Flowers is subject of pollination interaction with - - pollinates - http://eol.org/schema/terms/pollinates + + + - - - Chris Mungall - has polinator - is target of pollination interaction with - + pollinated by + Chris Mungall http://eol.org/schema/terms/hasPollinator + is target of pollination interaction with + has polinator + + - - - + + acquires nutrients from Chris Mungall Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. - - acquires nutrients from + + + - - - inverse of preys on - Chris Mungall - has predator - is target of predation interaction with - - + preyed upon by http://eol.org/schema/terms/HasPredator + inverse of preys on + is target of predation interaction with + has predator + Chris Mungall http://polytraits.lifewatchgreece.eu/terms/PRED + + + - - - - Anopheles is a vector for Plasmodium - Chris Mungall - a is a vector for b if a carries and transmits an infectious pathogen b into another living organism - + is vector for + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism + Chris Mungall + Anopheles is a vector for Plasmodium + + + - - - Chris Mungall - + has vector + Chris Mungall + + - - - Chris Mungall - Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + partner in + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + Chris Mungall + - - - Chris Mungall - Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + subject participant in + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + Chris Mungall + - - - Chris Mungall - Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + target participant in + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + Chris Mungall + - - Chris Mungall - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + Chris Mungall - - - Chris Mungall + is symbiosis + Chris Mungall + - - - Chris Mungall + is commensalism + Chris Mungall + - - - Chris Mungall + is mutualism + Chris Mungall + - - - Chris Mungall + is parasitism + Chris Mungall + - - - Chris Mungall - + provides nutrients for + Chris Mungall + + - - - Chris Mungall - is subject of eating interaction with - + eats + is subject of eating interaction with + Chris Mungall + + - - + + is eaten by + is target of eating interaction with Chris Mungall eaten by - is target of eating interaction with - - is eaten by + + - - - + + is evidence for + Chris Mungall A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. - Chris Mungall - - is evidence for + + + - - - - + + composed primarily of 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall + + + + + - - - composed primarily of - - - ABal nucleus child nucleus of ABa nucleus (in C elegans) - c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + + child nucleus of Chris Mungall This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. - child nucleus of + c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + ABal nucleus child nucleus of ABa nucleus (in C elegans) + - - + + child nucleus of in hermaphrodite A child nucleus relationship in which the cells are part of a hermaphroditic organism Chris Mungall - child nucleus of in hermaphrodite + - - - A child nucleus relationship in which the cells are part of a male organism - Chris Mungall + child nucleus of in male + Chris Mungall + A child nucleus relationship in which the cells are part of a male organism + - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - + has part that occurs in + Chris Mungall + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + + + - - - Chris Mungall + is kinase activity + Chris Mungall + - - - Chris Mungall + is ubiquitination + Chris Mungall + - - - - See notes for inverse relation - Chris Mungall + receives input from + Chris Mungall + See notes for inverse relation + + - - + + sends output to This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. Chris Mungall - sends output to + - - + + relation between structure and stage + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + + - - + + - - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. - relation between structure and stage - - - - x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - Chris Mungall + existence starts during + Chris Mungall + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + + - - - x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - Chris Mungall + existence starts with + Chris Mungall + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + - - + + existence overlaps x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence overlaps + Chris Mungall + - - - - x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + + existence starts and ends during Chris Mungall + x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts and ends during + + - - - - x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + + existence ends during Chris Mungall + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during + + - - + + existence ends with x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends with + Chris Mungall + - - - + + + transformation of x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall - transformation of + - - - + + immediate transformation of x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall - - immediate transformation of + + + - - - x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + + existence starts during or after Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts during or after + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + - - + + existence ends during or before x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during or before + Chris Mungall + - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - + causal agent in process + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + + - - - - - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + + + + - - Chris Mungall + depends on - + Chris Mungall + - - - q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + + towards This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + - towards - - + + has intermediate 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate - p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c Chris Mungall + p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c has intermediate product - - has intermediate + + - - - - - The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between material entities + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + + + + - - - - - - - + + determined by A coral reef environment is determined by a particular coral reef - s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. - The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + Pier Buttigieg Chris Mungall - - determined by (system to material entity) + The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. Chris Mungall - Pier Buttigieg - - determined by + determined by (system to material entity) + + + + + + + + - - - inverse of determined by - Chris Mungall - determines (material entity to system) - - + determines + determines (material entity to system) + Chris Mungall + inverse of determined by + + + - - - - - + + determined by part of s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall - - determined by part of + + + + + - - + + transcribed from + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + x is transcribed from y if and only if x is synthesized from template y + Chris Mungall + - - + + - - + + - - + + - - x is transcribed from y if and only if x is synthesized from template y - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - transcribed from + - - A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + sequentially related to + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + A relation that holds between two entities that have the property of being sequences or having sequences. - sequentially related to - - - Every UTR is adjacent to a CDS of the same transcript - Two consecutive DNA residues are sequentially adjacent - Two exons on a processed transcript that were previously connected by an intron are adjacent + + sequentially adjacent to + http://www.ncbi.nlm.nih.gov/pubmed/20226267 x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y + Two exons on a processed transcript that were previously connected by an intron are adjacent + Two consecutive DNA residues are sequentially adjacent + Every UTR is adjacent to a CDS of the same transcript Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - sequentially adjacent to + - - - - - Every CDS has as a start sequence the start codon for that transcript - x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + + + has start sequence + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall + Every CDS has as a start sequence the start codon for that transcript started by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 + x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - has start sequence + + - - - + + + is start sequence of + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + starts inverse of has start sequence Chris Mungall - starts - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - is start sequence of + + - - - - - Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) - x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + + + has end sequence + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall ended by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 + x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) - has end sequence + + - - - - inverse of has end sequence + + + is end sequence of + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall + inverse of has end sequence ends - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - is end sequence of + + - - - x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. - In the SO paper, this was defined as an instance-type relation + + is consecutive sequence of + http://www.ncbi.nlm.nih.gov/pubmed/20226267 Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 + In the SO paper, this was defined as an instance-type relation + x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. - is consecutive sequence of + - - - + + + is sequentially aligned with Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. - x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering Chris Mungall + x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - is sequentially aligned with + - - - - + + + bounds sequence of + Chris Mungall The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall - bounds sequence of + + - - - - inverse of bounds sequence of + + + is bound by sequence of Chris Mungall + inverse of bounds sequence of - - is bound by sequence of + + - - - - - - + + + has subsequence + http://www.ncbi.nlm.nih.gov/pubmed/20226267 x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall contains - http://www.ncbi.nlm.nih.gov/pubmed/20226267 + Chris Mungall - has subsequence + + + + - - - - - - inverse of has subsequence + + + is subsequence of Chris Mungall + inverse of has subsequence contained by - - is subsequence of + + + + - - - - + + + overlaps sequence of x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. Chris Mungall - overlaps sequence of + + - - - - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + + + does not overlap sequence of Chris Mungall disconnected from + x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - does not overlap sequence of + - - - - inverse of downstream of sequence of + + + is upstream of sequence of Chris Mungall + inverse of downstream of sequence of - is upstream of sequence of + - - - - - x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + + + is downstream of sequence of Chris Mungall + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - is downstream of sequence of + + - - - - A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript + + is immediately downstream of sequence of x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript Chris Mungall - - is immediately downstream of sequence of + + + - - - - A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript - inverse of immediately downstream of + + is immediately upstream of sequence of Chris Mungall + inverse of immediately downstream of + A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript - is immediately upstream of sequence of + + - - - - - - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' - A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall + + + + has skeleton has supporting framework + A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - has skeleton + Chris Mungall + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' + + + + - - - This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. + + + - - - + + results in ending of p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall - results in ending of + + - - - - - - - - x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y - Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + + hyperparasite of http://eol.org/schema/terms/hyperparasitoidOf + Chris Mungall https://en.wikipedia.org/wiki/Hyperparasite epiparasite of + x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism hyperparasitoid of - - hyperparasite of + + + + + + + - - - - - - - inverse of hyperparasite of - Chris Mungall + + hyperparasitized by has epiparasite has hyperparasite hyperparasitoidized by - - - hyperparasitized by + Chris Mungall + inverse of hyperparasite of + + + + + + + - - + + allelopath of Chris Mungall + x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y http://en.wikipedia.org/wiki/Allelopathy - - allelopath of http://eol.org/schema/terms/allelopathyYes - x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y + + - - - - Chris Mungall - + pathogen of + Chris Mungall + + + - - - Chris Mungall - + has pathogen + Chris Mungall + + - - - inverse of is evidence for + + has evidence Chris Mungall - - - + inverse of is evidence for x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. - has evidence + + + + - - - - Chris Mungall - - causally influenced by (material entity to material entity) + causally influenced by + causally influenced by (material entity to material entity) + Chris Mungall + + + - - - Chris Mungall + interaction relation helper property + https://github.com/oborel/obo-relations/wiki/InteractionRelations + Chris Mungall - https://github.com/oborel/obo-relations/wiki/InteractionRelations + - - - Chris Mungall + molecular interaction relation helper property + Chris Mungall + - - + + results in movement of Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall - results in movement of + Chris Mungall + - - + + causally influences Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall - causally influences (material entity to material entity) - causally influences + + - - + + has branching part inverse of branching part of Chris Mungall - - - has branching part + + + - - - - - x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - + conduit for + This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. + UBERON:cjm + Chris Mungall + x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. + + + + - - - - x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + + lumen of Chris Mungall + x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. GOC:cjm - - lumen of + + + - - - + + luminal space of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall - - luminal space of + + + - - - - A relation that holds between an attribute or a qualifier and another attribute. - Chris Mungall - - This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. - + has modifier + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + Chris Mungall + A relation that holds between an attribute or a qualifier and another attribute. + + + + - - - - - Chris Mungall - + participates in a biotic-biotic interaction with + Chris Mungall + + + + - - - - + + skeleton of inverse of has skeleton Chris Mungall - - skeleton of + + + + - - - - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + directly regulates Chris Mungall - directly regulates (processual) - - directly regulates + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + + + - - - x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + existence starts at point + x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + - - - + + has part structure that is capable of + Chris Mungall + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + + - - + + - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' - s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall - has part structure that is capable of - - - - p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. + results in closure of + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. + + - - - p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + results in breakdown of + p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + - - + results in synthesis of + - - - + results in assembly of + + - - - p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + results in catabolism of + p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + - - - + results in disassembly of + + - - - + results in remodeling of + + - - - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + results in organization of + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + - - - x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + existence ends at point + x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + - - - - + + causal relation between material entity and a process + Chris Mungall A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall - - causal relation between material entity and a process + + + + - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - + capable of regulating + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + pyrethroid -> growth + + - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - + capable of negatively regulating + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + - - + + capable of positively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - capable of positively regulating + + - - - pazopanib -> pathological angiogenesis - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + + capable of inhibiting or preventing pathological process treats - + pazopanib -> pathological angiogenesis The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. - capable of inhibiting or preventing pathological process + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + + - - - treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + treats + + - - - benzene -> cancer [CHEBI] - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. - causes disease - + capable of upregulating or causing pathological process + causes disease + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + benzene -> cancer [CHEBI] + + - - - c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. - treats - + is substance that treats + treats + c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. + + @@ -5876,509 +5897,509 @@ the a supports either the existence of b, or the truth value of b. - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI + is marker for + May be ceded to OBI + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. + - - - Inverse of 'causal agent in process' - + process has causal agent + Inverse of 'causal agent in process' + + - + + obsolete related via dependence to + true A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - obsolete related via dependence to - true - + + correlated with A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation - correlated with - - - An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. + + is evidence with support from A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. In the Gene Ontology association model, this corresponds to the With/From field - is evidence with support from + An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. + - - - Inverse of is-model-of + has model + Inverse of is-model-of + - - Do not use this relation directly. It is a grouping relation. + related via evidence or inference to + Do not use this relation directly. It is a grouping relation. - - - + visits - https://github.com/oborel/obo-relations/issues/74 + https://github.com/oborel/obo-relations/issues/74 + + - - + visited by + - - - + visits flowers of + + - - + has flowers visited by + - - - - + lays eggs in + + + - - - + has eggs laid in by + + - - - - https://github.com/jhpoelen/eol-globi-data/issues/143 + kills + https://github.com/jhpoelen/eol-globi-data/issues/143 + + - - + is killed by + - - - + + directly positively regulates Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. - directly positively regulates (process to process) - - directly positively regulates + + + + - - - - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. - - directly negatively regulates (process to process) - + directly negatively regulates + directly negatively regulates (process to process) + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + + + - - - + + ectoparasite of A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host + + - ectoparasite of - - - inverse of ectoparasite of - + has ectoparasite + inverse of ectoparasite of + + - - - - - A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system - lives inside of + endoparasite of + lives inside of + A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system + + + - - + has endoparasite + - - - - A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite + mesoparasite of + A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite + + - - - inverse of mesoparasite of - + has mesoparasite + inverse of mesoparasite of + + - - - + + intercellular endoparasite of A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. + + - intercellular endoparasite of - - - inverse of intercellular endoparasite of - + has intercellular endoparasite + inverse of intercellular endoparasite of + + - - - + + intracellular endoparasite of A sub-relation of endoparasite-of in which the parasite inhabits host cells. + + - intracellular endoparasite of - - - inverse of intracellular endoparasite of - + has intracellular endoparasite + inverse of intracellular endoparasite of + + - - - - - - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Melissa Haendel - - Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + Melissa Haendel + + + + + - - - - + + produced by a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel - - produced by + + + + - - - Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. - Logical axioms to be added after the relevant branch of GO is MIREOTed in + represses expression of + Logical axioms to be added after the relevant branch of GO is MIREOTed in + Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. + - - + + increases expression of Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. Logical axioms to be added after the relevant branch of GO is MIREOTed in - increases expression of + - - - - Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? - Matthew Brush - The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + + + is model of + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + Matthew Brush + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - - + + causes or contributes to condition + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. - Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - causes or contributes to condition + - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. + causes condition + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. + - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. + contributes to condition + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. + - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. - contributes to expressivity of condition + contributes to severity of condition + contributes to expressivity of condition + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. + - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. - contributes to penetrance of condition + contributes to frequency of condition + contributes to penetrance of condition + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. + - - + + ameliorates condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. - is preventative for condition Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - ameliorates condition + is preventative for condition + - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + - - - A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. + exacerbates condition + A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. + - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. + condition ameliorated by + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. + - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. + condition exacerbated by + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. + - - - - + + condition has genetic basis in + 2017-11-05T02:38:20Z + cjm + Do not use this relation directly. It is intended as a grouping for a more specific relations + + + - - - + + + - Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm - 2017-11-05T02:38:20Z - condition has genetic basis in - - - - cjm - 2017-11-05T02:45:20Z + has material basis in gain of function germline mutation in + 2017-11-05T02:45:20Z + cjm + + @@ -6387,24 +6408,24 @@ Environmental exposures include those imposed by natural environments, experimen - - - - cjm - 2017-11-05T02:45:37Z + has material basis in loss of function germline mutation in + 2017-11-05T02:45:37Z + cjm + + - - - - cjm - 2017-11-05T02:45:54Z + has material basis in germline mutation in + 2017-11-05T02:45:54Z + cjm + + @@ -6412,12 +6433,12 @@ Environmental exposures include those imposed by natural environments, experimen - - - - cjm - 2017-11-05T02:46:07Z + has material basis in somatic mutation in + 2017-11-05T02:46:07Z + cjm + + @@ -6425,107 +6446,107 @@ Environmental exposures include those imposed by natural environments, experimen - - - - cjm - 2017-11-05T02:46:26Z + has major susceptibility factor + 2017-11-05T02:46:26Z + cjm + + - - - - cjm - 2017-11-05T02:46:57Z + has partial material basis in germline mutation in + 2017-11-05T02:46:57Z + cjm + + - - - p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - cjm - 2018-12-13T11:26:17Z + has primary input or output + 2018-12-13T11:26:17Z + cjm + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + - - - - p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - cjm - 2018-12-13T11:26:32Z + has primary output + 2018-12-13T11:26:32Z + cjm + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + + - - p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm GOC:dph - GOC:kva GOC:pt + GOC:kva + GOC:cjm PMID:27812932 + + - - - - p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - cjm - 2018-12-13T11:26:56Z + has primary input + 2018-12-13T11:26:56Z + cjm + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + + - - - p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm GOC:dph - GOC:kva - GOC:pt + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. PMID:27812932 + GOC:pt + GOC:kva + GOC:cjm + + - - - - Do not use this relation directly. It is intended as a grouping for a more specific relations - cjm - 2017-11-05T02:53:08Z + is genetic basis for condition + 2017-11-05T02:53:08Z + cjm + Do not use this relation directly. It is intended as a grouping for a more specific relations + + - - - Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm - 2017-11-05T02:55:51Z + is causal gain of function germline mutation of in + 2017-11-05T02:55:51Z + cjm + Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + @@ -6533,12 +6554,12 @@ Environmental exposures include those imposed by natural environments, experimen - - - Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm - 2017-11-05T02:56:06Z + is causal loss of function germline mutation of in + 2017-11-05T02:56:06Z + cjm + Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + @@ -6546,12 +6567,12 @@ Environmental exposures include those imposed by natural environments, experimen - - - Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - cjm - 2017-11-05T02:56:40Z + is causal germline mutation in + 2017-11-05T02:56:40Z + cjm + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + @@ -6559,12 +6580,12 @@ Environmental exposures include those imposed by natural environments, experimen - - - Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - cjm - 2017-11-05T02:57:07Z + is causal somatic mutation in + 2017-11-05T02:57:07Z + cjm + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. + @@ -6572,12 +6593,12 @@ Environmental exposures include those imposed by natural environments, experimen - - - Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - cjm - 2017-11-05T02:57:43Z + is causal susceptibility factor for + 2017-11-05T02:57:43Z + cjm + Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. + @@ -6585,12 +6606,12 @@ Environmental exposures include those imposed by natural environments, experimen - - - Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - cjm - 2017-11-05T02:58:43Z + is causal germline mutation partially giving rise to + 2017-11-05T02:58:43Z + cjm + Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. + @@ -6598,202 +6619,202 @@ Environmental exposures include those imposed by natural environments, experimen - - - - cjm - 2017-11-05T03:20:01Z + realizable has basis in + 2017-11-05T03:20:01Z + cjm + + - - - cjm - 2017-11-05T03:20:29Z + is basis for realizable + 2017-11-05T03:20:29Z + cjm + - - - - cjm - 2017-11-05T03:26:47Z + disease has basis in + 2017-11-05T03:26:47Z + cjm + + - - - + + disease has basis in dysfunction of + 2017-11-05T03:29:32Z + cjm A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - cjm - 2017-11-05T03:29:32Z - disease has basis in dysfunction of + + - - - - A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. - disease has basis in disruption of (disease to process) - cjm - 2017-11-05T03:37:52Z + disease has basis in disruption of + 2017-11-05T03:37:52Z + cjm + disease has basis in disruption of (disease to process) + A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + + - - - - - A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm - 2017-11-05T03:46:07Z + disease has basis in feature + 2017-11-05T03:46:07Z + cjm + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. + + + - - - + + disease causes dysfunction of + 2017-11-05T03:58:20Z + cjm + disease causes dysfunction of (disease to anatomical entity) + + - - + + - disease causes dysfunction of (disease to anatomical entity) - cjm - 2017-11-05T03:58:20Z - disease causes dysfunction of - - - + + disease has location + 2017-11-05T04:06:02Z + cjm + TODO: complete range axiom once more of CARO has been mireoted in to this ontology + This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. + + - - + + - A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. - TODO: complete range axiom once more of CARO has been mireoted in to this ontology - This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm - 2017-11-05T04:06:02Z - disease has location - - - - - A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm - 2017-12-26T19:37:31Z + disease has inflammation site + 2017-12-26T19:37:31Z + cjm + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity + + + - - - - + + realized in response to stimulus + 2017-12-26T19:45:49Z + cjm + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + + + - - + + - A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm - 2017-12-26T19:45:49Z - realized in response to stimulus - - - A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - cjm - 2017-12-26T19:50:53Z + disease has feature + 2017-12-26T19:50:53Z + cjm + A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. + - - - - A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. - cjm - 2017-12-26T19:58:44Z + disease arises from structure + 2017-12-26T19:58:44Z + cjm + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. + + - - + + enables subfunction + 2018-01-25T23:20:13Z + cjm + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + - - + + - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm - 2018-01-25T23:20:13Z - enables subfunction - - - - cjm - 2018-01-26T23:49:30Z + acts upstream of or within, positive effect + 2018-01-26T23:49:30Z + cjm + + @@ -6801,26 +6822,26 @@ Environmental exposures include those imposed by natural environments, experimen - - - - cjm - 2018-01-26T23:49:51Z + acts upstream of or within, negative effect + 2018-01-26T23:49:51Z + cjm + + - - - - c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - - cjm - 2018-01-26T23:53:14Z + acts upstream of, positive effect + 2018-01-26T23:53:14Z + cjm + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + + @@ -6828,14 +6849,14 @@ Environmental exposures include those imposed by natural environments, experimen - - - - c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - - cjm - 2018-01-26T23:53:22Z + acts upstream of, negative effect + 2018-01-26T23:53:22Z + cjm + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + + @@ -6843,243 +6864,243 @@ Environmental exposures include those imposed by natural environments, experimen - - - - cjm - 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + 2018-03-13T23:55:05Z + cjm + + - - - - cjm - 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + 2018-03-13T23:55:19Z + cjm + + - - - + + epiphyte of An interaction relationship wherein a plant or algae is living on the outside surface of another plant. https://en.wikipedia.org/wiki/Epiphyte - epiphyte of + + - - - inverse of epiphyte of - + has epiphyte + inverse of epiphyte of + + - - - + + kleptoparasite of A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material https://en.wikipedia.org/wiki/Kleptoparasitism - kleptoparasite of + + - - - inverse of kleptoparasite of - + kleptoparasitized by + inverse of kleptoparasite of + + - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + lays eggs on + An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + + - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + has eggs laid on by + An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + - - - - - muffin 'has substance added' some 'baking soda' - + + + has substance added "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. Damion Dooley - has substance added + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + muffin 'has substance added' some 'baking soda' + + + - - - - - 'egg white' 'has substance removed' some 'egg yolk' - + + + has substance removed "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + 'egg white' 'has substance removed' some 'egg yolk' Damion Dooley - has substance removed + + + - - - - - sardines 'immersed in' some 'oil and mustard' - - "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - Damion Dooley + + immersed in + Damion Dooley + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + sardines 'immersed in' some 'oil and mustard' + + + - - - - bread 'has primary substance added' some 'flour' - + + + has primary substance added 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. Damion Dooley - has primary substance added + bread 'has primary substance added' some 'flour' + + - - - - - - - - - A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. - An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) - Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. + + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall David Osumi-Sutherland + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + Austin Meier Marie Angelique Laporte + Chris Mungall + Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) triggered by process - realized in response to - https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit + + + + + + + - - - triggered by process RO:cjm + triggered by process + + - - - - + + generically depends on + The pattern shared by chess boards generically depends on any chess board. + [072-ISO] Genetic information generically depend on molecules of DNA. The novel *War and Peace* generically depends on this copy of the novel. - The pattern shared by chess boards generically depends on any chess board. + g-depends on The score of a symphony g-depends on a copy of the score. - This pdf file generically depends on this server. A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. - [072-ISO] - g-depends on - generically depends on + This pdf file generically depends on this server. + + + - - - - Molecules of DNA are carriers of genetic information. - This copy of *War and Peace* is carrier of the novel written by Tolstoy. + + is carrier of This hard drive is carrier of these data items. - *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* [072-ISO] - is carrier of + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + Molecules of DNA are carriers of genetic information. + + - - + + has anatomical participant + 2018-09-26T01:08:58Z + cjm + p has anatomical participant c iff p has participant c, and c is an anatomical entity + - - + + - p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm - 2018-09-26T01:08:58Z - has anatomical participant - + @@ -7096,32 +7117,32 @@ Environmental exposures include those imposed by natural environments, experimen - + + has increased age-specific mortality rate + 2018-05-22T16:43:28Z + dos + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - + - 0 + 0 - 100 + 100 - Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - 2018-05-22T16:43:28Z - This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. - has increased age-specific mortality rate - dos - - + Wikipedia:Infant_mortality Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. PMID:24138933 - Wikipedia:Infant_mortality + + @@ -7140,97 +7161,97 @@ Environmental exposures include those imposed by natural environments, experimen - International Classification of Diseases + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + @@ -7239,17 +7260,17 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - - + + @@ -7258,104 +7279,104 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - + - - + + database extract, transform, and load process + - - + + - - + + - database extract, transform, and load process A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. - PERSON:Alan Ruttenberg ETL WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load - - - database extract, transform, and load process + PERSON:Alan Ruttenberg + database extract, transform, and load process + + - + - + - + - - + Systematized Nomenclature of Medicine + - + - + - - - - - - - + + - - + + + + + + + @@ -7364,29 +7385,29 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - + - + - + - - + + @@ -7399,271 +7420,271 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - + - + - + - + + discharge process - - + + - + - + Amanda Hicks a document act in which concludes an inpatient encounter - discharge process - + - + - + - + - + - + - - - An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0000047 - - biological sex + + biological sex + + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + PATO:0000047 + http://purl.obolibrary.org/obo/pato.owl + quality + - - - An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0000169 - - - viability + + viability + + An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. + PATO:0000169 + http://purl.obolibrary.org/obo/pato.owl + quality + + - - - A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0000383 - - - female + + female + + A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. + PATO:0000383 + http://purl.obolibrary.org/obo/pato.owl + quality + + - - - A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0000384 - - - male + + male + + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + PATO:0000384 + http://purl.obolibrary.org/obo/pato.owl + quality + + - - - A viability quality inhering in a bearer by virtue of the bearer's condition before death. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0001421 - - alive + + alive + + A viability quality inhering in a bearer by virtue of the bearer's condition before death. + PATO:0001421 + http://purl.obolibrary.org/obo/pato.owl + quality + - - - A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0001422 - - dead + + dead + + A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. + PATO:0001422 + http://purl.obolibrary.org/obo/pato.owl + quality + - - - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0001894 - - phenotypic sex + + phenotypic sex + + PATO:0001894 + http://purl.obolibrary.org/obo/pato.owl + quality + - - - A quality that inheres in an entire organism or part of an organism. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0001995 - organismal quality + + organismal quality + + A quality that inheres in an entire organism or part of an organism. + PATO:0001995 + http://purl.obolibrary.org/obo/pato.owl + quality - - - A material entity consisting of multiple components that are causally integrated. + + system + May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall + A material entity consisting of multiple components that are causally integrated. http://www.jbiomedsem.com/content/4/1/43 - system - - - An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. - uberon - UBERON:0000000 - - processual entity + + processual entity + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + UBERON:0000000 + uberon + - - - End of the life of an organism. - http://purl.obolibrary.org/obo/uberon.owl - ncit:Death is an outcome - XAO:0000437 - XtroDO:0000085 - uberon - death - UBERON:0000071 - death stage + + death stage + + End of the life of an organism. + UBERON:0000071 + XAO:0000437 + XtroDO:0000085 + death + http://purl.obolibrary.org/obo/uberon.owl + ncit:Death is an outcome + uberon - - - An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. - http://purl.obolibrary.org/obo/uberon.owl - FBdv:00000000 - HsapDv:0000001 - MmusDv:0000001 - OGES:000011 - ncithesaurus:Life - entire life cycle - entire lifespan - life - lifespan - uberon - UBERON:0000104 - - life cycle + + life cycle + + An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + FBdv:00000000 + HsapDv:0000001 + MmusDv:0000001 + OGES:000011 + UBERON:0000104 + entire life cycle + entire lifespan + http://purl.obolibrary.org/obo/uberon.owl + life + lifespan + ncithesaurus:Life + uberon + @@ -7671,66 +7692,66 @@ Environmental exposures include those imposed by natural environments, experimen - - - A spatiotemporal region encompassing some part of the life cycle of an organism. - this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here - http://purl.obolibrary.org/obo/uberon.owl - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage - BILS:0000105 - EFO:0000399 - FBdv:00007012 - FMA:24120 - HsapDv:0000000 - MmusDv:0000000 - OlatDv:0000010 - PdumDv:0000090 - WBls:0000002 - XAO:1000000 - ZFS:0000000 - ZFS:0100000 - ncithesaurus:Developmental_Stage - developmental stage - stage - uberon - UBERON:0000105 - - - life cycle stage + + life cycle stage + + A spatiotemporal region encompassing some part of the life cycle of an organism. + BILS:0000105 + EFO:0000399 + FBdv:00007012 + FMA:24120 + HsapDv:0000000 + MmusDv:0000000 + OlatDv:0000010 + PdumDv:0000090 + UBERON:0000105 + WBls:0000002 + XAO:1000000 + ZFS:0000000 + ZFS:0100000 + developmental stage + http://purl.obolibrary.org/obo/uberon.owl + ncithesaurus:Developmental_Stage + stage + the WBls class 'all stages' belongs here as it is the superclass of other WBls stages + this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here + uberon + we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage + + - - - Of or pertaining to the period of time immediately following birth, or to the newborn. - consider splitting infant/newborn - http://purl.obolibrary.org/obo/uberon.owl + + neonate stage + + BTO:0001762 + EV:0300037 + HsapDv:0000082 + MmusDv:0000096 + NIF_Organism:birnlex_695 + OGES:000025 + Of or pertaining to the period of time immediately following birth, or to the newborn. + UBERON:0007221 + consider splitting infant/newborn + fledgling stage + hatchling + hatchling stage + http://purl.obolibrary.org/obo/uberon.owl + infant stage + neonatal stage + nestling stage + newborn stage + pouch stage + puggle + puggle stage + uberon - BTO:0001762 - EV:0300037 - HsapDv:0000082 - MmusDv:0000096 - NIF_Organism:birnlex_695 - OGES:000025 - neonatal stage - fledgling stage - hatchling - hatchling stage - infant stage - nestling stage - pouch stage - puggle - puggle stage - uberon - newborn stage - UBERON:0007221 - neonate stage @@ -7738,69 +7759,64 @@ Environmental exposures include those imposed by natural environments, experimen - - - A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. - uberon - UBERON:0035943 - - life cycle temporal boundary + + life cycle temporal boundary + + A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. + UBERON:0035943 + uberon + - - - A life cycle temporal boundary that marks the end of the life cycle of the organism. - end of life cycle - moment of death - time of death - uberon - death - end of life - UBERON:0035944 - life-death temporal boundary + + life-death temporal boundary + + A life cycle temporal boundary that marks the end of the life cycle of the organism. + UBERON:0035944 + death + end of life + end of life cycle + moment of death + time of death + uberon - - - A life cycle temporal boundary that marks the start of the neonate stage of the organism. - moment of birth - time of birth - uberon - birth - UBERON:0035946 - start of neonate stage + + start of neonate stage + + A life cycle temporal boundary that marks the start of the neonate stage of the organism. + UBERON:0035946 + birth + moment of birth + time of birth + uberon - - - - - - - - + + admitting diagnosis + - + - + - - + + @@ -7809,201 +7825,207 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - - + + - - a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or during the admission of that patient + + + + + + + Amanda Hicks - S. Clint Dowland PCORnet CDM 4.1 - admitting diagnosis + S. Clint Dowland + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or during the admission of that patient - - - Amanda Hicks - A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process. + PCORnet racial identity datum + + A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process. + Amanda Hicks - - - Amanda Hicks + PCORnet American Indian or Alaska Native identity datum + + Amanda Hicks - - - Amanda Hicks + PCORnet Asian identity datum + + Amanda Hicks - - - Amanda Hicks + PCORnet black or African American identity datum PCORnet item + + Amanda Hicks - - + PCORnet CDM item identifier + - - + PCORnet item + - - - Amanda Hicks + PCORnet Native Hawaiian or other Pacific Islander identity datum + + Amanda Hicks - - - Amanda Hicks + PCORnet white identity datum + + Amanda Hicks - - - Amanda Hicks + PCORnet multiple race identity datum + + Amanda Hicks - - - + + PCORnet Hispanic identity datum + + Amanda Hicks From PCORnet CDM "A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." - PCORnet Hispanic identity datum - - - - Amanda Hicks + PCORnet not Hispanic identity datum + + + Amanda Hicks - - - Amanda Hicks + PCORnet ethnic identity datum + + Amanda Hicks - - + + PCORnet patient identifier + A centrally registered identifier that denotes a person in a PCORnet data mart and is used to link across tables. This identifier is not necessarily unique within PCORnet. Amanda Hicks - PCORnet patient identifier - - + + admission process + - - + + - - + + Amanda Hicks a social act in which a patient is registered with a health care provider for the purposes of recieving care in an inpatient encounter - admission process - - + + discharge diagnosis + - + - + - - + + @@ -8012,617 +8034,628 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - - + + - - a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or simultaneously with the discharge of that patient + Amanda Hicks - S. Clint Dowland PCORnet CDM 4.1 - discharge diagnosis + S. Clint Dowland + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or simultaneously with the discharge of that patient - - + + final diagnosis + - + - + - - + + - a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an outpatient encounter Amanda Hicks - S. Clint Dowland PCORnet CDM 4.1 - final diagnosis + S. Clint Dowland + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an outpatient encounter - - + + interim diagnosis + - + - + - - + + - a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge of that patient Amanda Hicks - S. Clint Dowland PCORnet CDM 4.1 - interim diagnosis + S. Clint Dowland + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge of that patient - - + PCORnet racial identification process + - - + PCORnet sexual orientation identity datum + - - + + ambulatory visit + - - + + - - + + - + + PCORnet CDM 4.1 + Amanda Hicks An outpatient encounter that occurs in an outpatient clinic, physician office, ambulatory surgery facility, urgent care facilitu, or a hospital encounters and that does not occur in an emergency department facillity. - Amanda Hicks - PCORnet CDM 4.1 Includes visits at outpatient clinics, physician offices, same day/ambulatory surgery centers, urgent care facilities, and other same-day ambulatory hospital encounters, but excludes emergency department encounters - ambulatory visit - - - A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility. + + deprecated emergency department encounter + + true Amanda Hicks - PCORnet CDM 4.1 Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known. - emergency department encounter + PCORnet CDM 4.1 + A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility. - - - A healthcare encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay - Amanda Hicks - PCORnet CDM 4.1 - Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished. - A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person. Unlike data items they are not necessilary contributed or acquired by a reliable method. + emergency department admit to inpatient hospital stay sexual orientation identity datum + + PCORnet CDM 4.1 + A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person. Unlike data items they are not necessilary contributed or acquired by a reliable method. + Amanda Hicks + A healthcare encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay + Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished. - - - + PCORnet asexual identity datum inpatient hospital encounter + + - - + PCORnet gay identity datum + - - + PCORnet lesbian identity datum + - - + PCORnet multiple sexual orientations identity datum + - - + PCORnet queer identity datum + - - + PCORnet questioning identity datum + - - + PCORnet something else identity datum + - - + PCORnet straight identity datum + - - - A gender identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the 2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the other does not have a multiple gender option, which changes the meaning of the values in the value set. + PCORnet gender identity datum + + A gender identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the 2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the other does not have a multiple gender option, which changes the meaning of the values in the value set. - - + PCORnet genderqueer identity datum + - - + PCORnet man identity datum + - - + PCORnet multiple genders datum + - - + PCORnet something else identity datum + - - + PCORnet transgenderfemale/transwoman/male-to-female identity datum + - - + PCORnet transgendermale/transman/female-to-male identity datum + - - + PCORnet woman identity datum + - - + PCORnet diagnosis identifier + - - + + code set + - - + + - - + + a set of non-lexical symbols with a conventionally agreed usage among a group for a particular purpose - code set - - + + PCORnet discharge status data item + A data item that is about a patient discharge (or lack thereof) and (where applicable) the type of facility or organization to which the patient was discharged. Matthew Diller S. Clint Dowland - PCORnet discharge status data item - - + + PCORnet skilled nursing facility discharge status data item + A PCORnet discharge status that is about a skilled nursing facility to which a patient was discharged. Matthew Diller S. Clint Dowland - PCORnet skilled nursing facility discharge status data item - - + + PCORnet adult foster home facility discharge status data item + A PCORnet discharge status that is about an adult foster home facility to which a patient was discharged. Matthew Diller S. Clint Dowland - PCORnet adult foster home facility discharge status data item - - + + PCORnet assisted living facility discharge status data item + A PCORnet discharge status that is about an assisted living facility to which a patient was discharged. Matthew Diller S. Clint Dowland - PCORnet assisted living facility discharge status data item - - + + PCORnet other acute inpatient hospital discharge status data item + A PCORnet discharge status that is about a hospital facility to which a patient was discharged and that is distinct from the discharging hospital. Amanda Hicks Matthew Diller S. Clint Dowland - PCORnet other acute inpatient hospital discharge status data item - - + + PCORnet nursing home facility discharge status data item + A PCORnet discharge status that is about a nursing home facility to which a patient was discharged. Matthew Diller S. Clint Dowland - PCORnet nursing home facility discharge status data item - - + + PCORnet rehabilitation facility discharge status data item + A PCORnet discharge status that is about a rehabilitation facility to which a patient was discharged. Matthew Diller S. Clint Dowland - PCORnet rehabilitation facility discharge status data item - - + + PCORnet residential facility discharge status data item + A PCORnet discharge status that is about a residential facility to which a patient was discharged. Matthew Diller S. Clint Dowland - PCORnet residential facility discharge status data item - - + + PCORnet hospice discharge status data item + A PCORnet discharge status that is about a hospice organization to which a patient was discharged. Matthew Diller S. Clint Dowland - PCORnet hospice discharge status data item - - + + PCORnet against medical advice discharge status data item + A PCORnet discharge status that is about a patient who is discharged upon deciding to leave against the advice of a health care provider. Matthew Diller S. Clint Dowland - PCORnet against medical advice discharge status data item - - + + PCORnet still in hospital discharge status data item + A PCORnet discharge status that is about a hospital facility in which a patient remains, having not been discharged. Matthew Diller S. Clint Dowland - PCORnet still in hospital discharge status data item - - + + PCORnet home health discharge status data item + A PCORnet discharge status that is about a home healthcare organization and the household to which a patient was discharged. Matthew Diller S. Clint Dowland - PCORnet home health discharge status data item - - + + PCORnet admitting source data item + A data item that is about a patient admission and the type of facility from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland - PCORnet admitting source data item - - + + PCORnet home health admitting source data item + A PCORnet data item that is about a home healthcare organization and the household from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland - PCORnet home health admitting source data item - - + + PCORnet skilled nursing facility admitting source data item + A PCORnet data item that is about a skilled nursing facility from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland - PCORnet skilled nursing facility admitting source data item - - + + PCORnet emergency department admitting source data item + A PCORnet data item that is about an emergency department from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland - PCORnet emergency department admitting source data item - - + + PCORnet intra-hospital admitting source data item + A PCORnet data item that is about another department in the same hospital from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland - PCORnet intra-hospital admitting source data item - - + + PCORnet ambulatory visit admitting source data item + A PCORnet data item that is about a patient admission that is causally upstream of an outpatient encounter. Matthew Diller S. Clint Dowland - PCORnet ambulatory visit admitting source data item - - + + PCORnet health care encounter identifier + A proper name that denotes a health care encounter and has part some symbol. Matthew Diller S. Clint Dowland - PCORnet health care encounter identifier - - + + PCORnet facility identifier + A proper name that denotes a health care facility and has part some symbol. Matthew Diller S. Clint Dowland - PCORnet facility identifier - - + + institutional professional consult + A health care encounter that realizes some health care provider role that inheres in some Homo sapiens. Matthew Diller S. Clint Dowland - institutional professional consult - - + + non-acute institutional stay + A health care encounter that occurs in some hospice facility, skilled nursing facility, rehabilitation facility, nursing home facility, residential home facility, overnight non-hospital dialysis facility, adult foster home facility, or assisted living facility. Matthew Diller S. Clint Dowland - non-acute institutional stay + + + + + + + + observation stay + + A health care encounter that occurs in some hospital facility or emergency department and that realizes some healthcare provider role that inheres in some organization. + Matthew Diller @@ -8640,101 +8673,101 @@ excludes emergency department encounters - + - An extension of the ICD-10 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. - NCI International Classification of Diseases, Tenth Revision, Clinical Modification + NCI + An extension of the ICD-10 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. - - - Published by the College of American Pathologists, the Systematized Nomenclature of Medicine Clinical Terms is a combination of content of SNOMED Reference Terminology and READ codes. - NCI + + Systematized Nomenclature of Medicine Clinical Terms + NCI + Published by the College of American Pathologists, the Systematized Nomenclature of Medicine Clinical Terms is a combination of content of SNOMED Reference Terminology and READ codes. - + + International Classification of Diseases, Ninth Revision, Clinical Modification An extension of the ICD-9 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. NCI - International Classification of Diseases, Ninth Revision, Clinical Modification - + - + - + - - - + + John Doe + - - - - + + John Doe's birth + + - - - - + + 23:59 + + - - - + + John Doe's neonate stage + - - + + 1D temporal interval occuped by John Doe's neonate stage @@ -8742,8 +8775,8 @@ excludes emergency department encounters - - + + 2000-02-02 @@ -8751,18 +8784,18 @@ excludes emergency department encounters - - - + rta1 + + - - + + eiqap1 @@ -8770,28 +8803,28 @@ excludes emergency department encounters - - - + + Jane Doe + - - - + + g + - - + + p4 @@ -8799,18 +8832,18 @@ excludes emergency department encounters - - - + + f1 + - - + + p5 @@ -8818,21 +8851,21 @@ excludes emergency department encounters - - - - - + + + John Doe's patient role m1 + + - - + + ridqap1 @@ -8840,8 +8873,8 @@ excludes emergency department encounters - - + + Jane Doe's American Indian or Alaska Native identity datum @@ -8849,28 +8882,28 @@ excludes emergency department encounters - - - + + p6 + - - - + rta2 + + - - + + Jane Doe's racial identification process @@ -8878,8 +8911,8 @@ excludes emergency department encounters - - + + ETL process of Jane Doe’s racial identity datum @@ -8887,20 +8920,20 @@ excludes emergency department encounters - - - - - + + John Doe's Hispanic or Latino identity datum + + + - - + + John Doe’s ethnic identification process @@ -8908,19 +8941,19 @@ excludes emergency department encounters - - - - + + John Doe’s PCORnet Hispanic identity datum + + - - + + ETL process of John Doe’s ethnic identity datum @@ -8928,20 +8961,20 @@ excludes emergency department encounters - - - - - + + Jane Doe's not Hispanic or Latino identity datum + + + - - + + Jane Doe’s ethnic identification process @@ -8949,19 +8982,19 @@ excludes emergency department encounters - - - - + + Jane Doe’s PCORnet not Hispanic identity datum + + - - + + ETL process of John Doe’s ethnic identity datum @@ -8969,8 +9002,8 @@ excludes emergency department encounters - - + + ETL process of Jane Doe’s ethnic identity datum @@ -8978,18 +9011,18 @@ excludes emergency department encounters - - - + + John Doe's patient role + - - + + 1234 @@ -8997,19 +9030,19 @@ excludes emergency department encounters - + - + - + @@ -9024,38 +9057,45 @@ excludes emergency department encounters /////////////////////////////////////////////////////////////////////////////////////// --> - - true + + David Osumi-Sutherland + - + + + + inverse of has disposition - + - - - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + + - - + + - - - David Osumi-Sutherland + + A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility. + Amanda Hicks + Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known. + PCORnet CDM 4.1 + emergency department encounter - - + + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + - - + + - - + + true - - + + - - + + @@ -9069,69 +9109,69 @@ excludes emergency department encounters --> - + - + - - + + - + + - - - + + + + + + + + - - - - - - - - + - + + - - + + - + + + + + + + - - - - - - - - + + + - - + - + From bf951102f2b99fdac5c92a3d00b3d9b24c2a7972 Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Mon, 9 Sep 2019 12:16:41 -0400 Subject: [PATCH 09/69] MIREOT'd 'vehicle' from ENVO. --- PCORnetCDM.owl | 7097 ++++++++++++++++++++++++------------------------ 1 file changed, 3572 insertions(+), 3525 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 64942d1..e3b7606 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1,59 +1,38 @@ - - - - - - - - - - - - - - - - - - -]> - - - - - 2019-08-03 - William R. Hogan - Josh Hanna + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> + + + + + + + + + + Amanda Hicks + Josh Hanna + William R. Hogan + 2019-08-03 RDFized PCORnet CDM - - - - - - - - - @@ -71,7 +50,7 @@ - + BFO OWL specification label BFO OWL specification label @@ -80,7 +59,7 @@ - + BFO CLIF specification label BFO CLIF specification label @@ -89,13 +68,13 @@ - + - + example of usage example of usage @@ -104,23 +83,23 @@ - + - - textual definition + definition definition + textual definition - + editor note editor note @@ -129,37 +108,39 @@ - + - + + alternative term + - + - + - + - + imported from @@ -167,22 +148,22 @@ - + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. - + - + - + elucidation elucidation @@ -191,7 +172,7 @@ - + has associated axiom(nl) has associated axiom(nl) @@ -200,7 +181,7 @@ - + has associated axiom(fol) has associated axiom(fol) @@ -209,56 +190,56 @@ - + - + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - + - - never in taxon + + tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - ?X DisjointWith RO_0002162 some ?Y Chris Mungall - tooth SubClassOf 'never in taxon' value 'Aves' - + ?X DisjointWith RO_0002162 some ?Y + never in taxon + - - mutually spatially disjoint with - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) non-overlapping with shares no parts with - - + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) + mutually spatially disjoint with + + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + - - taxonomic class assertion + An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + taxonomic class assertion @@ -266,73 +247,73 @@ - + - + defined by inverse - + - - logical macro assertion - https://github.com/oborel/obo-relations/wiki/ShortcutRelations + An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + logical macro assertion + https://github.com/oborel/obo-relations/wiki/ShortcutRelations - - annotation property cardinality + An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. - - + annotation property cardinality + + - - logical macro assertion on a class + A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL - + logical macro assertion on a class + - - logical macro assertion on a property + A logical macro assertion whose domain is an IRI for a property + logical macro assertion on a property - - logical macro assertion on an object property + Used to annotate object properties to describe a logical meta-property or characteristic of the object property. - + logical macro assertion on an object property + - + logical macro assertion on an annotation property @@ -340,30 +321,30 @@ - - dispositional interpretation + An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. - + dispositional interpretation + - - has no connections with + 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' + A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. shares no connection with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) - A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. - + has no connections with + - + inherited annotation property @@ -371,222 +352,220 @@ - - curator guidance link + Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) - + curator guidance link + - - always present in taxon + + brain always_present_in_taxon 'Vertebrata' + forelimb always_present_in_taxon Euarchontoglires S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. never lost in - brain always_present_in_taxon 'Vertebrata' - forelimb always_present_in_taxon Euarchontoglires - + always present in taxon + - - temporal logical macro assertion on a class + This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. - + temporal logical macro assertion on a class + - + measurement property has unit - + - + has start time value - + - + has end time value - + - - start, days post fertilization + Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. - + start, days post fertilization + - - end, days post fertilization + Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. - + end, days post fertilization + - - start, years post birth + Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. - + start, years post birth + - - end, years post birth + Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 - + end, years post birth + - - start, months post birth + Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. - + start, months post birth + - - end, months post birth + Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 - + end, months post birth + - - month of gestation + Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. - + month of gestation + - - has developmental stage marker + A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process - + has developmental stage marker + - - start, days post coitum - For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + Count of number of days intervening between the start of the stage and the time of coitum. - + For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + start, days post coitum + - - end, days post coitum + Count of number of days intervening between the end of the stage and the time of coitum. - + end, days post coitum + - + start, weeks post birth - + - + end, weeks post birth - + - - is asymmetric relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p - + is asymmetric relational form of process class + https://github.com/oborel/obo-relations/wiki/InteractionRelations + - - is symmetric relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p - + is symmetric relational form of process class + https://github.com/oborel/obo-relations/wiki/InteractionRelations + - - is relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations + R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process - + is relational form of process class + https://github.com/oborel/obo-relations/wiki/InteractionRelations + - - is direct form of - Chris Mungall + relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: @@ -597,218 +576,220 @@ Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - + Chris Mungall + is direct form of + - - is indirect form of + relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall - + is indirect form of + - + logical macro assertion on an axiom - + - - is a defining property chain axiom + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - + is a defining property chain axiom + - - is a defining property chain axiom where second argument is reflexive + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - + is a defining property chain axiom where second argument is reflexive + - - is relational form of a class + An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. - + is relational form of a class + - - logical macro assertion involving identity + A shortcut relationship that holds between two entities based on their identity criteria - + logical macro assertion involving identity + - - in approximate one to one relationship with + A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. - + in approximate one to one relationship with + - - is approximately equivalent to - The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y - + The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + is approximately equivalent to + - - is opposite of + 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - + is opposite of + - - is indistinguishable from + x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - + is indistinguishable from + - + evidential logical macro assertion on an axiom - + - - axiom has evidence - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom - + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom has evidence + - - axiom contradicted by evidence - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom - + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom contradicted by evidence + - - is representative IRI for equivalence set - OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member + In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. - If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. - + If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion + is representative IRI for equivalence set + OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member + - - is directional form of - 2018-03-13T23:59:29Z - cjm + Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" - + cjm + 2018-03-13T23:59:29Z + is directional form of + - + + cjm + 2018-03-14T00:03:16Z is positive form of - 2018-03-14T00:03:16Z - cjm - + - + + cjm + 2018-03-14T00:03:24Z is negative form of - 2018-03-14T00:03:24Z - cjm - + - - is homeomorphic for - 2018-10-21T19:46:34Z - cjm + + part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. + cjm + 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. - part-of is homeomorphic for independent continuants. - + is homeomorphic for + - - external_ontology_notes + + external_ontology_notes - + PCORnet CDM Comments @@ -816,122 +797,122 @@ Where we have an annotation assertion - + eco subset - + - + - + - + - - subset_property + + subset_property - + - + - - database_cross_reference + + database_cross_reference - - has_exact_synonym + + has_exact_synonym - - has_narrow_synonym + + has_narrow_synonym - - has_obo_namespace + + has_obo_namespace - - has_related_synonym + + has_related_synonym - + - - in_subset + + in_subset - + is defined by - This is an experimental annotation + + is defined by - - + This is an experimental annotation - + label @@ -939,21 +920,21 @@ Where we have an annotation assertion - - see also + + see also - + - + @@ -970,327 +951,327 @@ Where we have an annotation assertion - + + + + + + + + + - - - - - - - - - - + + - - + + - - - + + + - - exists at + + + + + exists-at + existsAt BFO2 Reference: entity BFO2 Reference: temporal region b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) - existsAt - exists-at - - - - + + exists at - - - has occurrent part - http://purl.obolibrary.org/obo/vo.owl - [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) - [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life - [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. + + + + + + o-has-part - (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] - [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent hasOccurrentPart + [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life + [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) - - - - - + [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. + [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent + http://purl.obolibrary.org/obo/vo.owl + [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) + (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] + + has occurrent part - - - has proper occurrent part - http://purl.obolibrary.org/obo/vo.owl + + + + + + o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 - - - - - + http://purl.obolibrary.org/obo/vo.owl + + has proper occurrent part - - - has temporal part - http://purl.obolibrary.org/obo/vo.owl + + + + + + + has-t-part [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life. + [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) - [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating - has-t-part - - - - - + http://purl.obolibrary.org/obo/vo.owl + + has temporal part - - - part of occurrent - http://purl.obolibrary.org/obo/vo.owl - BFO2 Reference: occurrent - occurrentPartOf + + + + + o-part-of - (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] - (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] - [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) - (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] - (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] - (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] - BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. + occurrentPartOf Mary’s 5th birthday occurrent_part_of Mary’s life The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. + the first set of the tennis match occurrent_part_of the tennis match. + [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) + BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. + BFO2 Reference: occurrent + http://purl.obolibrary.org/obo/vo.owl b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) - the first set of the tennis match occurrent_part_of the tennis match. - - - - + (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] + (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] + (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] + (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] + (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] + + part of occurrent - - - proper part of occurrent + + + + + + o-ppart-of + properOccurrentPartOf [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) - properOccurrentPartOf - o-ppart-of (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] - - - - + + proper part of occurrent - - - temporal part of - http://purl.obolibrary.org/obo/vo.owl - (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] - (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] - temporalPartOf + + + + + t-part-of - (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] - b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) - b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) - if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) + temporalPartOf the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life the process boundary which separates the 3rd and 4th years of your life. your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating - - - - + b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) + b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) + http://purl.obolibrary.org/obo/vo.owl + if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) + (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] + (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] + (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] + + temporal part of - - occupies temporal region + + + + + spans occupiesTemporalRegion p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) - - - - - + + occupies temporal region - - has temporal occupant + + + + span-of - [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) spanOf - - - - + [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) + + has temporal occupant - - during which exists - [copied from inverse property 'exists at'] BFO2 Reference: entity + + + during-which-exists + [copied from inverse property 'exists at'] BFO2 Reference: entity [copied from inverse property 'exists at'] BFO2 Reference: temporal region [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) - - - + + during which exists - + - + - + - - is_specified_input_of - PERSON:Bjoern Peters - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - Alan Ruttenberg + + + is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - - - + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_input_of - + - + - - + + - + - + - + - - - + + + - - + + @@ -1298,130 +1279,129 @@ Where we have an annotation assertion - + - - contained in + + + + + + + + + contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) - contained in contained_in - - - - - - - - - + + + contained in - - contains + contains - - + + + contains - - is allergic trigger for - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + + + + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) - - - + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is allergic trigger for - - is autoimmune trigger for + + + + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - - - + is autoimmune trigger for - - has allergic trigger - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) - - + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has allergic trigger - - has autoimmune trigger + + + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - - + has autoimmune trigger - - + + - + + David Osumi-Sutherland - - - tracheates - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + + + + + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). David Osumi-Sutherland - - - + tracheates - - bounding layer of - David Osumi-Sutherland - A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + + + X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y @@ -1431,268 +1411,267 @@ range: spatial region or site (immaterial continuant) has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - + David Osumi-Sutherland + + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + bounding layer of - - coincident with - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. - Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. - David Osumi-Sutherland + + + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - - + David Osumi-Sutherland + + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + coincident with - - regulates in other organism - David Osumi-Sutherland + + + + x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - - - + David Osumi-Sutherland + regulates in other organism - - regulates transport of - David Osumi-Sutherland - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - + - - + + + A relationship that holds between a process that regulates a transport process and the entity transported by that process. + David Osumi-Sutherland + + regulates transport of - - occurent part of + + + + + A part of relation that applies only between occurents. - - - - + occurent part of - - has regulatory component activity - 2017-05-24T09:30:46Z - dos + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - - + dos + 2017-05-24T09:30:46Z + has regulatory component activity - - has negative regulatory component activity - 2017-05-24T09:31:01Z - dos - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - - + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity - - has positive regulatory component activity - 2017-05-24T09:31:17Z - dos + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - - + has positive regulatory component activity - - has necessary component activity - 2017-05-24T09:36:08Z - dos + + + + dos + 2017-05-24T09:36:08Z A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. - - + has necessary component activity - - has component activity - 2017-05-24T09:44:33Z - dos + + + dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - + has component activity - - has component process - 2017-05-24T09:49:21Z - dos + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - - - + dos + 2017-05-24T09:49:21Z + has component process - - has ligand - 2017-07-19T17:30:36Z - dos + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - + dos + 2017-07-19T17:30:36Z + has ligand - - transports - 2017-07-20T17:11:08Z - dos + + Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - + dos + 2017-07-20T17:11:08Z + transports - - occurs across - 2017-07-20T17:19:37Z - dos + + A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - + dos + 2017-07-20T17:19:37Z + occurs across - - directly regulated by - 2017-09-17T13:52:24Z - dos + + + + dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - - + directly regulated by - GOC:dos + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - - + GOC:dos - - directly negatively regulated by - 2017-09-17T13:52:38Z - dos + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - - + dos + 2017-09-17T13:52:38Z + directly negatively regulated by - GOC:dos + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - - + GOC:dos - - directly positively regulated by - 2017-09-17T13:52:47Z - dos + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - - + dos + 2017-09-17T13:52:47Z + directly positively regulated by - GOC:dos + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - - + GOC:dos - - - has effector activity - 2017-09-22T14:14:36Z - dos - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - - + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos - - - - in register with - 2017-12-07T12:58:06Z - dos + + A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; @@ -1701,9 +1680,13 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - + 2017-12-07T12:58:06Z + in register with + dos + + A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; @@ -1713,77 +1696,93 @@ A and B are aligned in C according to a shared co-ordinate framework so that com Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. GOC:dos - - - - + + - - + + - - - encompasses - Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - di + + + + David Osumi-Sutherland - - + di + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses - - + + - - David Osumi-Sutherland - - + - - + + + David Osumi-Sutherland + + - - + + - - fasciculates with - (forall (?x ?y) + + + + + + + + + + + + + + + + + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + David Osumi-Sutherland + fasciculates with + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -1803,83 +1802,81 @@ Examples include: the relationship between two channels collected simultaneously ) (overlaps ?nps ?npbss) )))))) - fasciculates with - David Osumi-Sutherland - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - - - - - + - - - - - - - - - - - + fasciculates with - - has plasma membrane part - Lindsay Cowell - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - Chris Mungall + + + + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] + Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - - - - - + Chris Mungall + Lindsay Cowell + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) + + has plasma membrane part - - releases neurotransmitter + + + + + has neurotransmitter - - - - + releases neurotransmitter - - overlaps - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + x overlaps y if and only if there exists some z such that x has part z and z part of y - - - - + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + overlaps - - has fasciculating neuron projection - (forall (?x ?y) + + + + + + + + + + + + + + + + The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + David Osumi-Sutherland + has fasciculating component + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -1902,461 +1899,445 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - has fasciculating component - - - - + - - - - - - - - - - - + has fasciculating neuron projection - - continuous with - X continuous_with Y if and only if X and Y share a fiat boundary. + + + + + + X continuous_with Y if and only if X and Y share a fiat boundary. + David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + + continuous with FMA:85972 - David Osumi-Sutherland - - - - - - - partially overlaps - (forall (?x ?y) + + + + x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x))))) - proper overlaps - x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x - We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - - - - + + + partially overlaps - - spatially disjoint from - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy - BFO_0000051 exactly 0 (BFO_0000050 some ?Y) + + + A is spatially_disjoint_from B if and only if they have no parts in common - Chris Mungall There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - - + Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy + BFO_0000051 exactly 0 (BFO_0000050 some ?Y) + + + spatially disjoint from + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - connected to - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - - + + - - + + - - + + + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + + connected to + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - connects - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - The M8 connects Glasgow and Edinburgh - - - + + + - - + + + The M8 connects Glasgow and Edinburgh + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + + connects + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - attached to part of - attached to part of (anatomical structure to anatomical structure) + + + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - - - + attached to part of (anatomical structure to anatomical structure) + attached to part of - - supplies - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + + Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. - + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + supplies - - drains + + Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - + drains - - has component - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component - - - - - - has phenotype - A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall - - - - + + + - - - + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + Chris Mungall + + has phenotype - - - phenotype of - Chris Mungall + + + + inverse of has phenotype - - - - + Chris Mungall + + + phenotype of - - - develops from - Melissa Haendel + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - This is the transitive form of the develops from relation Chris Mungall David Osumi-Sutherland + Melissa Haendel Terry Meehan - - - - - + This is the transitive form of the develops from relation + develops from - - - develops into - Chris Mungall + + + + + + inverse of develops from + Chris Mungall David Osumi-Sutherland Terry Meehan - - - - - + + develops into - - has gene product + + + + every HOTAIR lncRNA is the gene product of some HOXC gene every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene + x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y Chris Mungall - every HOTAIR lncRNA is the gene product of some HOXC gene - - - + has gene product - - directly develops from - TODO - add child relations from DOS - FBbt - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - has developmental precursor - David Osumi-Sutherland - - - - - + + + + - - + + - - + + - - + + - + + + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. + Chris Mungall + David Osumi-Sutherland + has developmental precursor + FBbt + + TODO - add child relations from DOS + directly develops from - - parasitoid of + + + A parasite that kills or sterilizes its host - - + parasitoid of - - has parasitoid + + inverse of parasitoid of - - + + has parasitoid - - directly develops into - developmental precursor of + + + inverse of directly develops from - - - + developmental precursor of + + directly develops into - - - regulates - false + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall David Hill Tanya Berardini + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. - Chris Mungall regulates (processual) - GO - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - - - - - - + false + regulates - - negatively regulates - Chris Mungall + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + negatively regulates (process to process) - - - - - + + negatively regulates - - - positively regulates + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall + positively regulates (process to process) - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - - - - - + + positively regulates - - has prototype - This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') - 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) - Chris Mungall - x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. - TODO: add homeomorphy axiom - Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) - + - - + + + 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) + heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') + + x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + TODO: add homeomorphy axiom + This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. + Chris Mungall + has prototype - - capable of - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - RO_0000053 some (RO_0000054 only ?Y) - - - - + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + capable of - - capable of part of - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) - has function in + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall - - + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + capable of part of @@ -2364,69 +2345,69 @@ Examples include: the relationship between two channels collected simultaneously - - actively participates in + + + + x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in - x actively participates in y if and only if x participates in y and x realizes some active role - - + actively participates in - - obsolete has active participant - true + + 'heart development' has active participant some Shh protein - has agent - Chris Mungall - This may be obsoleted and replaced by the original 'has agent' relation + x has participant y if and only if x realizes some active role that inheres in y - - - + This may be obsoleted and replaced by the original 'has agent' relation + Chris Mungall + has agent + + obsolete has active participant + true - - surrounded by + + + + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x Chris Mungall - - - - + + surrounded by - - adjacent to - x adjacent to y if and only if x and y share a boundary. + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. - This relation acts as a join point with BSPO - Chris Mungall The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - - - - - + + x adjacent to y if and only if x and y share a boundary. + This relation acts as a join point with BSPO + Chris Mungall + + adjacent to + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -2434,419 +2415,419 @@ Examples include: the relationship between two channels collected simultaneously - - surrounds - Chris Mungall + + + inverse of surrounded by - - - - + Chris Mungall + + + surrounds - - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + - + + Chris Mungall - - + - + + Chris Mungall - - + - - develops from part of - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall - - + + - - + + + + x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + Chris Mungall + develops from part of - - develops in + + + + + + + + + x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 - x develops_in y if x is located in y whilst x is developing - - - - - - - + develops in - - obligate parasite of + + A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - + obligate parasite of - - facultative parasite of + + A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - + facultative parasite of - + + Chris Mungall - - + - + + Chris Mungall - - + - - has start location - starts with process that occurs in - Chris Mungall + + + + + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - - - - + Chris Mungall + starts with process that occurs in + + has start location - - has end location + + + + + + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - - - - + + has end location - - has input + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes - - - - - - + + has input - - has output - Chris Mungall + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + Chris Mungall produces - - - - + + has output - - stem parasite of + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - + stem parasite of - - root parasite of + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - + root parasite of - - hemiparasite of + + A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. - + hemiparasite of - - has exposure receptor + + A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. ExO:0000001 - + has exposure receptor - - has exposure stressor - ExO:0000000 + + A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. - + ExO:0000000 + has exposure stressor - - has exposure route + + A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 - + has exposure route - - has exposure transport path - http://purl.obolibrary.org/obo/ExO_0000004 + + A broad relationship between an exposure event or process and the course takes from the source to the target. - + http://purl.obolibrary.org/obo/ExO_0000004 + has exposure transport path - - related via exposure to + + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. - + related via exposure to - - has active ingredient - A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. + + + + + Any portion of roundup 'has active ingredient' some glyphosate + A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. has active substance has active pharmaceutical ingredient - - - - + has active ingredient - - active ingredient in' + + inverse of has active ingredient - - + + active ingredient in' - - connecting branch of + + + b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - + connecting branch of - - has connecting branch + + inverse of connecting branch of - - + + has connecting branch - - has developmental contribution from - Chris Mungall - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - - - - + + + + + - - + + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + + x has developmental contribution from y iff x has some part z such that z develops from y + Chris Mungall + has developmental contribution from - - developmentally contributes to - inverse of has developmental contribution from - Chris Mungall - - - - + + + - - + + + + inverse of has developmental contribution from + Chris Mungall + + developmentally contributes to - - developmentally induced by - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - David Osumi-Sutherland + + + + + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T - induced by - Melissa Haendel Chris Mungall - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - - - - - + David Osumi-Sutherland + Melissa Haendel + induced by + Developmental Biology, Gilbert, 8th edition, figure 6.5(F) + GO:0001759 + We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] + developmentally induced by - - developmentally induces - Chris Mungall + + + + Inverse of developmentally induced by - - - + Chris Mungall + developmentally induces - - developmentally preceded by - false + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - - - - + developmentally preceded by - - acts upstream of - c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. - + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of @@ -2854,12 +2835,12 @@ Examples include: the relationship between two channels collected simultaneously - - acts upstream of or within + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. - + acts upstream of or within @@ -2867,56 +2848,56 @@ Examples include: the relationship between two channels collected simultaneously - - developmentally replaces - replaces + + + x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall - - + replaces + developmentally replaces - - developmentally succeeded by + + + Inverse of developmentally preceded by Chris Mungall - - + developmentally succeeded by - - part of developmental precursor of - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall - - + + - - + + + 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue + + Chris Mungall + part of developmental precursor of - - results in developmental progression of - results_in_developmental_progression_of - Chris Mungall + + + p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - - + Chris Mungall + results_in_developmental_progression_of + results in developmental progression of @@ -2924,246 +2905,250 @@ Examples include: the relationship between two channels collected simultaneously - - results in development of - http://www.geneontology.org/GO.doc.development.shtml - results_in_development_of + + + + every flower development (GO:0009908) results in development of some flower (PO:0009046) + p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. Chris Mungall - every flower development (GO:0009908) results in development of some flower (PO:0009046) - - - + http://www.geneontology.org/GO.doc.development.shtml + results_in_development_of + results in development of - - results in formation of - results_in_formation_of + + + + an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - GOC:mtg_berkeley_2013 - Chris Mungall every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - - + + Chris Mungall + GOC:mtg_berkeley_2013 + results_in_formation_of + results in formation of - - results in morphogenesis of - results_in_morphogenesis_of - GOC:mtg_berkeley_2013 - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + + + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - Chris Mungall tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - - - + + The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + Chris Mungall + GOC:mtg_berkeley_2013 + results_in_morphogenesis_of + results in morphogenesis of - - results in maturation of - results_in_maturation_of - Chris Mungall - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + + + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - GOC:mtg_berkeley_2013 bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - - - + + The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + Chris Mungall + GOC:mtg_berkeley_2013 + results_in_maturation_of + results in maturation of - - results in disappearance of - results_in_disappearance_of - May be merged into parent relation - Chris Mungall + + foramen ovale closure SubClassOf results in disappearance of foramen ovale - - + + Chris Mungall + May be merged into parent relation + results_in_disappearance_of + results in disappearance of - - results in developmental regression of + + every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) + Chris Mungall May be merged into parent relation - - + results in developmental regression of - - is treated by substance - cjm + + + Inverse of 'is substance that treats' - - - + cjm + + is treated by substance - - causally upstream of, positive effect - cjm + + + + + cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y - - - + causally upstream of, positive effect - - causally upstream of, negative effect - cjm + + + + + cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y - - - + causally upstream of, negative effect - - has exposure stimulus - 2017-06-05T17:35:04Z - cjm - Chris Mungall + + A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. Austin Meier + Chris Mungall Marie Angelique Laporte - + cjm + 2017-06-05T17:35:04Z + has exposure stimulus - - transports or maintains localization of - regulates localization of + + + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall - - + regulates localization of + transports or maintains localization of - - inheres in part of - q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. - Chris Mungall - Because part_of is transitive, inheres in is a sub-relation of inheres in part of - - - - + + - - + + - - + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + Chris Mungall + + + inheres in part of + - true - - + + - - + + + true - - results in acquisition of features of - results_in_acquisition_of_features_of + + + + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - GOC:mtg_berkeley_2013 Chris Mungall - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. - - - + GOC:mtg_berkeley_2013 + results_in_acquisition_of_features_of + results in acquisition of features of - - mereotopologically related to + A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - + + mereotopologically related to - - colocalizes with + + + + Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Gene Ontology Consortium Chris Mungall http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - - - + Gene Ontology Consortium + colocalizes with - - contributes to + + + + ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. + Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. + eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if @@ -3175,70 +3160,66 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Chris Mungall - Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. - In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to - eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex - - + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + contributes to - - enables - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + + + a particular instances of akt-2 enables some instance of protein kinase activity - has - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - is executing Chris Mungall - executes catalyzes + executes + has is catalyzing - - + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables - - functionally related to + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function + functionally related to - - part of structure that is capable of - false + + this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall - + false + part of structure that is capable of - - involved in - actively involved in + + + c involved_in p if and only if c enables some process p', and p' is part of p - enables part of Chris Mungall - - + actively involved in + enables part of + involved in @@ -3246,718 +3227,716 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - regulates levels of - Chris Mungall + + + + + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c + Chris Mungall + regulates levels of (process to entity) - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid - - - - + regulates levels of - - enabled by + + + inverse of enables Chris Mungall - - + enabled by - - - regulated by + + + + + inverse of regulates Chris Mungall regulated by (processual) - - - - + + regulated by - - negatively regulated by - Chris Mungall + + inverse of negatively regulates - - + Chris Mungall + + negatively regulated by - - positively regulated by + + inverse of positively regulates Chris Mungall - - + + positively regulated by - - related via localization to - Chris Mungall + + + A relationship that holds via some process of localization + Chris Mungall Do not use this relation directly. It is a grouping relation. - - + related via localization to - - has target start location + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. Chris Mungall - + has target start location - - has target end location - Chris Mungall + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - + Chris Mungall + has target end location - - imports + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. Chris Mungall - + imports - - results in transport along - Chris Mungall + + Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - + Chris Mungall + results in transport along - - results in transport across - Chris Mungall + + + Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - - + Chris Mungall + results in transport across - - results in growth of - Chris Mungall + + + 'pollen tube growth' results_in growth_of some 'pollen tube' - - + Chris Mungall + results in growth of - - results in transport to from or in + + 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) Chris Mungall - + results in transport to from or in - - exports + + Chris Mungall - + exports - - results in commitment to - http://www.geneontology.org/GO.doc.development.shtml#fate - Chris Mungall + + + an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - - + Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml#fate + results in commitment to - - results in determination of - http://www.geneontology.org/GO.doc.development.shtml#fate - Chris Mungall + + + p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - - + Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml#fate + results in determination of - + - + - - input of - Chris Mungall + + + inverse of has input - - - - + Chris Mungall + + + input of - - output of + + + inverse of has output Chris Mungall - - - - + + + output of - - formed as result of + + Chris Mungall - + formed as result of - - results in structural organization of + + + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. Chris Mungall - - + results in structural organization of - - results in specification of - http://www.geneontology.org/GO.doc.development.shtml#fate - Chris Mungall + + + The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - - + Chris Mungall + http://www.geneontology.org/GO.doc.development.shtml#fate + results in specification of - - results in developmental induction of + + p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. Chris Mungall - + results in developmental induction of - - has dendrite location - http://neurolex.org/wiki/Property:DendriteLocation + + Chris Mungall - + http://neurolex.org/wiki/Property:DendriteLocation + has dendrite location - - - attached to + + + + a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) - - - + + attached to - - has muscle origin + + + + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) - m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + has muscle origin - - + + + We need to import uberon muscle to create a stricter domain constraint - - - - - has muscle insertion + + + + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) - m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + has muscle insertion - - + + + We need to import uberon muscle into RO to use as a stricter domain constraint - - - - - in branching relationship with - https://github.com/obophenotype/uberon/issues/170 - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - Chris Mungall + + + + + + A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - - - - - + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + in branching relationship with + + https://github.com/obophenotype/uberon/issues/170 - - tributary of - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - http://en.wikipedia.org/wiki/Tributary - tributary channel of - Chris Mungall - http://www.medindia.net/glossary/venous_tributary.htm - drains to - drains into + + Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein + x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. + Chris Mungall + drains into + drains to + tributary channel of http://en.wikipedia.org/wiki/Tributary + http://www.medindia.net/glossary/venous_tributary.htm + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) + + tributary of - - - + http://en.wikipedia.org/wiki/Tributary - - distributary of - x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes - http://en.wikipedia.org/wiki/Distributary + + Deschutes River distributary_of Little Lava Lake - branch of + + x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x Chris Mungall + branch of distributary channel of - - - + http://en.wikipedia.org/wiki/Distributary + + This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes + distributary of - - anabranch of - x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - anastomoses with - Chris Mungall - - - - - + + - + + + + + x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + Chris Mungall + anastomoses with + + anabranch of - - spatially coextensive with - x spatially_coextensive_with y if and inly if x and y have the same location - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios - A lump of clay and a statue - Chris Mungall - + + - + - + + A lump of clay and a statue + x spatially_coextensive_with y if and inly if x and y have the same location + Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + spatially coextensive with - - branching part of + + + + + x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y Chris Mungall + + branching part of FMA:85994 - - - - - - - main stem of + + + x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. Chris Mungall - - - + + main stem of - - proper distributary of - Chris Mungall + + + x proper_distributary_of y iff x distributary_of y and x does not flow back into y - - - + Chris Mungall + + proper distributary of - - proper tributary of - Chris Mungall + + + x proper_tributary_of y iff x tributary_of y and x does not originate from y - - - + Chris Mungall + + proper tributary of - - has developmental potential involving - Chris Mungall + + + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - - - + Chris Mungall + has developmental potential involving - - has potential to developmentally contribute to - Chris Mungall + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - + Chris Mungall + has potential to developmentally contribute to - - has potential to developmentally induce - Chris Mungall + + + x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - - + Chris Mungall + has potential to developmentally induce - - has potential to develop into - Chris Mungall + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - + Chris Mungall + has potential to develop into - - has potential to directly develop into - Chris Mungall + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - - + Chris Mungall + has potential to directly develop into - - has direct input + + 'protein catabolic process' SubClassOf has_direct_input some protein + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + Chris Mungall directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' - Chris Mungall - - + has direct input - - obsolete has indirect input - true + + + Chris Mungall Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - Chris Mungall - + obsolete has indirect input + true - - obsolete has direct output - true - p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + translation SubClassOf has_direct_output some protein + + p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. Chris Mungall directly produces - + obsolete has direct output + true - - obsolete has indirect output - true + + + + + + Chris Mungall Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - - - - - + obsolete has indirect output + true - - causally downstream of + + + + + inverse of upstream of Chris Mungall - - - - + causally downstream of - - immediately causally downstream of + + + + + Chris Mungall - - - - + immediately causally downstream of - - directly activates - directly positively regulates + + + p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - directly activates (process to process) Chris Mungall - - - + directly positively regulates + + directly activates (process to process) + directly activates - - - indirectly activates - indirectly positively regulates - Chris Mungall + + + p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - - + Chris Mungall + indirectly positively regulates + + indirectly activates - - directly inhibits + + + Chris Mungall directly negatively regulates + directly inhibits (process to process) - Chris Mungall - - + directly inhibits - - - indirectly inhibits - indirectly negatively regulates + + + + Chris Mungall - - - + indirectly negatively regulates + + indirectly inhibits - - causally related to + + This relation groups causal relations between material entities and causal relations between processes - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: @@ -3973,1923 +3952,1925 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to - - - causally upstream of - Chris Mungall + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain - - - + Chris Mungall + causally upstream of - - immediately causally upstream of + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall - - - - + + immediately causally upstream of - - directly provides input for - Chris Mungall - directly provides input for (process to process) + + + + p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - - - - + Chris Mungall + + directly provides input for (process to process) + directly provides input for - - - transitively provides input for - Chris Mungall + + + + + + transitive form of directly_provides_input_for + Chris Mungall This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) - - - - + transitively provides input for - - - causally upstream of or within - influences (processual) - Chris Mungall + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) affects - - + causally upstream of or within - - differs in - false - https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions - This is an exploratory relation + + false Chris Mungall + This is an exploratory relation + differs in + https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions - - differs in attribute of - Chris Mungall - + + - - + + + Chris Mungall + differs in attribute of - - differs in attribute + + + Chris Mungall - - + differs in attribute - - - causally downstream of or within - Chris Mungall + + + inverse of causally upstream of or within - - - + Chris Mungall + + + causally downstream of or within - - involved in regulation of + + + c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall - - + involved in regulation of - - - involved in positive regulation of - Chris Mungall + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - + Chris Mungall + + involved in positive regulation of - - involved in negative regulation of - Chris Mungall + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - - + Chris Mungall + + involved in negative regulation of - - involved in or involved in regulation of + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p - involved in or reguates OWL does not allow defining object properties via a Union Chris Mungall - - - + involved in or reguates + involved in or involved in regulation of - - is active in + + + A protein that enables activity in a cytosol. - Chris Mungall c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - enables activity in + Chris Mungall executes activity in - - + enables activity in + + is active in + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos - - - - contributes to morphology of + + p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall - + contributes to morphology of - - - interacts with - Considering relabeling as 'pairwise interacts with' - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations - Chris Mungall - in pairwise interaction with - This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Considering relabeling as 'pairwise interacts with' + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. - - - + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - biotically interacts with + + + + + An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - http://eol.org/schema/terms/interactsWith Chris Mungall interacts with on organism level + + biotically interacts with - - - - + http://eol.org/schema/terms/interactsWith - - trophically interacts with + + An interaction relationship in which the partners are related via a feeding relationship. Chris Mungall + + trophically interacts with - - - - preys on + + + + A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] + Baleen whale preys on krill + An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members + Chris Mungall + Jorrit Poelen Katja Shulz is subject of predation interaction with - Chris Mungall - An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] preys upon - http://www.inaturalist.org/observations/2942824 - Baleen whale preys on krill + + preys on http://eol.org/schema/terms/preysUpon - Jorrit Poelen - - - + http://www.inaturalist.org/observations/2942824 - - - symbiotically interacts with - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - A biotic interaction in which the two organisms live together in more or less intimate association. - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - Chris Mungall - - + + + - - + + - + + A biotic interaction in which the two organisms live together in more or less intimate association. + Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + + symbiotically interacts with - - commensually interacts with - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - Chris Mungall - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - - + + - - + + - + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + commensually interacts with - - mutualistically interacts with - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall - - + + - - + + - + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + mutualistically interacts with - - interacts with via parasite-host interaction - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - This relation groups a pair of inverse relations, parasite of and parasitized by - Chris Mungall - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - - + + - - + + - + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + This relation groups a pair of inverse relations, parasite of and parasitized by + + interacts with via parasite-host interaction - - parasite of - direct parasite of - http://eol.org/schema/terms/parasitizes - parasitizes - Chris Mungall - Pediculus humanus capitis parasite of human - - - - + + + + - - + + - + + Pediculus humanus capitis parasite of human + Chris Mungall + parasitizes + direct parasite of + + parasite of + http://eol.org/schema/terms/parasitizes - - parasitized by + + + Chris Mungall - directly parasitized by has parasite - http://eol.org/schema/terms/hasParasite parasitised by - - - + directly parasitized by + + parasitized by + http://eol.org/schema/terms/hasParasite - - participates in a abiotic-biotic interaction with - semibiotically interacts with - Chris Mungall + + Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. + Chris Mungall + semibiotically interacts with + + participates in a abiotic-biotic interaction with - - - - activity directly regulates activity of + + + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall molecularly controls - Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - + activity directly regulates activity of - - activity directly negatively regulates activity of - inhibits + + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - molecularly decreases activity of Chris Mungall - + inhibits + molecularly decreases activity of + activity directly negatively regulates activity of - - activity directly positively regulates activity of + + Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - activates Chris Mungall + activates molecularly increases activity of - + activity directly positively regulates activity of - - has symptom + + + A relation that holds between a disease or an organism and a phenotype Chris Mungall - - + has symptom - - host of - The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + + Chris Mungall - - + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + + host of - + + + Chris Mungall + has host http://eol.org/schema/terms/hasHost - Chris Mungall - - - - pollinates + + + + Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - http://eol.org/schema/terms/pollinates Chris Mungall - Bees pollinate Flowers is subject of pollination interaction with - - - + + pollinates + http://eol.org/schema/terms/pollinates - - pollinated by + + Chris Mungall - http://eol.org/schema/terms/hasPollinator - is target of pollination interaction with has polinator - - + is target of pollination interaction with + + pollinated by + http://eol.org/schema/terms/hasPollinator - - acquires nutrients from + + + Chris Mungall Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. - - - + + acquires nutrients from - - preyed upon by - http://eol.org/schema/terms/HasPredator + + inverse of preys on - is target of predation interaction with - has predator Chris Mungall + has predator + is target of predation interaction with + + + preyed upon by + http://eol.org/schema/terms/HasPredator http://polytraits.lifewatchgreece.eu/terms/PRED - - - - - is vector for - a is a vector for b if a carries and transmits an infectious pathogen b into another living organism - Chris Mungall + + + Anopheles is a vector for Plasmodium - - - + Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism + + is vector for - - has vector + + Chris Mungall - - + + has vector - - partner in - Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + + Chris Mungall - + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + partner in - - subject participant in - Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + + Chris Mungall - + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + subject participant in - - target participant in - Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + + Chris Mungall - + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + target participant in - - helper property (not for use in curation) - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) - - is symbiosis + + Chris Mungall - + is symbiosis - - is commensalism + + Chris Mungall - + is commensalism - - is mutualism + + Chris Mungall - + is mutualism - - is parasitism + + Chris Mungall - + is parasitism - - provides nutrients for + + Chris Mungall - - + + provides nutrients for - - eats - is subject of eating interaction with + + Chris Mungall - - + is subject of eating interaction with + + eats - - is eaten by - is target of eating interaction with + + Chris Mungall eaten by - - + is target of eating interaction with + + is eaten by - - is evidence for - Chris Mungall + + + A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b. - - - + Chris Mungall + + is evidence for - - composed primarily of + + + + 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall - - - - - + + + composed primarily of - - child nucleus of + + + ABal nucleus child nucleus of ABa nucleus (in C elegans) + c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d Chris Mungall This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. - c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - ABal nucleus child nucleus of ABa nucleus (in C elegans) - + child nucleus of - - child nucleus of in hermaphrodite + + A child nucleus relationship in which the cells are part of a hermaphroditic organism Chris Mungall - + child nucleus of in hermaphrodite - - child nucleus of in male - Chris Mungall + + A child nucleus relationship in which the cells are part of a male organism - + Chris Mungall + child nucleus of in male - - has part that occurs in - Chris Mungall + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - - - + Chris Mungall + + has part that occurs in - - is kinase activity + + Chris Mungall - + is kinase activity - - is ubiquitination + + Chris Mungall - + is ubiquitination - - receives input from - Chris Mungall + + + See notes for inverse relation - - + Chris Mungall + receives input from - - sends output to + + This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. Chris Mungall - + sends output to - - relation between structure and stage - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. - - + + - - + + + + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + relation between structure and stage - - existence starts during - Chris Mungall + + + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - + Chris Mungall + existence starts during - - existence starts with - Chris Mungall + + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - + Chris Mungall + existence starts with - - existence overlaps + + x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. Chris Mungall - + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence overlaps - - existence starts and ends during - Chris Mungall + + + x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - - + existence starts and ends during - - existence ends during - Chris Mungall + + + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - - + existence ends during - - existence ends with + + x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. Chris Mungall - + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends with - - - transformation of + + + x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall - + transformation of - - immediate transformation of + + + x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall - - - + + immediate transformation of - - existence starts during or after + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - + existence starts during or after - - existence ends during or before + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. Chris Mungall - + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during or before - - causal agent in process + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process - - - + + causal agent in process - - causal relation between processes - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. - - - - + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes - - depends on + Chris Mungall - + depends on + - - towards + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall - q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 - + towards - - has intermediate + + 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate - Chris Mungall p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c + Chris Mungall has intermediate product - - + + has intermediate - - causal relation between material entities - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - - + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between material entities - - determined by + + + + + + + A coral reef environment is determined by a particular coral reef - Pier Buttigieg - Chris Mungall - The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. - Chris Mungall - determined by (system to material entity) - - - - - - - + The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + Chris Mungall + determined by (system to material entity) + Chris Mungall + Pier Buttigieg + + determined by - - determines - determines (material entity to system) - Chris Mungall + + inverse of determined by - - - + Chris Mungall + determines (material entity to system) + + + determines - - determined by part of + + + + + s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall - - - - - + + determined by part of - - transcribed from - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - x is transcribed from y if and only if x is synthesized from template y - Chris Mungall - + + - - + + - - + + - - + + - + + x is transcribed from y if and only if x is synthesized from template y + Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed from - - sequentially related to - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + + A relation that holds between two entities that have the property of being sequences or having sequences. Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. - A relation that holds between two entities that have the property of being sequences or having sequences. + sequentially related to - - sequentially adjacent to - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Two exons on a processed transcript that were previously connected by an intron are adjacent - Two consecutive DNA residues are sequentially adjacent + + Every UTR is adjacent to a CDS of the same transcript + Two consecutive DNA residues are sequentially adjacent + Two exons on a processed transcript that were previously connected by an intron are adjacent + x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 - + sequentially adjacent to - - - has start sequence - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - Chris Mungall + + + + Every CDS has as a start sequence the start codon for that transcript - started by x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + Chris Mungall + started by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - + has start sequence - - - is start sequence of - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - starts + + + inverse of has start sequence Chris Mungall + starts + http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - + + is start sequence of - - - has end sequence - http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + + + Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) + x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence Chris Mungall ended by - x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) + http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - + has end sequence - - - is end sequence of - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - Chris Mungall + + + inverse of has end sequence + Chris Mungall ends + http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - + + is end sequence of - - is consecutive sequence of - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - Chris Mungall - In the SO paper, this was defined as an instance-type relation + + x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. + In the SO paper, this was defined as an instance-type relation + Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 - + is consecutive sequence of - - - is sequentially aligned with + + + Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. - Chris Mungall x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering + Chris Mungall - + is sequentially aligned with - - - bounds sequence of - Chris Mungall + + + + The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + Chris Mungall - - + bounds sequence of - - - is bound by sequence of - Chris Mungall + + + inverse of bounds sequence of + Chris Mungall - - + + is bound by sequence of - - - has subsequence - http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + + + + x has subsequence y iff all of the sequence parts of x are sequence parts of y - contains Chris Mungall + contains + http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - - + has subsequence - - - is subsequence of - Chris Mungall + + + + + inverse of has subsequence + Chris Mungall contained by - - - - + + is subsequence of - - - overlaps sequence of + + + + x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. Chris Mungall - - + overlaps sequence of - - - does not overlap sequence of + + + + x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. Chris Mungall disconnected from - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - + does not overlap sequence of - - - is upstream of sequence of - Chris Mungall + + + inverse of downstream of sequence of + Chris Mungall - + is upstream of sequence of - - - is downstream of sequence of - Chris Mungall + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + Chris Mungall - - + is downstream of sequence of - - is immediately downstream of sequence of - x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + + + A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript + x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y Chris Mungall + - - - + is immediately downstream of sequence of - - is immediately upstream of sequence of - Chris Mungall - inverse of immediately downstream of + + + A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript + inverse of immediately downstream of + Chris Mungall - - + is immediately upstream of sequence of - - - - has skeleton - has supporting framework + + + + + + + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). Chris Mungall - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' - - - - + has supporting framework + The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). + has skeleton + + + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. - - - - - results in ending of + + + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. Chris Mungall - - + results in ending of - - hyperparasite of - http://eol.org/schema/terms/hyperparasitoidOf + + + + + + + + x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite epiparasite of - x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y - Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism hyperparasitoid of - - - - - - - + + hyperparasite of - - hyperparasitized by + + + + + + + inverse of hyperparasite of + Chris Mungall has epiparasite has hyperparasite hyperparasitoidized by - Chris Mungall - inverse of hyperparasite of - - - - - - - + + + hyperparasitized by - - allelopath of + + Chris Mungall - x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y http://en.wikipedia.org/wiki/Allelopathy + + allelopath of http://eol.org/schema/terms/allelopathyYes - - + x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y - - pathogen of + + + Chris Mungall - - - + + pathogen of - - has pathogen + + Chris Mungall - - + + has pathogen - - has evidence - Chris Mungall + + inverse of is evidence for - x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. - - - + Chris Mungall + + + x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. + has evidence - - causally influenced by - causally influenced by (material entity to material entity) + + + Chris Mungall - - - + + causally influenced by (material entity to material entity) + causally influenced by - - interaction relation helper property - https://github.com/oborel/obo-relations/wiki/InteractionRelations + + Chris Mungall + interaction relation helper property - + https://github.com/oborel/obo-relations/wiki/InteractionRelations - - molecular interaction relation helper property + + Chris Mungall - + molecular interaction relation helper property - - results in movement of + + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall - + + results in movement of - - causally influences + + Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall + causally influences (material entity to material entity) - - + causally influences - - has branching part + + inverse of branching part of Chris Mungall - - - + + + has branching part - - conduit for - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - UBERON:cjm - Chris Mungall + + + + x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - - - + Chris Mungall + UBERON:cjm + This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. + + conduit for - - lumen of - Chris Mungall + + + x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + Chris Mungall GOC:cjm - - - + + lumen of - - luminal space of + + + s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall - - - + + luminal space of - - has modifier - This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. - Chris Mungall + + + A relation that holds between an attribute or a qualifier and another attribute. - - - + Chris Mungall + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + + has modifier - - participates in a biotic-biotic interaction with + + + + Chris Mungall + + participates in a biotic-biotic interaction with - - - - - - skeleton of + + + + inverse of has skeleton Chris Mungall - - - - + + skeleton of - - directly regulates + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall + directly regulates (processual) - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - - - - + + directly regulates - - existence starts at point + + x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. - + existence starts at point - - has part structure that is capable of - Chris Mungall - s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' - - + + + - - + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + Chris Mungall + has part structure that is capable of - - results in closure of + + + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. - - + results in closure of - - results in breakdown of + + p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p - + results in breakdown of - + + results in synthesis of - - + + + results in assembly of - - - - results in catabolism of + + p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. - + results in catabolism of - + + + results in disassembly of - - - + + + results in remodeling of - - - - results in organization of + + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c - + results in organization of - - existence ends at point + + x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. - + existence ends at point - - causal relation between material entity and a process - Chris Mungall + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - - - + Chris Mungall + + causal relation between material entity and a process - - capable of regulating - Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + pyrethroid -> growth - - + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating - - capable of negatively regulating + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - + + capable of negatively regulating - - capable of positively regulating + + renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - + + capable of positively regulating - - capable of inhibiting or preventing pathological process - treats + + pazopanib -> pathological angiogenesis - The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. - - + treats + + The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. + capable of inhibiting or preventing pathological process - Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + + treats - - + Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship - - capable of upregulating or causing pathological process - causes disease - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + + benzene -> cancer [CHEBI] - - + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + causes disease + + capable of upregulating or causing pathological process - - is substance that treats - treats + + c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. - - + treats + + is substance that treats @@ -5897,509 +5878,509 @@ the a supports either the existence of b, or the truth value of b. - - is marker for - May be ceded to OBI + + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - + May be ceded to OBI + is marker for - - process has causal agent + + Inverse of 'causal agent in process' - - + + process has causal agent - - obsolete related via dependence to - true + A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + obsolete related via dependence to + true - - correlated with + A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Groups both positive and negative correlation + correlated with - - is evidence with support from + + + An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. In the Gene Ontology association model, this corresponds to the With/From field - An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. - + is evidence with support from - - has model + + Inverse of is-model-of - + has model - - related via evidence or inference to + Do not use this relation directly. It is a grouping relation. + related via evidence or inference to - + + + visits - https://github.com/oborel/obo-relations/issues/74 - - + https://github.com/oborel/obo-relations/issues/74 - + + visited by - - + + + visits flowers of - - - + + has flowers visited by - - + + + + lays eggs in - - - - + + + has eggs laid in by - - - - kills + + + https://github.com/jhpoelen/eol-globi-data/issues/143 - - + kills - + + is killed by - - - directly positively regulates + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + directly positively regulates (process to process) - - - - + + directly positively regulates - - directly negatively regulates - directly negatively regulates (process to process) + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. - - - - + + directly negatively regulates (process to process) + + directly negatively regulates - - ectoparasite of + + + A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host - - + ectoparasite of - - has ectoparasite + + inverse of ectoparasite of - - + + has ectoparasite - - endoparasite of - lives inside of - A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system - - + + + + A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system + lives inside of + endoparasite of - + + has endoparasite - - - mesoparasite of + + + A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite - - + mesoparasite of - - has mesoparasite + + inverse of mesoparasite of - - + + has mesoparasite - - intercellular endoparasite of + + + A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. - - + intercellular endoparasite of - - has intercellular endoparasite + + inverse of intercellular endoparasite of - - + + has intercellular endoparasite - - intracellular endoparasite of + + + A sub-relation of endoparasite-of in which the parasite inhabits host cells. - - + intracellular endoparasite of - - has intracellular endoparasite + + inverse of intracellular endoparasite of - - + + has intracellular endoparasite - - produces - Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel - - - - - + + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces - - produced by + + + + a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel - - - - + + produced by - - represses expression of - Logical axioms to be added after the relevant branch of GO is MIREOTed in + + Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. - + Logical axioms to be added after the relevant branch of GO is MIREOTed in + represses expression of - - increases expression of + + Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. Logical axioms to be added after the relevant branch of GO is MIREOTed in - + increases expression of - - - - is model of - The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. - Matthew Brush - To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + Matthew Brush + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + is model of - - causes or contributes to condition - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. - + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + causes or contributes to condition - - causes condition + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. - + causes condition - - contributes to condition + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. - + contributes to condition - - contributes to severity of condition - contributes to expressivity of condition + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. - + contributes to expressivity of condition + contributes to severity of condition - - contributes to frequency of condition - contributes to penetrance of condition + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. - + contributes to penetrance of condition + contributes to frequency of condition - - ameliorates condition + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. + is preventative for condition Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - is preventative for condition - + ameliorates condition - - correlated with condition + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - + correlated with condition - - exacerbates condition + + A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. - + exacerbates condition - - condition ameliorated by + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. - + condition ameliorated by - - condition exacerbated by + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. - + condition exacerbated by - - condition has genetic basis in - 2017-11-05T02:38:20Z - cjm - Do not use this relation directly. It is intended as a grouping for a more specific relations - - - + + + + - - - + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + cjm + 2017-11-05T02:38:20Z + condition has genetic basis in - + + + + cjm + 2017-11-05T02:45:20Z has material basis in gain of function germline mutation in - 2017-11-05T02:45:20Z - cjm - - @@ -6408,24 +6389,24 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + cjm + 2017-11-05T02:45:37Z has material basis in loss of function germline mutation in - 2017-11-05T02:45:37Z - cjm - - - + + + + cjm + 2017-11-05T02:45:54Z has material basis in germline mutation in - 2017-11-05T02:45:54Z - cjm - - @@ -6433,12 +6414,12 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + cjm + 2017-11-05T02:46:07Z has material basis in somatic mutation in - 2017-11-05T02:46:07Z - cjm - - @@ -6446,107 +6427,107 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + cjm + 2017-11-05T02:46:26Z has major susceptibility factor - 2017-11-05T02:46:26Z - cjm - - - + + + + cjm + 2017-11-05T02:46:57Z has partial material basis in germline mutation in - 2017-11-05T02:46:57Z - cjm - - - - has primary input or output - 2018-12-13T11:26:17Z - cjm + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - + cjm + 2018-12-13T11:26:17Z + has primary input or output - - has primary output - 2018-12-13T11:26:32Z - cjm + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - - + cjm + 2018-12-13T11:26:32Z + has primary output + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + GOC:cjm GOC:dph - GOC:pt GOC:kva - GOC:cjm + GOC:pt PMID:27812932 - - - - has primary input - 2018-12-13T11:26:56Z - cjm + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - - + cjm + 2018-12-13T11:26:56Z + has primary input - GOC:dph + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - PMID:27812932 - GOC:pt - GOC:kva GOC:cjm - - + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 - - is genetic basis for condition - 2017-11-05T02:53:08Z - cjm + + + Do not use this relation directly. It is intended as a grouping for a more specific relations - - + cjm + 2017-11-05T02:53:08Z + is genetic basis for condition - - is causal gain of function germline mutation of in - 2017-11-05T02:55:51Z - cjm + + Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - + cjm + 2017-11-05T02:55:51Z + is causal gain of function germline mutation of in @@ -6554,12 +6535,12 @@ Environmental exposures include those imposed by natural environments, experimen - - is causal loss of function germline mutation of in - 2017-11-05T02:56:06Z - cjm + + Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - + cjm + 2017-11-05T02:56:06Z + is causal loss of function germline mutation of in @@ -6567,12 +6548,12 @@ Environmental exposures include those imposed by natural environments, experimen - - is causal germline mutation in - 2017-11-05T02:56:40Z - cjm + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - + cjm + 2017-11-05T02:56:40Z + is causal germline mutation in @@ -6580,12 +6561,12 @@ Environmental exposures include those imposed by natural environments, experimen - - is causal somatic mutation in - 2017-11-05T02:57:07Z - cjm + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - + cjm + 2017-11-05T02:57:07Z + is causal somatic mutation in @@ -6593,12 +6574,12 @@ Environmental exposures include those imposed by natural environments, experimen - - is causal susceptibility factor for - 2017-11-05T02:57:43Z - cjm + + Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - + cjm + 2017-11-05T02:57:43Z + is causal susceptibility factor for @@ -6606,12 +6587,12 @@ Environmental exposures include those imposed by natural environments, experimen - - is causal germline mutation partially giving rise to - 2017-11-05T02:58:43Z - cjm + + Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - + cjm + 2017-11-05T02:58:43Z + is causal germline mutation partially giving rise to @@ -6619,202 +6600,202 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + cjm + 2017-11-05T03:20:01Z realizable has basis in - 2017-11-05T03:20:01Z - cjm - - - + + + cjm + 2017-11-05T03:20:29Z is basis for realizable - 2017-11-05T03:20:29Z - cjm - - + + + + cjm + 2017-11-05T03:26:47Z disease has basis in - 2017-11-05T03:26:47Z - cjm - - - - disease has basis in dysfunction of - 2017-11-05T03:29:32Z - cjm + + + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) - - + cjm + 2017-11-05T03:29:32Z + disease has basis in dysfunction of - - disease has basis in disruption of - 2017-11-05T03:37:52Z - cjm - disease has basis in disruption of (disease to process) + + + A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. - - + disease has basis in disruption of (disease to process) + cjm + 2017-11-05T03:37:52Z + disease has basis in disruption of - - disease has basis in feature - 2017-11-05T03:46:07Z - cjm + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - - - + cjm + 2017-11-05T03:46:07Z + disease has basis in feature - - disease causes dysfunction of - 2017-11-05T03:58:20Z - cjm - disease causes dysfunction of (disease to anatomical entity) - - + + + - - + + + disease causes dysfunction of (disease to anatomical entity) + cjm + 2017-11-05T03:58:20Z + disease causes dysfunction of - - disease has location - 2017-11-05T04:06:02Z - cjm - TODO: complete range axiom once more of CARO has been mireoted in to this ontology - This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. - - + + + - - + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. + TODO: complete range axiom once more of CARO has been mireoted in to this ontology + This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. + cjm + 2017-11-05T04:06:02Z + disease has location - - disease has inflammation site - 2017-12-26T19:37:31Z - cjm + + + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - - - + cjm + 2017-12-26T19:37:31Z + disease has inflammation site - - realized in response to stimulus - 2017-12-26T19:45:49Z - cjm - A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - - - + + + + - - + + + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + cjm + 2017-12-26T19:45:49Z + realized in response to stimulus - - disease has feature - 2017-12-26T19:50:53Z - cjm + + A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - + cjm + 2017-12-26T19:50:53Z + disease has feature - - disease arises from structure - 2017-12-26T19:58:44Z - cjm + + + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. - - + cjm + 2017-12-26T19:58:44Z + disease arises from structure - - enables subfunction - 2018-01-25T23:20:13Z - cjm - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - + + - - + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + enables subfunction - + + + + cjm + 2018-01-26T23:49:30Z acts upstream of or within, positive effect - 2018-01-26T23:49:30Z - cjm - - @@ -6822,26 +6803,26 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + cjm + 2018-01-26T23:49:51Z acts upstream of or within, negative effect - 2018-01-26T23:49:51Z - cjm - - - - acts upstream of, positive effect - 2018-01-26T23:53:14Z - cjm + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - - - + + cjm + 2018-01-26T23:53:14Z + acts upstream of, positive effect @@ -6849,14 +6830,14 @@ Environmental exposures include those imposed by natural environments, experimen - - acts upstream of, negative effect - 2018-01-26T23:53:22Z - cjm + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - - - + + cjm + 2018-01-26T23:53:22Z + acts upstream of, negative effect @@ -6864,243 +6845,243 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + cjm + 2018-03-13T23:55:05Z causally upstream of or within, negative effect - 2018-03-13T23:55:05Z - cjm - - - + + + + cjm + 2018-03-13T23:55:19Z causally upstream of or within, positive effect - 2018-03-13T23:55:19Z - cjm - - - - epiphyte of + + + An interaction relationship wherein a plant or algae is living on the outside surface of another plant. https://en.wikipedia.org/wiki/Epiphyte - - + epiphyte of - - has epiphyte + + inverse of epiphyte of - - + + has epiphyte - - kleptoparasite of + + + A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material https://en.wikipedia.org/wiki/Kleptoparasitism - - + kleptoparasite of - - kleptoparasitized by + + inverse of kleptoparasite of - - + + kleptoparasitized by - - lays eggs on + + + An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - - + lays eggs on - - has eggs laid on by + + An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - + has eggs laid on by - - - has substance added + + + + + muffin 'has substance added' some 'baking soda' + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - Damion Dooley The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - muffin 'has substance added' some 'baking soda' - - - + Damion Dooley + has substance added - - - has substance removed - "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. Damion Dooley - - - + has substance removed - - - immersed in - Damion Dooley - "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + + + + sardines 'immersed in' some 'oil and mustard' - - - + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + Damion Dooley + immersed in - - - has primary substance added + + + + bread 'has primary substance added' some 'flour' + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. Damion Dooley - bread 'has primary substance added' some 'flour' - - + has primary substance added - - realized in response to - https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - David Osumi-Sutherland + + + + + + + + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. + r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. Austin Meier - Marie Angelique Laporte Chris Mungall - Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. - An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + David Osumi-Sutherland + Marie Angelique Laporte triggered by process - - - - - - - + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit - RO:cjm + + triggered by process - - + RO:cjm - - generically depends on - The pattern shared by chess boards generically depends on any chess board. - [072-ISO] + + + + Genetic information generically depend on molecules of DNA. The novel *War and Peace* generically depends on this copy of the novel. - g-depends on + The pattern shared by chess boards generically depends on any chess board. The score of a symphony g-depends on a copy of the score. - A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. This pdf file generically depends on this server. - - - + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on - - is carrier of + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. This hard drive is carrier of these data items. - [072-ISO] *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* - This copy of *War and Peace* is carrier of the novel written by Tolstoy. - Molecules of DNA are carriers of genetic information. - - + [072-ISO] + is carrier of - - has anatomical participant - 2018-09-26T01:08:58Z - cjm - p has anatomical participant c iff p has participant c, and c is an anatomical entity - + + - - + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + cjm + 2018-09-26T01:08:58Z + has anatomical participant - + @@ -7117,32 +7098,32 @@ Environmental exposures include those imposed by natural environments, experimen - - has increased age-specific mortality rate - 2018-05-22T16:43:28Z - dos - This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. - Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + - + - 0 + 0 - 100 + 100 + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + dos - Wikipedia:Infant_mortality + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. PMID:24138933 - - + Wikipedia:Infant_mortality @@ -7161,97 +7142,97 @@ Environmental exposures include those imposed by natural environments, experimen + International Classification of Diseases - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + @@ -7260,17 +7241,83 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + + + + + An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff. + An object which is large enough to be visible to humans, but small enough that humans can handle the object (i.e. transport it, examine it, etc) in its entirety with little to no technological assistance. + mesoscopic physical object + http://purl.obolibrary.org/obo/envo.owl + MA:ma + This is a legacy class from ENVO's early versions. It will be depopulated and filled in by inference using a PATO quality. Not to be confused with "mesoscopic" as defined in physics, which deals with objects typically between 10e-6 and 10-8 meters in diameter. + https://en.oxforddictionaries.com/definition/mesoscopic + mesoscopic physical object + physical object of mesoscopic geological size + + + + + + + + + A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. + http://purl.obolibrary.org/obo/envo.owl + manufactured good + https://en.wikipedia.org/wiki/Manufactured_product + manufactured product + + + + + + + + + http://purl.obolibrary.org/obo/envo.owl + ENVO + ENVO:00003075 + anthropogenic abiotic mesoscopic feature + + + + + + + + + http://purl.obolibrary.org/obo/envo.owl + ENVO + ENVO:01000010 + abiotic mesoscopic physical object + + + + + + + + + A vehicle is a mobile machine which transports people or cargo. + http://purl.obolibrary.org/obo/envo.owl + https://en.wikipedia.org/wiki/Vehicle + vehicle + - + - - + + @@ -7279,135 +7326,135 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - + - - database extract, transform, and load process - + + - - + + - - + + + database extract, transform, and load process A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. + PERSON:Alan Ruttenberg ETL WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load - PERSON:Alan Ruttenberg - database extract, transform, and load process - - + + database extract, transform, and load process + - + - + - + - + + Systematized Nomenclature of Medicine - - + - - - - - - - + - + - - + + + + + + + + - + - + - + - + - + - - + + @@ -7420,271 +7467,271 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - + - + - + - - discharge process + - - + + - + - + Amanda Hicks a document act in which concludes an inpatient encounter + discharge process - + - + - + - + - + - + - - biological sex - - An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. - PATO:0000047 - http://purl.obolibrary.org/obo/pato.owl - quality - + + + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + http://purl.obolibrary.org/obo/pato.owl + quality + PATO:0000047 + + biological sex - - viability - - An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. - PATO:0000169 - http://purl.obolibrary.org/obo/pato.owl - quality - - + + + An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. + http://purl.obolibrary.org/obo/pato.owl + quality + PATO:0000169 + + + viability - - female - - A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. - PATO:0000383 - http://purl.obolibrary.org/obo/pato.owl - quality - - + + + A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. + http://purl.obolibrary.org/obo/pato.owl + quality + PATO:0000383 + + + female - - male - - A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. - PATO:0000384 - http://purl.obolibrary.org/obo/pato.owl - quality - - + + + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + http://purl.obolibrary.org/obo/pato.owl + quality + PATO:0000384 + + + male - - alive - - A viability quality inhering in a bearer by virtue of the bearer's condition before death. - PATO:0001421 - http://purl.obolibrary.org/obo/pato.owl - quality - + + + A viability quality inhering in a bearer by virtue of the bearer's condition before death. + http://purl.obolibrary.org/obo/pato.owl + quality + PATO:0001421 + + alive - - dead - - A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. - PATO:0001422 - http://purl.obolibrary.org/obo/pato.owl - quality - + + + A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. + http://purl.obolibrary.org/obo/pato.owl + quality + PATO:0001422 + + dead - - phenotypic sex - - PATO:0001894 - http://purl.obolibrary.org/obo/pato.owl - quality - + + + http://purl.obolibrary.org/obo/pato.owl + quality + PATO:0001894 + + phenotypic sex - - organismal quality - - A quality that inheres in an entire organism or part of an organism. - PATO:0001995 - http://purl.obolibrary.org/obo/pato.owl - quality + + + A quality that inheres in an entire organism or part of an organism. + http://purl.obolibrary.org/obo/pato.owl + quality + PATO:0001995 + organismal quality - - system - + + + A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall - A material entity consisting of multiple components that are causally integrated. http://www.jbiomedsem.com/content/4/1/43 + system - - processual entity - - An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. - UBERON:0000000 - uberon - + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + uberon + UBERON:0000000 + + processual entity - - death stage - - End of the life of an organism. - UBERON:0000071 - XAO:0000437 - XtroDO:0000085 - death - http://purl.obolibrary.org/obo/uberon.owl - ncit:Death is an outcome - uberon + + + End of the life of an organism. + http://purl.obolibrary.org/obo/uberon.owl + ncit:Death is an outcome + XAO:0000437 + XtroDO:0000085 + uberon + death + UBERON:0000071 + death stage - - life cycle - - An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. - FBdv:00000000 - HsapDv:0000001 - MmusDv:0000001 - OGES:000011 - UBERON:0000104 - entire life cycle - entire lifespan - http://purl.obolibrary.org/obo/uberon.owl - life - lifespan - ncithesaurus:Life - uberon - + + + An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + http://purl.obolibrary.org/obo/uberon.owl + FBdv:00000000 + HsapDv:0000001 + MmusDv:0000001 + OGES:000011 + ncithesaurus:Life + entire life cycle + entire lifespan + life + lifespan + uberon + UBERON:0000104 + + life cycle @@ -7692,66 +7739,66 @@ Environmental exposures include those imposed by natural environments, experimen - - life cycle stage - - A spatiotemporal region encompassing some part of the life cycle of an organism. - BILS:0000105 - EFO:0000399 - FBdv:00007012 - FMA:24120 - HsapDv:0000000 - MmusDv:0000000 - OlatDv:0000010 - PdumDv:0000090 - UBERON:0000105 - WBls:0000002 - XAO:1000000 - ZFS:0000000 - ZFS:0100000 - developmental stage - http://purl.obolibrary.org/obo/uberon.owl - ncithesaurus:Developmental_Stage - stage - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here - uberon - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage - - + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here + http://purl.obolibrary.org/obo/uberon.owl + the WBls class 'all stages' belongs here as it is the superclass of other WBls stages + we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage + BILS:0000105 + EFO:0000399 + FBdv:00007012 + FMA:24120 + HsapDv:0000000 + MmusDv:0000000 + OlatDv:0000010 + PdumDv:0000090 + WBls:0000002 + XAO:1000000 + ZFS:0000000 + ZFS:0100000 + ncithesaurus:Developmental_Stage + developmental stage + stage + uberon + UBERON:0000105 + + + life cycle stage - - neonate stage - - BTO:0001762 - EV:0300037 - HsapDv:0000082 - MmusDv:0000096 - NIF_Organism:birnlex_695 - OGES:000025 - Of or pertaining to the period of time immediately following birth, or to the newborn. - UBERON:0007221 - consider splitting infant/newborn - fledgling stage - hatchling - hatchling stage - http://purl.obolibrary.org/obo/uberon.owl - infant stage - neonatal stage - nestling stage - newborn stage - pouch stage - puggle - puggle stage - uberon + + + Of or pertaining to the period of time immediately following birth, or to the newborn. + consider splitting infant/newborn + http://purl.obolibrary.org/obo/uberon.owl + BTO:0001762 + EV:0300037 + HsapDv:0000082 + MmusDv:0000096 + NIF_Organism:birnlex_695 + OGES:000025 + neonatal stage + fledgling stage + hatchling + hatchling stage + infant stage + nestling stage + pouch stage + puggle + puggle stage + uberon + newborn stage + UBERON:0007221 + neonate stage @@ -7759,64 +7806,69 @@ Environmental exposures include those imposed by natural environments, experimen - - life cycle temporal boundary - - A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. - UBERON:0035943 - uberon - + + + A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. + uberon + UBERON:0035943 + + life cycle temporal boundary - - life-death temporal boundary - - A life cycle temporal boundary that marks the end of the life cycle of the organism. - UBERON:0035944 - death - end of life - end of life cycle - moment of death - time of death - uberon + + + A life cycle temporal boundary that marks the end of the life cycle of the organism. + end of life cycle + moment of death + time of death + uberon + death + end of life + UBERON:0035944 + life-death temporal boundary - - start of neonate stage - - A life cycle temporal boundary that marks the start of the neonate stage of the organism. - UBERON:0035946 - birth - moment of birth - time of birth - uberon + + + A life cycle temporal boundary that marks the start of the neonate stage of the organism. + moment of birth + time of birth + uberon + birth + UBERON:0035946 + start of neonate stage - - admitting diagnosis - + + + + + + + + - + - + - - + + @@ -7825,207 +7877,201 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - - + + - - - - - - - + + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or during the admission of that patient Amanda Hicks - PCORnet CDM 4.1 S. Clint Dowland - a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or during the admission of that patient + PCORnet CDM 4.1 + admitting diagnosis - - PCORnet racial identity datum - - A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process. + + Amanda Hicks + A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process. + PCORnet racial identity datum - - PCORnet American Indian or Alaska Native identity datum - + + Amanda Hicks + PCORnet American Indian or Alaska Native identity datum - - PCORnet Asian identity datum - + + Amanda Hicks + PCORnet Asian identity datum - + + + Amanda Hicks PCORnet black or African American identity datum PCORnet item - - Amanda Hicks - + + PCORnet CDM item identifier - - + + PCORnet item - - - PCORnet Native Hawaiian or other Pacific Islander identity datum - + + Amanda Hicks + PCORnet Native Hawaiian or other Pacific Islander identity datum - - PCORnet white identity datum - + + Amanda Hicks + PCORnet white identity datum - - PCORnet multiple race identity datum - + + Amanda Hicks + PCORnet multiple race identity datum - - PCORnet Hispanic identity datum - - + + + Amanda Hicks From PCORnet CDM "A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." + PCORnet Hispanic identity datum - - PCORnet not Hispanic identity datum - - + + + Amanda Hicks + PCORnet not Hispanic identity datum - - PCORnet ethnic identity datum - + + Amanda Hicks + PCORnet ethnic identity datum - - PCORnet patient identifier - + + A centrally registered identifier that denotes a person in a PCORnet data mart and is used to link across tables. This identifier is not necessarily unique within PCORnet. Amanda Hicks + PCORnet patient identifier - - admission process - + + - - + + - - + + Amanda Hicks a social act in which a patient is registered with a health care provider for the purposes of recieving care in an inpatient encounter + admission process - - discharge diagnosis - + + - + - + - - + + @@ -8034,628 +8080,629 @@ Environmental exposures include those imposed by natural environments, experimen - + - + - - + + - + + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or simultaneously with the discharge of that patient Amanda Hicks - PCORnet CDM 4.1 S. Clint Dowland - a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs before or simultaneously with the discharge of that patient + PCORnet CDM 4.1 + discharge diagnosis - - final diagnosis - + + - + - + - - + + + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an outpatient encounter Amanda Hicks - PCORnet CDM 4.1 S. Clint Dowland - a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an outpatient encounter + PCORnet CDM 4.1 + final diagnosis - - interim diagnosis - + + - + - + - - + + + a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge of that patient Amanda Hicks - PCORnet CDM 4.1 S. Clint Dowland - a diagnosis that is about some patient and that is the specified output of a diagnostic process that occurs during an inpatient encounter, after admission, and before discharge of that patient + PCORnet CDM 4.1 + interim diagnosis - + + PCORnet racial identification process - - + + PCORnet sexual orientation identity datum - - - ambulatory visit - + + - - + + - - + + - - PCORnet CDM 4.1 - Amanda Hicks + An outpatient encounter that occurs in an outpatient clinic, physician office, ambulatory surgery facility, urgent care facilitu, or a hospital encounters and that does not occur in an emergency department facillity. + Amanda Hicks + PCORnet CDM 4.1 Includes visits at outpatient clinics, physician offices, same day/ambulatory surgery centers, urgent care facilities, and other same-day ambulatory hospital encounters, but excludes emergency department encounters + ambulatory visit - - deprecated emergency department encounter - - true + + + A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility. Amanda Hicks - Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known. PCORnet CDM 4.1 - A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility. + Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known. + deprecated emergency department encounter + true - - emergency department admit to inpatient hospital stay - sexual orientation identity datum - - PCORnet CDM 4.1 - A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person. Unlike data items they are not necessilary contributed or acquired by a reliable method. - Amanda Hicks + + A healthcare encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay + Amanda Hicks + PCORnet CDM 4.1 Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished. + A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person. Unlike data items they are not necessilary contributed or acquired by a reliable method. + emergency department admit to inpatient hospital stay + sexual orientation identity datum - + + + PCORnet asexual identity datum inpatient hospital encounter - - - + + PCORnet gay identity datum - - + + PCORnet lesbian identity datum - - + + PCORnet multiple sexual orientations identity datum - - + + PCORnet queer identity datum - - + + PCORnet questioning identity datum - - + + PCORnet something else identity datum - - + + PCORnet straight identity datum - - - PCORnet gender identity datum - + + A gender identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the 2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the other does not have a multiple gender option, which changes the meaning of the values in the value set. + PCORnet gender identity datum - + + PCORnet genderqueer identity datum - - + + PCORnet man identity datum - - + + PCORnet multiple genders datum - - + + PCORnet something else identity datum - - + + PCORnet transgenderfemale/transwoman/male-to-female identity datum - - + + PCORnet transgendermale/transman/female-to-male identity datum - - + + PCORnet woman identity datum - - + + PCORnet diagnosis identifier - - - code set - + + - - + + - - + + a set of non-lexical symbols with a conventionally agreed usage among a group for a particular purpose + code set - - PCORnet discharge status data item - + + A data item that is about a patient discharge (or lack thereof) and (where applicable) the type of facility or organization to which the patient was discharged. Matthew Diller S. Clint Dowland + PCORnet discharge status data item - - PCORnet skilled nursing facility discharge status data item - + + A PCORnet discharge status that is about a skilled nursing facility to which a patient was discharged. Matthew Diller S. Clint Dowland + PCORnet skilled nursing facility discharge status data item - - PCORnet adult foster home facility discharge status data item - + + A PCORnet discharge status that is about an adult foster home facility to which a patient was discharged. Matthew Diller S. Clint Dowland + PCORnet adult foster home facility discharge status data item - - PCORnet assisted living facility discharge status data item - + + A PCORnet discharge status that is about an assisted living facility to which a patient was discharged. Matthew Diller S. Clint Dowland + PCORnet assisted living facility discharge status data item - - PCORnet other acute inpatient hospital discharge status data item - + + A PCORnet discharge status that is about a hospital facility to which a patient was discharged and that is distinct from the discharging hospital. Amanda Hicks Matthew Diller S. Clint Dowland + PCORnet other acute inpatient hospital discharge status data item - - PCORnet nursing home facility discharge status data item - + + A PCORnet discharge status that is about a nursing home facility to which a patient was discharged. Matthew Diller S. Clint Dowland + PCORnet nursing home facility discharge status data item - - PCORnet rehabilitation facility discharge status data item - + + A PCORnet discharge status that is about a rehabilitation facility to which a patient was discharged. Matthew Diller S. Clint Dowland + PCORnet rehabilitation facility discharge status data item - - PCORnet residential facility discharge status data item - + + A PCORnet discharge status that is about a residential facility to which a patient was discharged. Matthew Diller S. Clint Dowland + PCORnet residential facility discharge status data item - - PCORnet hospice discharge status data item - + + A PCORnet discharge status that is about a hospice organization to which a patient was discharged. Matthew Diller S. Clint Dowland + PCORnet hospice discharge status data item - - PCORnet against medical advice discharge status data item - + + A PCORnet discharge status that is about a patient who is discharged upon deciding to leave against the advice of a health care provider. Matthew Diller S. Clint Dowland + PCORnet against medical advice discharge status data item - - PCORnet still in hospital discharge status data item - + + A PCORnet discharge status that is about a hospital facility in which a patient remains, having not been discharged. Matthew Diller S. Clint Dowland + PCORnet still in hospital discharge status data item - - PCORnet home health discharge status data item - + + A PCORnet discharge status that is about a home healthcare organization and the household to which a patient was discharged. Matthew Diller S. Clint Dowland + PCORnet home health discharge status data item - - PCORnet admitting source data item - + + A data item that is about a patient admission and the type of facility from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland + PCORnet admitting source data item - - PCORnet home health admitting source data item - + + A PCORnet data item that is about a home healthcare organization and the household from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland + PCORnet home health admitting source data item - - PCORnet skilled nursing facility admitting source data item - + + A PCORnet data item that is about a skilled nursing facility from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland + PCORnet skilled nursing facility admitting source data item - - PCORnet emergency department admitting source data item - + + A PCORnet data item that is about an emergency department from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland + PCORnet emergency department admitting source data item - - PCORnet intra-hospital admitting source data item - + + A PCORnet data item that is about another department in the same hospital from which a patient was discharged prior to admission. Matthew Diller S. Clint Dowland + PCORnet intra-hospital admitting source data item - - PCORnet ambulatory visit admitting source data item - + + A PCORnet data item that is about a patient admission that is causally upstream of an outpatient encounter. Matthew Diller S. Clint Dowland + PCORnet ambulatory visit admitting source data item - - PCORnet health care encounter identifier - + + A proper name that denotes a health care encounter and has part some symbol. Matthew Diller S. Clint Dowland + PCORnet health care encounter identifier - - PCORnet facility identifier - + + A proper name that denotes a health care facility and has part some symbol. Matthew Diller S. Clint Dowland + PCORnet facility identifier - - institutional professional consult - + + A health care encounter that realizes some health care provider role that inheres in some Homo sapiens. Matthew Diller S. Clint Dowland + institutional professional consult - - non-acute institutional stay - + + A health care encounter that occurs in some hospice facility, skilled nursing facility, rehabilitation facility, nursing home facility, residential home facility, overnight non-hospital dialysis facility, adult foster home facility, or assisted living facility. Matthew Diller S. Clint Dowland + non-acute institutional stay - - observation stay - + + A health care encounter that occurs in some hospital facility or emergency department and that realizes some healthcare provider role that inheres in some organization. Matthew Diller + observation stay @@ -8673,101 +8720,101 @@ excludes emergency department encounters - + - International Classification of Diseases, Tenth Revision, Clinical Modification - NCI An extension of the ICD-10 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. + NCI + International Classification of Diseases, Tenth Revision, Clinical Modification - - - Systematized Nomenclature of Medicine Clinical Terms - NCI + + Published by the College of American Pathologists, the Systematized Nomenclature of Medicine Clinical Terms is a combination of content of SNOMED Reference Terminology and READ codes. + NCI + Systematized Nomenclature of Medicine Clinical Terms - + - International Classification of Diseases, Ninth Revision, Clinical Modification An extension of the ICD-9 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. NCI + International Classification of Diseases, Ninth Revision, Clinical Modification - + - + - + - - + + + John Doe - - - + + + + John Doe's birth - - - - + + + + 23:59 - - - - + + + John Doe's neonate stage - - - + + 1D temporal interval occuped by John Doe's neonate stage @@ -8775,8 +8822,8 @@ excludes emergency department encounters - - + + 2000-02-02 @@ -8784,18 +8831,18 @@ excludes emergency department encounters - + + + rta1 - - - - + + eiqap1 @@ -8803,28 +8850,28 @@ excludes emergency department encounters - - + + + Jane Doe - - - + + + g - - - + + p4 @@ -8832,18 +8879,18 @@ excludes emergency department encounters - - + + + f1 - - - + + p5 @@ -8851,21 +8898,21 @@ excludes emergency department encounters - - - + + + + + John Doe's patient role m1 - - - - + + ridqap1 @@ -8873,8 +8920,8 @@ excludes emergency department encounters - - + + Jane Doe's American Indian or Alaska Native identity datum @@ -8882,28 +8929,28 @@ excludes emergency department encounters - - + + + p6 - - + + + rta2 - - - - + + Jane Doe's racial identification process @@ -8911,8 +8958,8 @@ excludes emergency department encounters - - + + ETL process of Jane Doe’s racial identity datum @@ -8920,20 +8967,20 @@ excludes emergency department encounters - - + + + + + John Doe's Hispanic or Latino identity datum - - - - - + + John Doe’s ethnic identification process @@ -8941,19 +8988,19 @@ excludes emergency department encounters - - + + + + John Doe’s PCORnet Hispanic identity datum - - - - + + ETL process of John Doe’s ethnic identity datum @@ -8961,20 +9008,20 @@ excludes emergency department encounters - - + + + + + Jane Doe's not Hispanic or Latino identity datum - - - - - + + Jane Doe’s ethnic identification process @@ -8982,19 +9029,19 @@ excludes emergency department encounters - - + + + + Jane Doe’s PCORnet not Hispanic identity datum - - - - + + ETL process of John Doe’s ethnic identity datum @@ -9002,8 +9049,8 @@ excludes emergency department encounters - - + + ETL process of Jane Doe’s ethnic identity datum @@ -9011,18 +9058,18 @@ excludes emergency department encounters - - + + + John Doe's patient role - - - + + 1234 @@ -9030,19 +9077,19 @@ excludes emergency department encounters - + - + - + @@ -9057,45 +9104,45 @@ excludes emergency department encounters /////////////////////////////////////////////////////////////////////////////////////// --> - - David Osumi-Sutherland - + + true - - + + A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility. + PCORnet CDM 4.1 + Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known. + emergency department encounter + Amanda Hicks - + inverse of has disposition - + - - + + + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. - - + + - - A health care encounter that occurs in an emergency department facillity and realizes the health care provider role of an organization and the emergency department function of the facility. - Amanda Hicks - Includes ED encounters that become inpatient stays (in which case inpatient stays would be a separate encounter). Excludes urgent care facility visits. ED claims should be pulled before hospitalization claims to ensure that ED with subsequent admission won't be rolled up in the hospital event. Does not include observation stays, where known. - PCORnet CDM 4.1 - emergency department encounter + + + David Osumi-Sutherland - - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. - + + - - + + - - true + + - - + + - - + + @@ -9109,69 +9156,69 @@ excludes emergency department encounters --> - + - + - - + + - - + - - - + + + - - - - - - + + + + + + + + - - + - - + + + - - - - - - - + + + + + - - - + + + + - + - + From 550733cf8a213c872b4eadd34509f3845cf7d8b0 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Tue, 10 Sep 2019 15:12:01 -0400 Subject: [PATCH 10/69] Updated defintion for PCORnet discharge status data item, and added PCORnet absent without leave discharge status data item. --- PCORnetCDM.owl | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index e3b7606..83c6172 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -9,6 +9,7 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:cito="http://purl.org/spar/cito/" xmlns:foaf="http://xmlns.com/foaf/0.1/" + xmlns:obda="https://w3id.org/obda/vocabulary#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" @@ -8435,7 +8436,7 @@ excludes emergency department encounters - A data item that is about a patient discharge (or lack thereof) and (where applicable) the type of facility or organization to which the patient was discharged. + A data item that is about a patient discharge, or lack thereof, and the type of facility or organization, if any, to which the patient was discharged. Matthew Diller S. Clint Dowland PCORnet discharge status data item @@ -8696,6 +8697,19 @@ excludes emergency department encounters + + + + + A discharge status that is about a patient’s terminating a healthcare encounter without being discharged. + Mathias Brochhausen + Matt Diller + S. Clint Dowland + PCORnet absent without leave discharge status data item + + + + From a13f73ef1561668925273f3bf01e9d655ada966d Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Thu, 12 Sep 2019 15:48:23 -0400 Subject: [PATCH 11/69] Added class PCORnet provider identifier. --- PCORnetCDM.owl | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 83c6172..a52b1b2 100644 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -8721,6 +8721,18 @@ excludes emergency department encounters + + + + + A proper name that denotes a human being who is a bearer of a person healthcare provider role. + Matthew Diller + S. Clint Dowland + PCORnet provider identifier + + + + - + rta1 @@ -8966,8 +8967,8 @@ excludes emergency department encounters - + rta2 @@ -8995,9 +8996,9 @@ excludes emergency department encounters + - John Doe's Hispanic or Latino identity datum @@ -9016,8 +9017,8 @@ excludes emergency department encounters - + John Doe’s PCORnet Hispanic identity datum @@ -9036,9 +9037,9 @@ excludes emergency department encounters + - Jane Doe's not Hispanic or Latino identity datum @@ -9057,8 +9058,8 @@ excludes emergency department encounters - + Jane Doe’s PCORnet not Hispanic identity datum From dc1e8024325a0dd29fe116a2c66e880f05beaf67 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 23 Oct 2019 14:53:34 -0400 Subject: [PATCH 14/69] Updated definitions for PCORnet discharge status data item and its subclasses. --- PCORnetCDM.owl | 34 ++++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 14 deletions(-) mode change 100644 => 100755 PCORnetCDM.owl diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl old mode 100644 new mode 100755 index 980212e..b1f28fe --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -8437,9 +8437,12 @@ excludes emergency department encounters - A data item that is about a patient discharge, or lack thereof, and the type of facility or organization, if any, to which the patient was discharged. + A data item that is about a documentation activity that records either (i) that some healthcare encounter ends with a patient discharge; (ii) that some healthcare encounter is terminated by a patient without any patient discharge; or (iii) that some healthcare encounter continues while the patient remains in the same hospital and while the hospital is billing a healthcare payor for services after a specified period. + If the healthcare encounter ends with a patient discharge, then the status might also indicate the type of facility or organization, if any, to which the patient is discharged. + Mathias Brochhausen Matthew Diller S. Clint Dowland + William R. Hogan PCORnet discharge status data item @@ -8449,7 +8452,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about a skilled nursing facility to which a patient was discharged. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a skilled nursing facility. Matthew Diller S. Clint Dowland PCORnet skilled nursing facility discharge status data item @@ -8461,7 +8464,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about an adult foster home facility to which a patient was discharged. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to an adult foster home facility. Matthew Diller S. Clint Dowland PCORnet adult foster home facility discharge status data item @@ -8473,7 +8476,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about an assisted living facility to which a patient was discharged. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to an assisted living facility. Matthew Diller S. Clint Dowland PCORnet assisted living facility discharge status data item @@ -8485,7 +8488,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about a hospital facility to which a patient was discharged and that is distinct from the discharging hospital. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to another hospital. Amanda Hicks Matthew Diller S. Clint Dowland @@ -8498,7 +8501,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about a nursing home facility to which a patient was discharged. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a nursing home facility. Matthew Diller S. Clint Dowland PCORnet nursing home facility discharge status data item @@ -8510,7 +8513,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about a rehabilitation facility to which a patient was discharged. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a rehabilitation facility. Matthew Diller S. Clint Dowland PCORnet rehabilitation facility discharge status data item @@ -8522,7 +8525,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about a residential facility to which a patient was discharged. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged to a residential facility. Matthew Diller S. Clint Dowland PCORnet residential facility discharge status data item @@ -8534,7 +8537,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about a hospice organization to which a patient was discharged. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged under the care of a hospice organization. Matthew Diller S. Clint Dowland PCORnet hospice discharge status data item @@ -8546,7 +8549,7 @@ excludes emergency department encounters - A PCORnet discharge status that is about a patient who is discharged upon deciding to leave against the advice of a health care provider. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged upon deciding to end the encounter against the advice of a healthcare provider. Matthew Diller S. Clint Dowland PCORnet against medical advice discharge status data item @@ -8558,9 +8561,10 @@ excludes emergency department encounters - A PCORnet discharge status that is about a hospital facility in which a patient remains, having not been discharged. + A PCORnet discharge status data item that is about a healthcare encounter that continues while the patient remains in the same hospital, and while the hospital is billing a healthcare payor for services after a specified period (typically 90 days). Matthew Diller S. Clint Dowland + William R. Hogan PCORnet still in hospital discharge status data item @@ -8570,9 +8574,10 @@ excludes emergency department encounters - A PCORnet discharge status that is about a home healthcare organization and the household to which a patient was discharged. + A PCORnet discharge status data item that is about a discharge process in which a patient is discharged (i) to a housing unit, and (ii) under the care of a home healthcare organization. Matthew Diller S. Clint Dowland + William R. Hogan PCORnet home health discharge status data item @@ -8702,10 +8707,11 @@ excludes emergency department encounters - A discharge status that is about a patient’s terminating a healthcare encounter without being discharged. + A PCORnet discharge status data item that is about a termination of an inpatient encounter, initiated by the patient, that lacks a discharge process as a proper part. Mathias Brochhausen - Matt Diller + Matthew Diller S. Clint Dowland + William R. Hogan PCORnet absent without leave discharge status data item From a34069fc51a731a482ef2aa362aff59c4df71f0d Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Thu, 31 Oct 2019 14:33:40 -0400 Subject: [PATCH 15/69] Deprecated 'PCORnet item' and 'PCORnet CDM item identifier', added definition to 'PCORnet diagnosis identifier', and made the class a subclass of 'identifier'. --- PCORnetCDM.owl | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index b1f28fe..50f2d9c 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -7949,7 +7949,8 @@ Environmental exposures include those imposed by natural environments, experimen - PCORnet CDM item identifier + obsolete PCORnet CDM item identifier + true @@ -7958,7 +7959,8 @@ Environmental exposures include those imposed by natural environments, experimen - PCORnet item + obsolete PCORnet item + true @@ -8403,7 +8405,8 @@ excludes emergency department encounters - + + An identifier that denotes a diagnosis. PCORnet diagnosis identifier @@ -8659,7 +8662,7 @@ excludes emergency department encounters - A proper name that denotes a health care encounter and has part some symbol. + An identifier that denotes a health care encounter and has part some symbol. Matthew Diller S. Clint Dowland PCORnet health care encounter identifier @@ -8671,7 +8674,7 @@ excludes emergency department encounters - A proper name that denotes a health care facility and has part some symbol. + An identifier that denotes a health care facility and has part some symbol. Matthew Diller S. Clint Dowland PCORnet facility identifier @@ -8732,7 +8735,7 @@ excludes emergency department encounters - A proper name that denotes a human being who is a bearer of a person healthcare provider role. + An identifier that denotes a human being who is a bearer of a person healthcare provider role. Matthew Diller S. Clint Dowland PCORnet provider identifier From 192a79831dc8a679b474a07209d60d857728b74e Mon Sep 17 00:00:00 2001 From: William Hogan Date: Sun, 1 Dec 2019 11:29:12 -0500 Subject: [PATCH 16/69] removed catalog-v001.xml from the repository. It's causing issues. --- catalog-v001.xml | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 catalog-v001.xml diff --git a/catalog-v001.xml b/catalog-v001.xml deleted file mode 100644 index 2b4af81..0000000 --- a/catalog-v001.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - From 6482076875d11329aa5b8f7ce1460b0d559529f0 Mon Sep 17 00:00:00 2001 From: William Hogan Date: Sun, 1 Dec 2019 12:04:48 -0500 Subject: [PATCH 17/69] fixed parentage of PCORnet CDM patient identifier --- PCORnetCDM.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 50f2d9c..deea0c5 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -8031,7 +8031,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A centrally registered identifier that denotes a person in a PCORnet data mart and is used to link across tables. This identifier is not necessarily unique within PCORnet. Amanda Hicks PCORnet patient identifier From af07985a379607d2a207927e40e511bfb1486c72 Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Wed, 1 Jan 2020 12:11:29 -0500 Subject: [PATCH 18/69] MIREOT'd the following classes and their superclasses from UBERON: 'blood', 'brain', 'breast', 'colon', 'ear', 'eye', 'hair', 'kidney', 'liver', 'lung', 'feather', 'meconium', 'milk', 'mouth', 'nail', 'nose', 'ovary', 'pancreas', 'penis', 'peritoneum', 'pharynx', 'pleura', 'prostate', 'pus', 'rectum', 'saliva', 'semen', 'serum', 'skin', 'spleen', 'sputum', 'stomach', 'stool', 'sweat', 'tear', 'testis', 'thyroid', 'tissue', 'urethra', 'urine', 'uterus', and 'vomitus'. --- PCORnetCDM.owl | 3618 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 3561 insertions(+), 57 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index deea0c5..355dd00 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -129,7 +129,9 @@ - + + curator notes + @@ -248,7 +250,9 @@ - + + present_in_taxon + @@ -780,6 +784,70 @@ Where we have an annotation assertion + + + + external_definition + + + + + + + + axiom_lost_from_external_ontology + + + + + + + + homology_notes + + + + + + + + has_relational_adjective + + + + + + + + taxon_notes + + + + + + + + function_notes + + + + + + + + structure_notes + + + + + + + + development_notes + + + + @@ -788,6 +856,14 @@ Where we have an annotation assertion + + + + fma_set_term + + + + @@ -805,6 +881,14 @@ Where we have an annotation assertion + + + + contributor + + + + @@ -843,6 +927,40 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + + has_alternative_id + + + + + + + + has_broad_synonym + + + + @@ -883,6 +1001,22 @@ Where we have an annotation assertion + + + + has_scope + + + + + + + + has_synonym_type + + + + @@ -897,6 +1031,24 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + @@ -927,6 +1079,12 @@ Where we have an annotation assertion + + + + + + @@ -7698,6 +7856,393 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. + a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. + the organ that is specialized for smell and is part of the respiratory system + the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359] + + + + BTO:0000840 + CALOHA:TS-2037 + EHDAA2:0001274 + EHDAA:1502 + EMAPA:16542 + EV:0100037 + EV:0100370 + FMA:46472 + GAID:77 + MA:0000281 + MAT:0000139 + MESH:D009666 + MIAA:0000139 + NCIT:C12756 + OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA + TAO:0000047 + UBERON:cjm + UMLS:C0028429 + ZFA:0000047 + galen:Nose + nasal sac + nose + peripheral olfactory organ + uberon + nasus + olfactory apparatus + proboscis + + + + UBERON:0000004 + + + + + + + MP:0002233 + ZFA:0000047 + ncithesaurus:Nose + nose + + + + + + + + + + Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. + Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] + we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive + 2012-09-17 + VHOG:0000860 + + + + EHDAA2:0001844 + EHDAA:6530 + EMAPA:17525 + EV:0100152 + FMA:86166 + GAID:933 + MA:0000151 + MAT:0000284 + MESH:D012867 + MIAA:0000284 + OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA + VHOG:0000860 + portion of skin + region of skin + skin + skin region + skin zone + uberon + UBERON:0000014 + + VHOG + + DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) + zone of skin + + + + + + + + + + + An organ that is capable of transducing sensory stimulus to the nervous system. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + + + + AEO:0000094 + BSA:0000121 + BTO:0000202 + CALOHA:TS-2043 + EHDAA2:0001824 + EHDAA:500 + EMAPA:35955 + FBbt:00005155 + GAID:63 + HAO:0000930 + MA:0000017 + MESH:D012679 + NCIT:C33224 + OBOL:accepted + OBOL:automatic + UMLS:C0935626 + VHOG:0001407 + WBbt:0006929 + organ of sense organ system + organ of sensory organ system + organ of sensory system + sense organ system organ + sensory organ + sensory organ system organ + sensory system organ + sensillum + uberon + Sinnesorgan + sensor + UBERON:0000020 + + ncithesaurus:Organ_of_the_Special_Sense + sense organ + + + + + + + + + + Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. + Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + CALOHA:TS-0051 + FMA:71012 + skin appendage + epidermal appendage + uberon + epidermal growth + UBERON:0000021 + + cutaneous appendage + + + + + + + + + one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Among the characteristics that distinguish the extant Aves from other living groups. Feathers have also been noticed in those Theropoda which have been termed feathered dinosaurs. Although feathers cover most parts of the body of birds, they arise only from certain well-defined tracts on the skin. They aid in flight, thermal insulation, waterproofing and coloration that helps in communication and protection + The beta-keratins in feathers, beaks and claws - and the claws, scales and shells of reptiles - are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the alpha-keratins of mammalian hair, horns and hoof. + + + BTO:0000447 + EFO:0000955 + GAID:1214 + MAT:0000156 + MESH:D005241 + OpenCyc:Mx4rvVjW-5wpEbGdrcN5Y29ycA + uberon + UBERON:0000022 + + + feather + http://xkcd.com/1104/ + + + + + + + + + + multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] + a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] + in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. + + 2012-08-14 + TAO:0005425 + FMA + + + + + FMA:9581 + GAID:19 + MESH:D012704 + NCIT:C13169 + TAO:0005425 + UMLS:C0036760 + ZFA:0005425 + tunica serosa + wall of serous sac + uberon + serosa + + UBERON:0000042 + + + TAO + + ncithesaurus:Serosa + serous membrane + + + + + + + + + + + the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + urethral + In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. + + + + BTO:0001426 + CALOHA:TS-1132 + EFO:0000931 + EMAPA:30901 + EV:0100099 + FMA:19667 + GAID:390 + MA:0000379 + MAT:0000121 + MESH:D014521 + MGI:anna + MIAA:0000121 + MP:0000537 + NCIT:C12417 + OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA + UMLS:C0041967 + VHOG:0001264 + XAO:0000153 + galen:Urethra + uberon + UBERON:0000057 + + + + + + ncithesaurus:Urethra + urethra + + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:305751 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:D000825 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + XAO:0003000 + ZFA:0000037 + biological structure + connected biological structure + uberon + UBERON:0000061 + + anatomical structure + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 + + + + + + CARO:0020004 + EFO:0000634 + EMAPA:35949 + ENVO:01000162 + FMA:67498 + MA:0003001 + NCIT:C13018 + OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA + OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA + UMLS:C0178784 + WBbt:0003760 + uberon + anatomical unit + body organ + element + UBERON:0000062 + + GO:0048513 + ncithesaurus:Organ + organ + + + + + + + + + A multicellular structure that is a part of an organ. + currently defined in a very broad sense, may be replaced by more specific classes in the future + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + + + AAO:0011124 + EFO:0000635 + FMA:82472 + NIFSTD:birnlex_16 + cardinal organ part + uberon + regional part of organ + UBERON:0000064 + + + + organ part + + + + @@ -7715,6 +8260,67 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + The organs associated with producing offspring in the gender that produces spermatozoa. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] + 2012-09-17 + VHOG:0000725 + + + + + BTO:0000082 + CALOHA:TS-1310 + EFO:0000970 + EHDAA2:0001054 + EHDAA:8136 + EMAPA:17968 + EV:0100101 + FBbt:00004927 + FMA:45664 + GAID:386 + HAO:0000505 + MA:0000396 + MESH:D005837 + MP:0001145 + NCIT:C12722 + OBOL:automatic + OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA + TGMA:0000634 + UMLS:C0017422 + UMLS:C1963704 + VHOG:0000725 + WBbt:0008423 + XAO:0000155 + genitalia of male organism + male genital system + male genitalia + male genitals + male organism genitalia + male organism reproductive system + reproductive system of male organism + uberon + male genital organ + male genital tract + male reproductive tract + systema genitale masculinum + UBERON:0000079 + + + VHOG + + ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 + ncithesaurus:Male_Genitalia + ncithesaurus:Male_Reproductive_System + male reproductive system + + + + @@ -7772,81 +8378,2979 @@ Environmental exposures include those imposed by natural environments, experimen - + + + + + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] + Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] + oral + some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives + in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips + 2012-06-20 + 2012-09-17 + AAO:0010355 + VHOG:0000812 + FMA + + + + + + AAO:0010355 + BTO:0001090 + BTO:0004698 + CALOHA:TS-1315 + EFO:0000825 + EHDAA2:0001326 + EHDAA:542 + EMAPA:16262 + FBbt:00003126 + FMA:49184 + FMA:TA + GAID:75 + MA:0000341 + MA:0002474 + MAT:0000038 + MESH:D009055 + MIAA:0000038 + OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA + TADS:0000040 + TAO:0000547 + TAO:0000590 + TGMA:0000131 + VHOG:0000280 + VHOG:0000812 + XAO:0003029 + ZFA:0000547 + ZFA:0000590 + galen:Mouth + regio oralis + adult mouth + uberon + cavital oralis + cavitas oris + cavum oris + mouth cavity + oral region + oral vestibule + rima oris + stoma + stomatodaeum + trophic apparatus + vestibule of mouth + vestibulum oris + + UBERON:0000165 + + + + + + AAO + VHOG + + AAO:BJB + DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) + mouth + + + + - - - Of or pertaining to the period of time immediately following birth, or to the newborn. - consider splitting infant/newborn - http://purl.obolibrary.org/obo/uberon.owl - - - - BTO:0001762 - EV:0300037 - HsapDv:0000082 - MmusDv:0000096 - NIF_Organism:birnlex_695 - OGES:000025 - neonatal stage - fledgling stage - hatchling - hatchling stage - infant stage - nestling stage - pouch stage - puggle - puggle stage + + + + + + A bodily fluid consisting of the expulsed contents of the stomach disgorged through the mouth or nose that happens as a result of a vomit reflex. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + ENVO:00000338 + NCIT:C77666 + OpenCyc:Mx4rvViQTJwpEbGdrcN5Y29ycA + UBERON:cjm + galen:Vomitus + vomitus uberon - newborn stage - UBERON:0007221 - neonate stage - + + UBERON:0000172 + vomit - + + + + + A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + UBERON:0000324 + UBERON:0007550 + + AEO:0000184 + BTO:0000491 + EHDAA2_RETIRED:0003184 + ENVO:02000022 + FMA:9674 + GO:0007588 + galen:Excretion + excreted substance + portion of excreted substance + waste substance + uberon + excretion + UBERON:0000174 + excreta + + - - - A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. + + + + + + Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + biospecimen in NCIT + NCIT + + ENVO:02000038 + OpenCyc:Mx4rvVjG6ZwpEbGdrcN5Y29ycA + galen:Pus + ncithesaurus:Pus uberon - UBERON:0035943 - - life cycle temporal boundary + purulent exudate + UBERON:0000177 + pus + - + + + + + A fluid that is composed of blood plasma and erythrocytes. + This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] + Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] + relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] + Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] + + + 2012-06-20 + 2012-08-14 + 2012-09-17 + AAO:0000046 + TAO:0000007 + VHOG:0000224 + + + + + AAO:0000046 + BTO:0000089 + CALOHA:TS-0079 + EFO:0000296 + EHDAA2:0000176 + EHDAA:418 + EMAPA:16332 + ENVO:02000027 + EV:0100047 + FMA:9670 + GAID:965 + MA:0000059 + MESH:D001769 + MIAA:0000315 + NCIT:C12434 + OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA + TAO:0000007 + UMLS:C0005767 + VHOG:0000224 + XAO:0000124 + ZFA:0000007 + galen:Blood + portion of blood + vertebrate blood + uberon + whole blood + UBERON:0000178 + + + + + AAO + TAO + VHOG + + AAO:LAP + DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) + ZFIN:curator + ncithesaurus:Blood + blood + + - - - A life cycle temporal boundary that marks the end of the life cycle of the organism. - end of life cycle - moment of death - time of death + + + + + + Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + cjm + 2009-04-08T04:38:19Z + + CARO:0000081 uberon - death - end of life - UBERON:0035944 - life-death temporal boundary + blood or blood analog + circulating fluid + UBERON:0000179 + haemolymphatic fluid - + + + + + The upper ventral region of the torso of an organism. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. + + + + BTO:0000149 + CALOHA:TS-2083 + EV:0100124 + FMA:9601 + GAID:33 + MESH:D001940 + NCIT:C12971 + OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA + UMLS:C0006141 + galen:Breast + mammary part of chest + mammary region + uberon + mamma + + UBERON:0000310 + + WP,unvetted + ncithesaurus:Breast + breast + + + - - - A life cycle temporal boundary that marks the start of the neonate stage of the organism. - moment of birth - time of birth + + + + + + A portion of organism substance that is produced by exocrine glands. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions + BTO + UBERON:0006540 + secretion + + + AEO:0001005 + BTO:0002977 + BTO:0002979 + EMAPA:36535 + FMA:9675 + MA:0002504 + MESH:D012634 + NCIT:C34062 + UMLS:C1516992 + galen:Secretion + bodily secretion + exocrine gland fluid/secretion + secreted substance uberon - birth - UBERON:0035946 - start of neonate stage + exocrine gland fluid + exocrine gland fluid or secretion + exocrine gland secretion + external secretion + UBERON:0000456 + ncithesaurus:Exocrine_Gland_Fluid_or_Secretion + secretion of exocrine gland + + + + + + + + + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + AAO:0010839 + AEO:0000004 + BILA:0000004 + CALOHA:TS-2101 + CARO:0000004 + EHDAA2:0003004 + EMAPA:35178 + FBbt:00007019 + FMA:9669 + HAO:0000004 + MA:0002450 + NCIT:C13236 + SPD:0000008 + TAO:0001487 + TGMA:0001824 + VHOG:0001726 + XAO:0004001 + ZFA:0001487 + galen:BodySubstance + body fluid or substance + body substance + organism substance + portion of body substance + portion of organism substance + uberon + UBERON:0000463 + + + organism substance + + + + + + + + + Anatomical entity that has mass. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + uberon + UBERON:0000465 + + material anatomical entity + + + + + + + + + A gonad of a male animal. A gonad produces and releases sperm. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Male reproductive organ.[TAO] + (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] + testicular + The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally + 2012-08-14 + 2012-09-17 + TAO:0000598 + VHOG:0000252 + UBERON:0002117 + + + + + AAO:0000606 + BILA:0000124 + BSA:0000085 + BTO:0001363 + CALOHA:TS-1030 + EFO:0000984 + EHDAA2:0002007 + EHDAA:8146 + EMAPA:17972 + EV:0100102 + FBbt:00004928 + FMA:7210 + GAID:396 + HAO:0001007 + MA:0000411 + MAT:0000132 + MESH:D013737 + MIAA:0000132 + NCIT:C12412 + OBOL:automatic + OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA + TAO:0000598 + UMLS:C0039597 + VHOG:0000252 + WBbt:0006794 + XAO:0000157 + ZFA:0000598 + galen:Testis + gonad of male genitalia + gonad of male reproductive system + male gonad + testicle + uberon + orchis + testes + testiculus + + + UBERON:0000473 + + + + + + TAO + VHOG + + DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) + ISBN-10:0123971756 + ZFIN:curator + ncithesaurus:Testis + NCBITaxon:40674 + testis + + + + + + + + + + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + changed label and definition to reflect CARO2 + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + AAO:0000607 + AAO:0010054 + AEO:0000043 + BILA:0000043 + CALOHA:TS-2090 + CARO:0000043 + EHDAA2:0003043 + EMAPA:35868 + FBbt:00007003 + FMA:9637 + HAO:0000043 + MA:0003002 + MESH:D014024 + NCIT:C12801 + TAO:0001477 + TGMA:0001844 + UMLS:C0040300 + VHOG:0001757 + WBbt:0005729 + XAO:0003040 + ZFA:0001477 + galen:Tissue + portion of tissue + tissue portion + simple tissue + uberon + UBERON:0000479 + + + ncithesaurus:Tissue + tissue + + + + + + + + + Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + AAO:0010048 + AEO:0000055 + BILA:0000055 + CARO:0000055 + EHDAA2:0003055 + FBbt:00007010 + HAO:0000055 + TAO:0001488 + TGMA:0001847 + VHOG:0001762 + XAO:0003037 + ZFA:0001488 + uberon + multi-tissue structures + + UBERON:0000481 + + multi-tissue structure + + + + + + + + + An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] + It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] + We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa + 2012-06-20 + 2012-09-17 + AAO:0000579 + VHOG:0000408 + + + + + AAO:0000579 + ANISEED:1235297 + BTO:0001307 + CALOHA:TS-0980 + EFO:0000837 + EHDAA2:0001915 + EHDAA:2993 + EMAPA:17021 + EV:0100070 + FMA:7148 + GAID:293 + ISBN10:0073040584 + MA:0000353 + MAT:0000051 + MESH:A03.492.766 + MIAA:0000051 + NCIT:C12391 + OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA + TAO:0002121 + UMLS:C0038351 + VHOG:0000408 + XAO:0000128 + galen:Stomach + stomach chamber + uberon + anterior intestine + gaster + mesenteron + ventriculus + + UBERON:0000945 + + + + + + + AAO + VHOG + + AAO:EJS + DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000) + WP:Stomach#In_other_animals + ncithesaurus:Stomach + stomach + + + + + + + + + + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. + requires review for applicability to invertebrate structures, e.g. synganglion + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] + Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] + The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] + + 2012-06-20 + 2012-08-14 + 2012-09-17 + AAO:0010478 + TAO:0000008 + VHOG:0000157 + + + + + + + + AAO:0010478 + ABA:Brain + BAMS:Br + BAMS:Brain + BILA:0000135 + BTO:0000142 + CALOHA:TS-0095 + DHBA:10155 + EFO:0000302 + EHDAA2:0000183 + EHDAA:2641 + EHDAA:6485 + EMAPA:16894 + EV:0100164 + FBbt:00005095 + FMA:50801 + GAID:571 + HBA:4005 + MA:0000168 + MAT:0000098 + MBA:8 + MBA:997 + MESH:D001921 + MIAA:0000098 + NCIT:C12439 + NeuroNames:21 + OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA + PBA:3999 + TAO:0000008 + UMLS:C0006104 + UMLS:C1269537 + VHOG:0000157 + XAO:0000010 + ZFA:0000008 + galen:Brain + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 + uberon + encephalon + suprasegmental levels of nervous system + suprasegmental structures + synganglion + the brain + UBERON:0000955 + + + + + + + AAO + TAO + VHOG + + + AAO:BJB + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 + NIFSTD:birnlex_796 + ZFIN:curator + ncithesaurus:Brain + brain + + + + + + + + + An organ that detects light. + This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + ocular + optic + Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, + + + BILA:0000017 + BTO:0000439 + CALOHA:TS-0309 + EFO:0000827 + EV:0100336 + FBbt:00005162 + GAID:69 + MAT:0000140 + MESH:D005123 + MIAA:0000140 + OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA + uberon + light-detecting organ + visual apparatus + UBERON:0000970 + + + + + + eye + + + + + + + + + The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] + pleural + In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86 + 2012-09-17 + VHOG:0000394 + + + + + + BTO:0001791 + CALOHA:TS-2081 + EFO:0001980 + EMAPA:16775 + EV:0100044 + FMA:9583 + GAID:360 + ISBN:0-683-40008-8 + MA:0000433 + MESH:D010994 + MP:0010820 + NCIT:C12469 + OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA + UBERON:cjm + UMLS:C0032225 + VHOG:0000394 + wall of pleural sac + uberon + pleura + pleural tissue + UBERON:0000977 + + + + VHOG + + BGEE:AN + ISBN10:0124020607 + ISBN:978-0030223693 + ncithesaurus:Pleural_Tissue + pleura + + + + + + + + + + A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + penile + phallic + Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca + + + + + BTO:0000405 + CALOHA:TS-0758 + EFO:0000987 + EHDAA2:0001433 + EHDAA:9380 + EMAPA:18682 + EMAPA_RETIRED:18996 + EV:0100107 + FMA:9707 + GAID:389 + ISBN:0-683-40008-8 + MA:0000408 + MAT:0000186 + MESH:D010413 + MIAA:0000186 + MP:0005187 + NCIT:C12409 + OpenCyc:Mx4rvVjkCZwpEbGdrcN5Y29ycA + UMLS:C0030851 + VHOG:0000727 + galen:Penis + uberon + penes + phallus + + UBERON:0000989 + + + + + WP + ncithesaurus:Penis + penis + + + + + + + + + + Reproductive organ that produces and releases eggs (ovary) or sperm (testis). + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] + The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] + Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] + gonadal + FMA xref is a 'general anatomical term' + 2012-06-20 + 2012-08-14 + 2012-09-17 + AAO:0000213 + TAO:0000413 + VHOG:0000397 + FMA + + + + AAO:0000213 + BILA:0000123 + BSA:0000079 + BTO:0000534 + EMAPA:17383 + FBbt:00004858 + FMA:18250 + GAID:368 + HAO:0000379 + ISBN:0140512888 + MA:0002420 + MESH:D006066 + NCIT:C12725 + OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA + TAO:0000413 + UMLS:C0018067 + VHOG:0000397 + WBbt:0005175 + XAO:0003146 + ZFA:0000413 + ZFIN:curator + gonada + uberon + gonads + + UBERON:0000991 + + + + + + AAO + TAO + VHOG + + AAO:BJB + DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) + ZFIN:curator + ncithesaurus:Gonad + gonad + + + + + + + + + the gonad of a female organism which contains germ cells + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] + Female reproductive organ.[TAO] + (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] + ovarian + Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo + 2012-06-20 + 2012-08-14 + 2012-09-17 + AAO:0000371 + TAO:0000403 + VHOG:0000251 + + + + AAO:0000371 + BILA:0000125 + BSA:0000080 + BTO:0000975 + CALOHA:TS-0730 + EFO:0000973 + EHDAA2:0001360 + EHDAA:8124 + EMAPA:17962 + EV:0100111 + FBbt:00004865 + FMA:7209 + GAID:367 + GO:0061039 + ISBN:0-683-40008-8 + MA:0000384 + MESH:D010053 + MIAA:0000125 + MP:0001126 + NCIT:C12404 + OBOL:automatic + OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA + TAO:0000403 + UMLS:C0029939 + VHOG:0000251 + XAO:0000258 + ZFA:0000403 + animal ovary + female gonad + female organism genitalia gonad + female organism genitalia gonada + female organism reproductive system gonad + female organism reproductive system gonada + female reproductive system gonad + female reproductive system gonada + genitalia of female organism gonad + genitalia of female organism gonada + gonad of female organism genitalia + gonad of female organism reproductive system + gonad of female reproductive system + gonad of genitalia of female organism + gonad of reproductive system of female organism + gonada of female organism genitalia + gonada of female organism reproductive system + gonada of female reproductive system + gonada of genitalia of female organism + gonada of reproductive system of female organism + ovum-producing ovary + reproductive system of female organism gonad + reproductive system of female organism gonada + uberon + ovaries + ovarium + + + + UBERON:0000992 + + + + + + AAO + TAO + VHOG + + AAO:BJB + DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) + WP + ZFIN:curator + ncithesaurus:Ovary + ovary + + + + + + + + + + + the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] + An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] + uterine + Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. + Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus] + 2012-09-17 + VHOG:0001137 + + + + BTO:0001424 + CALOHA:TS-1102 + EFO:0000975 + EMAPA:29915 + EV:0100113 + FMA:17558 + GAID:172 + MA:0000389 + MAT:0000127 + MESH:D014599 + MGI:csmith + MIAA:0000127 + MP:0001120 + NCIT:C12405 + OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA + UMLS:C0042149 + VHOG:0001137 + galen:Uterus + uberon + UBERON:0000995 + + + + + VHOG + + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678 + ncithesaurus:Uterus + uterus + + + + + + + + + + + A filament, mostly protein, that grows from follicles found in the dermis[WP]. + TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales) + this class defines an individual hair + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + + BTO:0001501 + CALOHA:TS-0430 + EFO:0000958 + EMAPA:18769 + EV:0100157 + FMA:53667 + GAID:71 + MA:0000155 + MAT:0000160 + MESH:D006197 + MIAA:0000160 + NCIT:C32705 + OpenCyc:Mx4rvVjOX5wpEbGdrcN5Y29ycA-Mp88EdaAAACgycbRww + UMLS:C0018494 + VHOG:0001191 + hair + uberon + coat hair + coat/ hair + fur + microchaeta + quill + setulae + vibrissa + whisker + + UBERON:0001037 + + + + ncithesaurus:Hair + strand of hair + + + + + + + + + + the terminal portion of the intestinal tube, terminating with the anus + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] + rectal + In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html + 2012-09-17 + VHOG:0001751 + + + + + AAO:0010401 + BTO:0001158 + CALOHA:TS-1180 + EFO:0000848 + EHDAA2:0001592 + EHDAA:5836 + EMAPA:17896 + EV:0100081 + FMA:14544 + GAID:311 + ISBN:0-683-40008-8 + MA:0000336 + MAT:0000050 + MESH:A03.492.411.495.767 + MIAA:0000050 + MP:0000492 + NCIT:C12390 + OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA + UMLS:C0034896 + VHOG:0001751 + XAO:0000238 + galen:Rectum + terminal portion of intestine + uberon + intestinum rectum + rectal sac + terminal portion of large intestine + UBERON:0001052 + + + + VHOG + + ncithesaurus:Rectum + rectum + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FBbt_root:00000000 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + uberon + UBERON:0001062 + + ncithesaurus:Anatomic_Structure_System_or_Substance + anatomical entity + + + + + + + + + Excretion that is the output of a kidney + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + kidney excreta from some taxa (e.g. in aves) may not be liquid + + + + BTO:0001419 + CALOHA:TS-1092 + EFO:0001939 + EMAPA:36554 + ENVO:00002047 + FMA:12274 + GAID:1189 + MA:0002545 + MAT:0000058 + MESH:D014556 + MIAA:0000058 + NCIT:C13283 + OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA + UMLS:C0042036 + galen:Urine + uberon + UBERON:0001088 + + + + ncithesaurus:Urine + urine + + + + + + + + + Secretion produced by a sweat gland. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + BTO:0001254 + ENVO:02000025 + FMA:12275 + GAID:1172 + MA:0002539 + MESH:D013542 + NCIT:C13280 + OpenCyc:Mx4rvVjJtZwpEbGdrcN5Y29ycA + UMLS:C0038984 + uberon + skin exudate + UBERON:0001089 + + + ncithesaurus:Sweat + sweat + + + + + + + + + Last portion of the large intestine before it becomes the rectum. + TODO - abstract this such that it legitimately covers all vertebrates + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] + The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] + Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] + colonic + In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] + In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] + it extracts water and salt from solid wastes before they are eliminated from the body[WP] + 2012-06-20 + 2012-08-14 + 2012-09-17 + AAO:0010400 + TAO:0000706 + VHOG:0000648 + + + + + AAO:0010400 + BTO:0000269 + CALOHA:TS-0158 + EFO:0000361 + EMAPA:18939 + EV:0100079 + FMA:14543 + GAID:309 + MA:0000335 + MAP:0000001 + MAT:0000526 + MESH:A03.492.411.495.356 + NCIT:C12382 + OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA + TAO:0000706 + UMLS:C0009368 + VHOG:0000648 + XAO:0000243 + ZFA:0000706 + ZFIN:curator + galen:Colon + large bowel + posterior intestine + uberon + hindgut + UBERON:0001155 + + + + + AAO + TAO + VHOG + + ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 + UBERON:0001155 + ZFIN:curator + ncithesaurus:Colon + colon + + + + + + + + + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] + In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] + pancreatic + As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) + The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm + The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans + 2012-06-20 + 2012-09-17 + AAO:0010112 + VHOG:0000050 + + + + AAO:0010112 + BTO:0000988 + CALOHA:TS-0736 + EFO:0000855 + EHDAA2:0001367 + EHDAA:6893 + EMAPA:17503 + EV:0100092 + FMA:7198 + GAID:334 + GO:0031016 + MA:0000120 + MAT:0000075 + MESH:D010179 + MIAA:0000075 + NCIT:C12393 + OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA + TAO:0000140 + UMLS:C0030274 + VHOG:0000050 + XAO:0000136 + ZFA:0000140 + galen:Pancreas + uberon + UBERON:0001264 + + + + + + + AAO + VHOG + + + + AAO:BJB + DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) + ncithesaurus:Pancreas + pancreas + + + + + + + + + + Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + The organ of hearing and of equilibrium. [TFD][VHOG] + Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] + auricular + 2012-09-17 + VHOG:0000330 + + + + + + AAO:0011014 + BTO:0000368 + CALOHA:TS-1165 + EFO:0000826 + EHDAA2:0000423 + EHDAA:502 + EMAPA:16193 + EV:0100353 + FMA:52780 + GAID:62 + GO:0042471 + MA:0000236 + MAT:0000138 + MESH:D004423 + MIAA:0000138 + NCIT:C12394 + OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA + OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA + UMLS:C0013443 + UMLS:C0521421 + VHOG:0000330 + XAO:0000189 + galen:Ear + uberon + auditory apparatus + auris + UBERON:0001690 + + + + + VHOG + + + DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005) + NIFSTD:birnlex_1062 + ncithesaurus:Ear + ear + + + + + + + + + + A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP]. + Use this class for both the nails of primates and the homologous claws of mammals such as mouse. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + A primate's nail consists of the unguis alone; the subunguis has disappeared + + + + + + + + + BTO:0001719 + CALOHA:TS-2034 + EFO:0000956 + EMAPA:35580 + EV:0100159 + FMA:54326 + GAID:1320 + MA:0002703 + MAT:0000158 + MESH:D009262 + MIAA:0000158 + NCIT:C33156 + OpenCyc:Mx4rvVjJv5wpEbGdrcN5Y29ycA + UMLS:C0027342 + VHOG:0001361 + XAO:0003103 + galen:Nail + nail/claw + claw + uberon + talon + + UBERON:0001705 + + + + ncithesaurus:Nail + The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226] + nail + + + + + + + + + Aqueous substance secreted by the lacrimal gland. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + + BTO:0001499 + CALOHA:TS-1016 + EMAPA:36537 + ENVO:02000034 + FMA:59756 + GAID:1173 + MA:0002508 + MESH:D013666 + NCIT:C33739 + UMLS:C0039409 + galen:Tear + galen:Tears + lacrimal fluid + lacrimal gland secretion + lacrimal secretion + tear + tears + uberon + tear fluid + + UBERON:0001827 + + ncithesaurus:Tear + secretion of lacrimal gland + + + + + + + + + A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + salivary + We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin + + + BTO:0001202 + CALOHA:TS-0891 + EMAPA:36536 + ENVO:02000036 + FMA:59862 + GAID:1167 + GO:0046541 + MA:0002507 + MAT:0000444 + MESH:D012463 + NCIT:C13275 + OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA + UMLS:C0036087 + galen:Saliva + salivary gland secretion + uberon + sailva normalis + saliva atomaris + saliva molecularis + + UBERON:0001836 + + GO + ncithesaurus:Saliva + saliva + + + + + + + + + An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. + to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] + ncit:Milk refers specifically to cow milk + 2012-09-17 + VHOG:0001263 + ncit + + + + BTO:0000868 + CALOHA:TS-0636 + EMAPA:36540 + ENVO:02000031 + EV:0100126 + FMA:62100 + GAID:1230 + MA:0002552 + MAT:0000056 + MESH:A13.622 + MIAA:0000056 + NCIT:C13401 + OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA + UMLS:C1511310 + VHOG:0001263 + galen:Milk + mammary gland milk + uberon + UBERON:0001913 + + + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224 + ncithesaurus:Breast_Fluid_or_Secretion + milk + + + + + + + + + Organism substance that is composed of sperm cells suspended in seminal fluid. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + seminal + Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530). + + + + + BTO:0001230 + CALOHA:TS-0917 + EMAPA:31488 + FMA:62966 + GAID:1169 + MA:0002522 + MESH:D012661 + NCIT:C13277 + NCIT:C13713 + OpenCyc:Mx4rvgC-zpwpEbGdrcN5Y29ycA + UMLS:C1518159 + UMLS:C2756969 + uberon + ejaculate + sperm + UBERON:0001968 + + + ncithesaurus:Male_Genital_System_Fluid_or_Secretion + ncithesaurus:Semen + semen + + + + + + + + + + The portion of blood plasma that excludes clotting factors. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + + BTO:0000133 + BTO:0001239 + CALOHA:TS-0923 + EHDAA2:0004728 + EMAPA:35770 + FMA:63083 + MA:0002502 + NCIT:C13325 + UMLS:C0229671 + serum + uberon + UBERON:0001977 + + + ncithesaurus:Serum + blood serum + + + + + + + + + Portion of semisolid bodily waste discharged through the anus[MW,modified] + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Excretion in semisolid state processed by the intestine.[FMA] + fecal + excreta + + + + + + + + + + BTO:0000440 + CALOHA:TS-2345 + ENVO:00002003 + FMA:64183 + GAID:1199 + MA:0002509 + MAT:0000053 + MESH:D005243 + MIAA:0000053 + NCIT:C13234 + OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA + UMLS:C0015733 + galen:Feces + faeces + fecal material + fecal matter + matières fécales@fr + merde@fr + partie de la merde@fr + piece of shit + porción de mierda@es + portion of excrement + portion of faeces + portion of fecal material + portion of fecal matter + portion of feces + portionem cacas + stool + teil der fäkalien@de + cow dung + cow pat + dung + fewmet + frass + guano + portion of dung + portion of guano + portion of scat + scat + spraint + uberon + droppings + excrement + ordure + spoor + + UBERON:0001988 + + + FMA:64183 + ncithesaurus:Feces + feces + + + + + + + + + A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] + In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes + In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) + In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species + 2012-06-20 + 2012-09-17 + AAO:0010544 + VHOG:0000418 + + + + AAO:0010544 + BTO:0001379 + CALOHA:TS-1047 + EFO:0000861 + EHDAA2:0002028 + EHDAA:2148 + EHDAA:2975 + EMAPA:17068 + EV:0100133 + FMA:9603 + GAID:465 + MA:0000129 + MAT:0000081 + MESH:D013961 + MIAA:0000081 + NCIT:C12400 + OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA + UMLS:C0040132 + VHOG:0000418 + XAO:0000162 + galen:ThyroidGland + thyroid + uberon + glandula thyroidea + NCBITaxon:32443 + NCBITaxon:32523 + NCBITaxon:7746 + + UBERON:0002046 + + + + + AAO + VHOG + + + AAO:BJB + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + Romer + ncithesaurus:Thyroid_Gland + thyroid gland + + + + + + + + + + + Respiration organ that develops as an oupocketing of the esophagus. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] + Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] + pulmonary + respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi + 2012-06-20 + 2012-09-17 + AAO:0010567 + VHOG:0000310 + + + + + AAO:0000275 + AAO:0010567 + BTO:0000763 + CALOHA:TS-0568 + EFO:0000934 + EHDAA2:0001042 + EHDAA:1554 + EHDAA:2205 + EMAPA:16728 + EV:0100042 + FMA:7195 + GAID:345 + MA:0000415 + MAT:0000135 + MESH:D008168 + MIAA:0000135 + NCIT:C12468 + OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA + UMLS:C0024109 + VHOG:0000310 + XAO:0000119 + galen:Lung + pulmo + uberon + + UBERON:0002048 + + + + + + AAO + VHOG + + AAO:SBH + ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011) + ncithesaurus:Lung + Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] + lung + + + + + + + + + + An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] + general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. + 2012-06-20 + AAO:0010386 + FMA + + + + + AAO:0010386 + BTO:0001491 + EHDAA:512 + EMAPA:16245 + FMA:7085 + MA:0000019 + MESH:D014781 + NCIT:C28287 + RETIRED_EHDAA2:0002201 + UMLS:C0042779 + XAO:0003034 + visceral organ + visceral organ system + uberon + Organsystem@de + splanchnic tissue + viscera + visceral tissue + UBERON:0002075 + + + + + AAO + BTO:0001491 + ncithesaurus:Viscera + viscus + + + + + + + + + the organ that functions to filter blood and to store red corpuscles and platelets + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + An organ involved in red blood cell filtration and immune response.[AAO] + With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG] + lienal + splenic + In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron + Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) + It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells + 2012-06-20 + 2012-09-17 + AAO:0010395 + VHOG:0000120 + + + + AAO:0010395 + BTO:0001281 + CALOHA:TS-0956 + EFO:0000869 + EMAPA:18767 + EV:0100055 + FMA:7196 + GAID:1289 + ISBN:0-683-40008-8 + MA:0000141 + MAT:0000085 + MESH:A15.382.520.604.713 + MIAA:0000085 + MP:0000689 + NCIT:C12432 + OpenCyc:Mx4rvVjgw5wpEbGdrcN5Y29ycA + TAO:0000436 + UMLS:C0037993 + VHOG:0000120 + XAO:0000328 + ZFA:0000436 + galen:Spleen + uberon + lien + + UBERON:0002106 + + + + + + AAO + VHOG + + + AAO:BMZ + ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94 + ncithesaurus:Spleen + spleen + + + + + + + + + + An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Organ which secretes bile and participates in formation of certain blood proteins.[AAO] + relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] + All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] + hepatic + An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). + The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. + secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. + Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. + 2012-06-20 + 2012-09-17 + AAO:0010111 + VHOG:0000257 + ZFA + + + + AAO:0010111 + BTO:0000759 + CALOHA:TS-0564 + EFO:0000887 + EHDAA2:0000997 + EHDAA:2197 + EMAPA:16846 + EV:0100089 + FMA:7197 + GAID:288 + MA:0000358 + MAT:0000097 + MESH:D008099 + MIAA:0000097 + NCIT:C12392 + OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA + TAO:0000123 + UMLS:C0023884 + VHOG:0000257 + XAO:0000133 + ZFA:0000123 + galen:Liver + uberon + iecur + jecur + + UBERON:0002107 + + + + + + + AAO + VHOG + + AAO:BJB + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 + ncithesaurus:Liver + liver + + + + + + + + + + A paired organ of the urinary tract which has the production of urine as its primary function. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] + renal + + 2012-06-20 + AAO:0000250 + + + + + + AAO:0000250 + BTO:0000671 + CALOHA:TS-0510 + EFO:0000929 + EMAPA:17373 + EV:0100096 + FMA:7203 + GAID:423 + MA:0000368 + MAT:0000119 + MESH:D007668 + MIAA:0000119 + NCIT:C12415 + OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA + UMLS:C0022646 + XAO:0003267 + galen:Kidney + reniculate kidney + uberon + + UBERON:0002113 + + + + + + + AAO + AAO:BJB + ncithesaurus:Kidney + kidney + + + + + + + + + An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. + An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint + AAO:0010180 + BTO:0001772 + FBbt:00005158 + FMA:77659 + UBERON:cjm + VHOG:0000287 + XAO:0000273 + olfactory organ + olfactory sense organ + olfactory sensory organ + main olfactory organ + primary olfactory organ + uberon + olfactory neuroepithelium + organ olfactus + organum olfactorium + UBERON:0002268 + + olfactory organ + + + + + + + + + A serous membrane that lines the peritoneal cavity[VHOG,modified]. + TODO - in ZFA is_a epithelium + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + An epithelium that lines the peritoneal cavity.[TAO] + Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] + peritoneal + todo: check MA/EMAPA. + 2012-06-20 + 2012-08-14 + AAO:0010814 + TAO:0005120 + MA + + + AAO:0010814 + BTO:0001472 + CALOHA:TS-2072 + EV:0100087 + FMA:9584 + GAID:18 + MA:0000449 + MESH:A01.047.025.600 + NCIT:C12770 + OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA + TAO:0005120 + UMLS:C0031153 + VHOG:0001257 + XAO:0000139 + ZFA:0005120 + galen:Peritoneum + uberon + peritonaeum + UBERON:0002358 + + + + AAO + TAO + AAO:JMG + ZFIN:curator + ncithesaurus:Peritoneum + peritoneum + + + + + + + + + + The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. + TODO - FMA treats the gland as part of the prostate - see also FMA:74119. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + prostatic + + + + + BTO:0001129 + CALOHA:TS-0828 + EFO:0000858 + EMAPA:19287 + EV:0100104 + FMA:9600 + GAID:392 + GO:0030850 + MA:0000404 + MAT:0000078 + MESH:D011467 + MIAA:0000078 + NCIT:C12410 + OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA + UMLS:C0033572 + VHOG:0001261 + galen:ProstateGland + male prostate + prostate + uberon + prostata + + UBERON:0002367 + + + + + + ncithesaurus:Prostate_Gland + prostate gland + + + + + + + + + + Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + + + AEO:0000098 + BTO:0001488 + CALOHA:TS-1300 + EHDAA2:0003098 + EMAPA:35999 + FMA:9602 + GAID:335 + MA:0002563 + MESH:D004702 + NCIT:C12704 + OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA + UMLS:C0014133 + ductless gland + glandula endocrina + uberon + ductless gland + glandulae endocrinae + + UBERON:0002368 + + + + ncithesaurus:Endocrine_Gland + endocrine gland + + + + + + + + + + an organ that functions as a secretory or excretory organ + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + glandular + UBERON:MIAA_0000021 + + + + + AAO:0000212 + AEO:0000096 + BTO:0000522 + EFO:0000797 + EHDAA2:0003096 + EHDAA:2161 + EHDAA:4475 + EHDAA:6522 + EMAPA:18425 + FBbt:00100317 + FMA:7146 + FMA:86294 + HAO:0000375 + MA:0003038 + MAT:0000021 + MGI:csmith + MIAA:0000021 + MP:0002163 + NCIT:C13319 + OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA + UMLS:C1285092 + WikipediaCategory:Glands + galen:Gland + glandular organ + uberon + Druese + glandula + + UBERON:0002530 + + + + ncithesaurus:Gland + gland + + + + + + + + + + An organ involved in reproduction + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + GO uses genitalia for the singular organ + GO + + + EMAPA:17381 + EMAPA:37731 + MA:0001752 + MESH:D005835 + NCIT:C25177 + OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA + TGMA:0000591 + UBERON:xp + UMLS:C0017420 + WBbt:0008422 + genital organ + reproductive system organ + sex organ + uberon + genitalia + + UBERON:0003133 + + + + MA:th + ncithesaurus:Genitalia + reproductive organ + + + + + + + + + Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + MA:0001751 + MP:0000653 + OBOL:automatic + genitalia gland + gland of genitalia + gland of reproductive system + reproductive gland + reproductive system gland + sex gland + uberon + UBERON:0003937 + + + reproductive gland + + + + + + + + + A proximal-distal subdivision of the digestive tract. + intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + FBbt:00100315 + FMA:71131 + uberon + alimentary system subdivision + intestinal tract + segment of intestinal tract + subdivision of alimentary system + UBERON:0004921 + + subdivision of digestive tract + + + + + + + + + An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + + MA:0000522 + abdomen organ + uberon + UBERON:0005172 + + abdomen element + + + + + + + + + An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + EMAPA:37062 + MA:0000529 + abdominal segment organ + uberon + UBERON:0005173 + + MA:th + abdominal segment element + + + + + + + + + An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + EMAPA:37270 + MA:0000516 + trunk organ + uberon + UBERON:0005177 + + + MA:th + trunk region element + + + + + + + + + An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + EMAPA:37273 + MA:0000557 + thoracic cavity organ + uberon + UBERON:0005178 + + + MA:th + thoracic cavity element + + + + + + + + + An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + EMAPA:37271 + MA:0000563 + uberon + upper body organ + UBERON:0005181 + + MA:th + thoracic segment organ + + + + + + + + + A sex gland that is part of a male reproductive system. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + BTO:0000080 + EMAPA:19285 + MA:0000399 + OBOL:automatic + uberon + accessory sex gland + UBERON:0005399 + + + male reproductive gland + + + + + + + + + Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. + add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] + + + + EMAPA:37883 + GO:GO + body hair or bristle + uberon + adnexae cutis + skin adnexa + skin adnexal structure + skin appendage + + UBERON:0006003 + + MA:th + MP:0010678 + integumentary adnexa + + + + + + + + + Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + fluid + + + EMAPA:37441 + FMA:280556 + GAID:266 + MESH:A12.207 + MESH:D001826 + galen:BodyFluid + body fluid + uberon + UBERON:0006314 + + MA:th + bodily fluid + + + + + + + + + A portion of organism substance that secreted_by a respiratory system. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + EMAPA:36550 + MA:0002533 + NCIT:C13722 + OBOL:automatic + UMLS:C1514899 + uberon + respiratory system fluid + respiratory system secretion + UBERON:0006538 + ncithesaurus:Respiratory_System_Fluid_or_Secretion + respiratory system fluid/secretion + + + + + + + + + A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + EMAPA:36538 + MA:0002505 + uberon + lactiferous gland fluid + lactiferous gland secretion + mammary gland fluid + mammary gland secreted fluid + mammary gland secretion + secretion of mammary gland + UBERON:0006539 + mammary gland fluid/secretion + + + + + + + + + The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. + currently this is an extremely generic class, encompassing both protostomes and deuterostomes. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + branchial + pharyngeal + FBbt:00005380 + GO:0060465 + MAT:0000049 + MIAA:0000049 + uberon + anterior part of foregut + pharyngeal tube + UBERON:0006562 + + + pharynx + + + + + + + + + Any gland that is part of the digestive system. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + AAO:0000130 + BTO:0000345 + UBERON:cjm + uberon + digestive gland + UBERON:0006925 + + digestive system gland + + + + + + + + + A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + BTO:0000838 + ncithesaurus:Meconium + uberon + UBERON:0007109 + meconium + + + + + + + + + Of or pertaining to the period of time immediately following birth, or to the newborn. + consider splitting infant/newborn + http://purl.obolibrary.org/obo/uberon.owl + + + + BTO:0001762 + EV:0300037 + HsapDv:0000082 + MmusDv:0000096 + NIF_Organism:birnlex_695 + OGES:000025 + neonatal stage + fledgling stage + hatchling + hatchling stage + infant stage + nestling stage + pouch stage + puggle + puggle stage + uberon + newborn stage + UBERON:0007221 + neonate stage + + + + + + + + + + Matter ejected from the lungs, bronchi, and trachea, through the mouth. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + BTO:0001297 + CALOHA:TS-0963 + Dorlands_Medical_Dictionary:MerckSource + EMAPA:36553 + FMA:312401 + GAID:1171 + MA:0002536 + MESH:D013183 + NCIT:C13278 + UMLS:C0038056 + uberon + expectoration + UBERON:0007311 + ncithesaurus:Sputum + sputum + + + + + + + + + An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]. + this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO] + 2012-08-14 + TAO:0002036 + + AAO:0010255 + FBbt:00004850 + HAO:0000091 + TAO:0002036 + TGMA:0000585 + aedeagus + penis + uberon + copulatory organ + + UBERON:0008811 + + + TAO + TAO:wd + intromittent organ + + + + + + + + + A nail, hoof or claw. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + MESH:D006724 + uberon + hoof or claw + hoof, claw or nail + keratin plate + keratin sheath + unguis + UBERON:0009564 + distal limb integumentary appendage + + + + + + + + + An anatomical structure that has more than one cell as a part. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + multicellular anatomical structure + + + + + + + + + Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + BTO:0004798 + uberon + male accessory gland + male accessory reproductive gland + UBERON:0010147 + + male accessory sex gland + + + + + + + + + A section through the tube or network of tubes that connects the ovaries to the outside of the body. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + FMA class may only represent the uterine portion + FMA + + FMA:18302 + subdivision of oviduct + subdivision of uterine tube + uterine tube zone + zone of uterine tube + subdivision of fallopian tube + uberon + UBERON:0013515 + + subdivision of oviduct + + + + + + + + + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + uberon + UBERON:0013522 + subdivision of tube + + + + + + + + + Anatomical projection that is part of the integumentl system. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + skin projection + uberon + UBERON:0013703 + integumentary projection + + + + + + + + + A viscus that is part of a abdomen. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + FMA:32413 + FMA:67355 + OBOL:automatic + abdominal viscera + abdominal viscera set + set of abdominal viscera + uberon + UBERON:0017672 + + abdominal viscera + + + + + + + + + A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + + uberon + UBERON:0034929 + external soft tissue zone + + + + + + + + + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + FMA:55268 + organ sector + organ zonal region + organ zone + uberon + organ region with floating fiat boundary + UBERON:0034944 + zone of organ + + + + + + + + + A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. + uberon + UBERON:0035943 + + life cycle temporal boundary + + + + + + + + + A life cycle temporal boundary that marks the end of the life cycle of the organism. + end of life cycle + moment of death + time of death + uberon + death + end of life + UBERON:0035944 + life-death temporal boundary + + + + + + + + + A life cycle temporal boundary that marks the start of the neonate stage of the organism. + moment of birth + time of birth + uberon + birth + UBERON:0035946 + start of neonate stage + + + + + + + + + A bodily fluid consisting of the contents of the digestive tract expulsed through the anterior portion of the digestive tract. + http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl + UBERON:cjm + uberon + regurgitate + UBERON:0036017 + regurgitated substance From bcdae2dfd5a03e2754c59ba2653a4027b31f6c51 Mon Sep 17 00:00:00 2001 From: William Hogan Date: Sun, 5 Jan 2020 15:01:36 -0500 Subject: [PATCH 19/69] added class called 'Internationalized Resource Identifier' to represent IRIs in RT applications. And otherwise. --- PCORnetCDM.owl | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 355dd00..3e94f2b 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -11940,6 +11940,19 @@ excludes emergency department encounters + + + + + Internationalized Resource Identifier + An identifier that is the specified output of a planned process that realizes the Internet standard RFC 3987 which is available from http://www.ietf.org/rfc/rfc3987.txt. + IRI + RFC 3987 has the title "Internationalized Resource Identifiers (IRIs)". It was published in 2005. + Internationalized Resource Identifier + + + + From 8d5936b46990d3acffd1a21e4d89af51f99efdb0 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 15 Jan 2020 11:33:53 -0500 Subject: [PATCH 20/69] Removed UBERON: processual entity, and changed its subclasses to subclasses of BFO: process boundary. --- PCORnetCDM.owl | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 3e94f2b..90678e6 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -7843,19 +7843,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. - uberon - UBERON:0000000 - - processual entity - - - - @@ -11298,7 +11285,7 @@ Environmental exposures include those imposed by natural environments, experimen - + A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. uberon UBERON:0035943 From 51264b71ce486121fc2dcbd9edbb381a2085fe35 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 22 Jan 2020 11:41:31 -0500 Subject: [PATCH 21/69] Changed UBERON: anatomical entity to a child of BFO: independenet continuant. Removed myself as a term editor for OMRSE: patient discharge. --- PCORnetCDM.owl | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 90678e6..f1d285b 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -7674,7 +7674,6 @@ Environmental exposures include those imposed by natural environments, experimen Amanda Hicks - S. Clint Dowland a document act that concludes an inpatient encounter discharge process @@ -9510,7 +9509,7 @@ Environmental exposures include those imposed by natural environments, experimen - + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl From 4bd42f7e18f8e08206d5669fa4b555c9fb27bb6b Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 22 Jan 2020 13:32:35 -0500 Subject: [PATCH 22/69] Removed purl.obolibrary.org/obo/ro/other_import.owl from list of Direct Imports. Then, re-imported ENVO: environmental system and OGMS: disease via MIREOT. --- PCORnetCDM.owl | 73 +++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 70 insertions(+), 3 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index f1d285b..a038664 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -25,7 +25,6 @@ - @@ -109,7 +108,10 @@ - + + definition editor + term editor + @@ -123,13 +125,18 @@ - + + definition source + definition source + + curator note + curator note curator notes @@ -7404,6 +7411,36 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -7458,6 +7495,22 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + A system which has the disposition to environ one or more material entities. + http://purl.obolibrary.org/obo/envo.owl + 2013-09-23T16:04:08Z + DOI:10.1186/2041-1480-4-43 + EcoLexicon:environment + environment + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + @@ -7565,6 +7618,20 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:21:20Z + https://github.com/OGMS/ogms/releases/tag/v2019-04-30 + disease + + + + From a7c6528c966fefea04788111dfb80dc53def9be5 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Tue, 28 Jan 2020 16:54:31 -0500 Subject: [PATCH 23/69] Removed unnecessary CARO and CL classes that were appearing without annotations, as well as the object properties that were causing them to appear. --- PCORnetCDM.owl | 2172 ++---------------------------------------------- 1 file changed, 63 insertions(+), 2109 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index a038664..0be0445 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1550,19 +1550,6 @@ range: spatial region or site (immaterial continuant) - - - - - - - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - David Osumi-Sutherland - tracheates - - - - @@ -1615,10 +1602,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. David Osumi-Sutherland @@ -1732,18 +1715,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - - Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos - 2017-07-20T17:11:08Z - transports - - - - @@ -1926,88 +1897,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - - - - - - - - - - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - David Osumi-Sutherland - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - fasciculates with - - - - - - - - - - - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - - has plasma membrane part - - - - - - - - - - - - has neurotransmitter - releases neurotransmitter - - - - @@ -2022,56 +1911,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - - - - - - - - - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - - has fasciculating neuron projection - - - - @@ -2179,19 +2018,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - attached to part of - - - - @@ -2204,18 +2030,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - drains - - - - @@ -2232,29 +2046,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - - - - - - - A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall - - has phenotype - - - - @@ -2270,44 +2061,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan - This is the transitive form of the develops from relation - develops from - - - - - - - - - - - - - inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan - - develops into - - - - @@ -2323,75 +2076,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - - - - - - - - - - - - - - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor - FBbt - - TODO - add child relations from DOS - directly develops from - - - - - - - - - - A parasite that kills or sterilizes its host - parasitoid of - - - - - - - - - inverse of parasitoid of - - has parasitoid - - - - - - - - - - inverse of directly develops from - developmental precursor of - - directly develops into - - - - @@ -2624,61 +2308,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall - develops from part of - - - - - - - - - - - - - - - x develops_in y if x is located in y whilst x is developing - Chris Mungall - EHDAA2 - Jonathan Bard, EHDAA2 - develops in - - - - - - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - obligate parasite of - - - - - - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - facultative parasite of - - - - @@ -2763,36 +2392,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - stem parasite of - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - root parasite of - - - - - - - - - A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. - hemiparasite of - - - - @@ -2897,96 +2496,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - - - - - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - - x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall - has developmental contribution from - - - - - - - - - - - - - - - inverse of has developmental contribution from - Chris Mungall - - developmentally contributes to - - - - - - - - - - - - - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - developmentally induced by - - - - - - - - - - - Inverse of developmentally induced by - Chris Mungall - developmentally induces - - - - - - - - - - - - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p - false - Chris Mungall - In general you should not use this relation to make assertions - use one of the more specific relations below this one - This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by - - - - @@ -3012,158 +2521,7 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else - This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall - replaces - developmentally replaces - - - - - - - - - - Inverse of developmentally preceded by - Chris Mungall - developmentally succeeded by - - - - - - - - - - - - - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - Chris Mungall - part of developmental precursor of - - - - - - - - - - p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). - This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall - results_in_developmental_progression_of - results in developmental progression of - - - - - - - - - - - every flower development (GO:0009908) results in development of some flower (PO:0009046) - - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml - results_in_development_of - results in development of - - - - - - - - - - - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_formation_of - results in formation of - - - - - - - - - - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_morphogenesis_of - results in morphogenesis of - - - - - - - - - - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_maturation_of - results in maturation of - - - - - - - - - foramen ovale closure SubClassOf results in disappearance of foramen ovale - - Chris Mungall - May be merged into parent relation - results_in_disappearance_of - results in disappearance of - - - - - - - - - every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - - Chris Mungall - May be merged into parent relation - results in developmental regression of - - - - - + @@ -3217,19 +2575,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - Chris Mungall - regulates localization of - transports or maintains localization of - - - - @@ -3262,22 +2607,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. - The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_acquisition_of_features_of - results in acquisition of features of - - - - @@ -3494,17 +2823,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall - imports - - - - @@ -3528,18 +2846,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall - results in growth of - - - - @@ -3551,43 +2857,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - Chris Mungall - exports - - - - - - - - - - an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. - p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in commitment to - - - - - - - - - - p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in determination of - - - - @@ -3638,42 +2907,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall - results in structural organization of - - - - - - - - - - The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in specification of - - - - - - - - - p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall - results in developmental induction of - - - - @@ -3685,61 +2918,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - - a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall - attached to (anatomical structure to anatomical structure) - - attached to - - - - - - - - - - m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall - Wikipedia:Insertion_(anatomy) - has muscle origin - - - - - - - We need to import uberon muscle to create a stricter domain constraint - - - - - - - - - - m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall - Wikipedia:Insertion_(anatomy) - has muscle insertion - - - - - - - We need to import uberon muscle into RO to use as a stricter domain constraint - - - - @@ -3895,67 +3073,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - - - - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall - has developmental potential involving - - - - - - - - - - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall - has potential to developmentally contribute to - - - - - - - - - - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall - has potential to developmentally induce - - - - - - - - - - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall - has potential to develop into - - - - - - - - - - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall - has potential to directly develop into - - - - @@ -4380,363 +3497,85 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - - An interaction relationship in which the partners are related via a feeding relationship. + + + Porifiera attaches to substrate + A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. Chris Mungall + semibiotically interacts with - trophically interacts with + participates in a abiotic-biotic interaction with - + - - - - A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] - Baleen whale preys on krill - An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members + + + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall - Jorrit Poelen - Katja Shulz - is subject of predation interaction with - preys upon - - preys on - http://eol.org/schema/terms/preysUpon - http://www.inaturalist.org/observations/2942824 + molecularly controls + activity directly regulates activity of - + - - - - - - - - - - - A biotic interaction in which the two organisms live together in more or less intimate association. + + + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - - symbiotically interacts with + inhibits + molecularly decreases activity of + activity directly negatively regulates activity of - + - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + + + Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - commensually interacts with + activates + molecularly increases activity of + activity directly positively regulates activity of - + - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + + Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - mutualistically interacts with + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + partner in - + - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + + Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - This relation groups a pair of inverse relations, parasite of and parasitized by - - interacts with via parasite-host interaction + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + subject participant in - + - - - - - - - - - - - - Pediculus humanus capitis parasite of human - Chris Mungall - parasitizes - direct parasite of - - parasite of - http://eol.org/schema/terms/parasitizes - - - - - - - - - - Chris Mungall - has parasite - parasitised by - directly parasitized by - - parasitized by - http://eol.org/schema/terms/hasParasite - - - - - - - - - Porifiera attaches to substrate - A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall - semibiotically interacts with - - participates in a abiotic-biotic interaction with - - - - - - - - - - Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - Chris Mungall - molecularly controls - activity directly regulates activity of - - - - - - - - - Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - inhibits - molecularly decreases activity of - activity directly negatively regulates activity of - - - - - - - - - Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - activates - molecularly increases activity of - activity directly positively regulates activity of - - - - - - - - - - A relation that holds between a disease or an organism and a phenotype - Chris Mungall - has symptom - - - - - - - - - Chris Mungall - The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) - - host of - - - - - - - - - Chris Mungall - - has host - http://eol.org/schema/terms/hasHost - - - - - - - - - - Bees pollinate Flowers - This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall - is subject of pollination interaction with - - pollinates - http://eol.org/schema/terms/pollinates - - - - - - - - - Chris Mungall - has polinator - is target of pollination interaction with - - pollinated by - http://eol.org/schema/terms/hasPollinator - - - - - - - - - - Chris Mungall - Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. - - acquires nutrients from - - - - - - - - - inverse of preys on - Chris Mungall - has predator - is target of predation interaction with - - - preyed upon by - http://eol.org/schema/terms/HasPredator - http://polytraits.lifewatchgreece.eu/terms/PRED - - - - - - - - - - Anopheles is a vector for Plasmodium - Chris Mungall - a is a vector for b if a carries and transmits an infectious pathogen b into another living organism - - is vector for - - - - - - - - - Chris Mungall - - has vector - - - - - - - - - Chris Mungall - Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target - partner in - - - - - - - - - Chris Mungall - Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. - subject participant in - - - - - - - - + + Chris Mungall Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. target participant in @@ -4794,42 +3633,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - Chris Mungall - - provides nutrients for - - - - - - - - - Chris Mungall - is subject of eating interaction with - - eats - - - - - - - - - Chris Mungall - eaten by - is target of eating interaction with - - is eaten by - - - - @@ -4861,41 +3664,6 @@ the a supports either the existence of b, or the truth value of b. - - - - ABal nucleus child nucleus of ABa nucleus (in C elegans) - c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall - This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. - child nucleus of - - - - - - - - - A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall - child nucleus of in hermaphrodite - - - - - - - - - A child nucleus relationship in which the cells are part of a male organism - Chris Mungall - child nucleus of in male - - - - @@ -4952,148 +3720,6 @@ the a supports either the existence of b, or the truth value of b. - - - - - - - - - - - - - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. - relation between structure and stage - - - - - - - - - - x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - Chris Mungall - existence starts during - - - - - - - - - x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - Chris Mungall - existence starts with - - - - - - - - - x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence overlaps - - - - - - - - - - x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts and ends during - - - - - - - - - - x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during - - - - - - - - - x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends with - - - - - - - - - - x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall - transformation of - - - - - - - - - - x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall - - immediate transformation of - - - - - - - - - x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts during or after - - - - - - - - - x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during or before - - - - @@ -5524,122 +4150,6 @@ the a supports either the existence of b, or the truth value of b. - - - - - - - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' - A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - has skeleton - - - - - - This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. - - - - - - - - - - p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall - results in ending of - - - - - - - - - - - - - - x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y - Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall - http://eol.org/schema/terms/hyperparasitoidOf - https://en.wikipedia.org/wiki/Hyperparasite - epiparasite of - hyperparasitoid of - - hyperparasite of - - - - - - - - - - - - - inverse of hyperparasite of - Chris Mungall - has epiparasite - has hyperparasite - hyperparasitoidized by - - - hyperparasitized by - - - - - - - - - Chris Mungall - http://en.wikipedia.org/wiki/Allelopathy - - allelopath of - http://eol.org/schema/terms/allelopathyYes - x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y - - - - - - - - - - Chris Mungall - - pathogen of - - - - - - - - - Chris Mungall - - has pathogen - - - - @@ -5690,18 +4200,6 @@ the a supports either the existence of b, or the truth value of b. - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall - - results in movement of - - - - @@ -5786,34 +4284,6 @@ the a supports either the existence of b, or the truth value of b. - - - - - - Chris Mungall - - participates in a biotic-biotic interaction with - - - - - - - - - - - - inverse of has skeleton - Chris Mungall - - skeleton of - - - - @@ -5829,119 +4299,39 @@ the a supports either the existence of b, or the truth value of b. - - - - x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. - existence starts at point - - - - - - - - - - - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' - s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall - has part structure that is capable of - - - - - - - - - - p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. - results in closure of - - - - - - - - - p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p - results in breakdown of - - - - - - - - - results in synthesis of - - - - - - - - - - results in assembly of - - - - - - - - - p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. - results in catabolism of - - - - - - - - - - results in disassembly of - - - - - + - - - - results in remodeling of + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + Chris Mungall + has part structure that is capable of - + - - - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c - results in organization of + + + p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + results in breakdown of - + - - - x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. - existence ends at point + + + p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + results in catabolism of @@ -6116,86 +4506,6 @@ the a supports either the existence of b, or the truth value of b. - - - - - visits - https://github.com/oborel/obo-relations/issues/74 - - - - - - - - - visited by - - - - - - - - - - visits flowers of - - - - - - - - - has flowers visited by - - - - - - - - - - - lays eggs in - - - - - - - - - - has eggs laid in by - - - - - - - - - - https://github.com/jhpoelen/eol-globi-data/issues/143 - kills - - - - - - - - - is killed by - - - - @@ -6224,119 +4534,6 @@ the a supports either the existence of b, or the truth value of b. - - - - - A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host - - ectoparasite of - - - - - - - - - inverse of ectoparasite of - - has ectoparasite - - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system - lives inside of - endoparasite of - - - - - - - - - has endoparasite - - - - - - - - - - A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite - mesoparasite of - - - - - - - - - inverse of mesoparasite of - - has mesoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. - - intercellular endoparasite of - - - - - - - - - inverse of intercellular endoparasite of - - has intercellular endoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits host cells. - - intracellular endoparasite of - - - - - - - - - inverse of intracellular endoparasite of - - has intracellular endoparasite - - - - @@ -6799,20 +4996,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. - disease has basis in dysfunction of (disease to anatomical structure) - cjm - 2017-11-05T03:29:32Z - disease has basis in dysfunction of - - - - @@ -6827,74 +5010,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - cjm - 2017-11-05T03:46:07Z - disease has basis in feature - - - - - - - - - - - - - - disease causes dysfunction of (disease to anatomical entity) - cjm - 2017-11-05T03:58:20Z - disease causes dysfunction of - - - - - - - - - - - - - - - - - - A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. - TODO: complete range axiom once more of CARO has been mireoted in to this ontology - This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - cjm - 2017-11-05T04:06:02Z - disease has location - - - - - - - - - - - A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - cjm - 2017-12-26T19:37:31Z - disease has inflammation site - - - - @@ -6925,19 +5040,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. - cjm - 2017-12-26T19:58:44Z - disease arises from structure - - - - @@ -7033,73 +5135,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - An interaction relationship wherein a plant or algae is living on the outside surface of another plant. - https://en.wikipedia.org/wiki/Epiphyte - epiphyte of - - - - - - - - - inverse of epiphyte of - - has epiphyte - - - - - - - - - - A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material - https://en.wikipedia.org/wiki/Kleptoparasitism - kleptoparasite of - - - - - - - - - inverse of kleptoparasite of - - kleptoparasitized by - - - - - - - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - lays eggs on - - - - - - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - has eggs laid on by - - - - @@ -7225,26 +5260,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - - - - - - p has anatomical participant c iff p has participant c, and c is an anatomical entity - cjm - 2018-09-26T01:08:58Z - has anatomical participant - - - - @@ -7380,67 +5395,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From 8b8d9e89d407f1011b8f70352bf56372d8774e71 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Tue, 10 Mar 2020 13:44:12 -0400 Subject: [PATCH 24/69] =?UTF-8?q?Removed=20=E2=80=98subclass=20of=20PCORne?= =?UTF-8?q?t=20ethnic=20identity=20datum=E2=80=99=20from=20axioms=20of=20P?= =?UTF-8?q?CORnet=20Hispanic=20identity=20datum=20and=20PCORnet=20not=20Hi?= =?UTF-8?q?spanic=20identity=20datum,=20and=20then=20deprecated=20PCORnet?= =?UTF-8?q?=20ethnic=20identity=20datum.=20Reason:=20to=20avoid=20multiple?= =?UTF-8?q?=20inheritance=20and=20eliminate=20a=20superfluous=20class.=20V?= =?UTF-8?q?ia=20MIREOT,=20added=20the=20following=20OGMS=20classes:=20diag?= =?UTF-8?q?nosis,=20clinical=20data=20item,=20diagnostic=20process,=20heal?= =?UTF-8?q?th=20care=20process,=20inpatient=20encounter,=20and=20outpatien?= =?UTF-8?q?t=20encounter.=20Reason:=20four=20of=20those=20six=20were=20use?= =?UTF-8?q?d=20in=20PCOR,=20but=20appeared=20without=20annotations;=20and?= =?UTF-8?q?=20each=20of=20the=20other=20two=20is=20a=20parent=20of=20one?= =?UTF-8?q?=20of=20the=20first=20four.=20Removed=20the=20OGMS=20link=20fro?= =?UTF-8?q?m=20list=20of=20imports=20because=20(a)=20it=20does=20not=20con?= =?UTF-8?q?nect=20to=20an=20OWL=20file,=20and=20thus=20imports=20nothing,?= =?UTF-8?q?=20and=20(b)=20we=20do=20not=20wish=20to=20import=20OGMS=20at?= =?UTF-8?q?=20this=20time.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- PCORnetCDM.owl | 67 ++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 62 insertions(+), 5 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 0be0445..7045e93 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -27,7 +27,6 @@ - Amanda Hicks Josh Hanna William R. Hogan @@ -5589,6 +5588,7 @@ Environmental exposures include those imposed by natural environments, experimen + @@ -5606,25 +5606,65 @@ Environmental exposures include those imposed by natural environments, experimen + The representation of a conclusion of a diagnostic process. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T12:42:23Z + https://github.com/OGMS/ogms/releases/tag/v2019-04-30 + diagnosis + + + + + + + + + A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient + Albert Goldfain +Sagar Jain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z +editor date: 2017-04-18 + + https://github.com/OGMS/ogms/releases/tag/v2019-04-30 + health care process - + + + TODO + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z + https://github.com/OGMS/ogms/releases/tag/v2019-04-30 + outpatient encounter + - + + + TODO + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z + https://github.com/OGMS/ogms/releases/tag/v2019-04-30 + inpatient encounter + + @@ -5641,6 +5681,24 @@ Environmental exposures include those imposed by natural environments, experimen + A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output). + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e + creation date: 2011-09-20T09:57:44Z + https://github.com/OGMS/ogms/releases/tag/v2019-04-30 + diagnostic process + + + + + + + + + a data item that is about a patient and is the specified output of a health care process assay or diagnostic process + creation date: 2018-11-27 + https://github.com/OGMS/ogms/releases/tag/v2019-04-30 + clinical data item @@ -9510,7 +9568,6 @@ Environmental exposures include those imposed by natural environments, experimen - Amanda Hicks From PCORnet CDM "A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." PCORnet Hispanic identity datum @@ -9522,7 +9579,6 @@ Environmental exposures include those imposed by natural environments, experimen - Amanda Hicks PCORnet not Hispanic identity datum @@ -9535,6 +9591,7 @@ Environmental exposures include those imposed by natural environments, experimen Amanda Hicks PCORnet ethnic identity datum + true From e6338f456b93385242cc93d7bd2432f7d5c8783e Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Wed, 11 Mar 2020 16:37:35 -0400 Subject: [PATCH 25/69] MIREOT'd 'cerebrospinal fluid', 'blood plasma', and 'uterine cervix' from UBERON. --- PCORnetCDM.owl | 188 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 188 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 7045e93..d774fd1 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5921,6 +5921,63 @@ editor date: 2017-04-18 + + + + + Lower, narrow portion of the uterus where it joins with the top end of the vagina. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] + The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] + cervical + 2012-09-17 + VHOG:0001359 + cervix + + + + + BTO:0001421 + BTO:0002249 + CALOHA:TS-0134 + EFO:0000979 + EMAPA:29927 + EV:0100114 + FMA:17740 + FMA:TA + GAID:376 + MA:0000392 + MAT:0000292 + MESH:D002584 + NCIT:C12311 + OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA + UMLS:C0007874 + VHOG:0001359 + galen:CervixUteri + canalis cervicis uteri + caudal segment of uterus + cervical canal of uterus + cervix uteri + neck of uterus + uterine cervix + uberon + cervical canal + cervix of uterus + + UBERON:0000002 + + + + VHOG + + + DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004) + ncithesaurus:Cervix + uterine cervix + + + + @@ -7815,6 +7872,79 @@ editor date: 2017-04-18 + + + + + A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. + many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6] + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] + In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] + EHDAA2 models this as developing from CP, which is wrong + the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. + 2012-08-14 + 2012-09-17 + TAO:0002184 + VHOG:0001278 + EHDAA2 + FMA + + + BIRNLEX:1798 + BTO:0000237 + CALOHA:TS-0130 + EFO:0000329 + EHDAA2:0004441 + ENVO:02000029 + EV:0100311 + FMA:20935 + GAID:1181 + MA:0002503 + MAT:0000499 + MESH:A12.207.268 + NCIT:C12692 + TAO:0002184 + UMLS:C0007806 + VHOG:0001278 + ZFA:0001626 + CSF + cerebral spinal fluid + uberon + liquor cerebrospinalis + spinal fluid + UBERON:0001359 + + + + + TAO + VHOG + + BIRNLEX:1798 + DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005) + ZFIN:curator + ncithesaurus:Cerebrospinal_Fluid + cerebrospinal fluid + + + + + + + + + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + FMA:45733 + organ neck + uberon + UBERON:0001560 + + neck of organ + + + + @@ -8082,6 +8212,43 @@ editor date: 2017-04-18 + + + + + The liquid component of blood, in which erythrocytes are suspended. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + plasma + portion of plasma + + + + BTO:0000131 + CALOHA:TS-0800 + EFO:0001905 + EMAPA:35690 + FMA:62970 + GAID:1178 + MA:0002501 + MAT:0000052 + MESH:D010949 + MIAA:0000052 + NCIT:C13356 + OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw + UMLS:C0032105 + blood plasm + portion of blood plasma + uberon + UBERON:0001969 + + + + ncithesaurus:Plasma + blood plasma + + + + @@ -9174,6 +9341,27 @@ editor date: 2017-04-18 + + + + + Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + transudative + characteristically low in protein and cellular content (unless there has been secondary concentration) + + FMA:12276 + GAID:1195 + MESH:D005122 + ncithesaurus:Transudate + uberon + plasma ultrafiltrate + UBERON:0007779 + transudate + + + + From 95671c06dbcb9d4b2c908d51d9a58d3b43e8cf3a Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Wed, 25 Mar 2020 17:23:47 -0400 Subject: [PATCH 26/69] MIREOT'd 'vagina' and 'pericardial fluid' from UBERON. --- PCORnetCDM.owl | 97 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 96 insertions(+), 1 deletion(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index d774fd1..3bfe78b 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1087,7 +1087,9 @@ Where we have an annotation assertion - + + depicted by + @@ -7539,6 +7541,63 @@ editor date: 2017-04-18 + + + + + A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] + The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] + The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] + vaginal + 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688 + 2012-09-17 + 2012-11-29 + FMA:19949 + VHOG:0001138 + + + + + BTO:0000243 + CALOHA:TS-1103 + EFO:0000976 + EMAPA:18986 + EV:0100117 + FMA:19949 + GAID:381 + MA:0000394 + MAT:0000128 + MESH:D014621 + MIAA:0000128 + NCIT:C12407 + OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA + UMLS:C0042232 + VHOG:0001138 + galen:Vagina + uberon + distal oviductal region + distal portion of oviduct + vaginae + + UBERON:0000996 + + + + FMA + VHOG + + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 + ncithesaurus:Vagina + vagina + + + + + + @@ -8876,6 +8935,24 @@ editor date: 2017-04-18 + + + + + Transudate contained in the pericardial cavity.[FMA] + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + + BTO:0001016 + FMA:9887 + MA:0002530 + uberon + UBERON:0002409 + + pericardial fluid + + + + @@ -9362,6 +9439,24 @@ editor date: 2017-04-18 + + + + + Any fluid produced by a serous gland. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + serous fluid + + UBERON:cjm + serosal fluid + serous gland fluid + uberon + UBERON:0007794 + secretion of serous gland + + + + From 40e0cb516ee64f62135ddea01fb4624c48c3d3c7 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Sat, 18 Apr 2020 15:18:26 -0400 Subject: [PATCH 27/69] =?UTF-8?q?Obsoleted=20and=20deprecated=20PCOR:=20?= =?UTF-8?q?=E2=80=98code=20set,=E2=80=99=20as=20it=20was=20decided=20we=20?= =?UTF-8?q?would=20do=20upon=20the=20addition=20of=20PNO:=20=E2=80=98code?= =?UTF-8?q?=20set.=E2=80=99=20Made=20the=20children=20of=20PCOR:=20?= =?UTF-8?q?=E2=80=98code=20set=E2=80=99=20into=20children=20of=20PNO:=20?= =?UTF-8?q?=E2=80=98code=20set.=E2=80=99?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- PCORnetCDM.owl | 25 ++++++------------------- 1 file changed, 6 insertions(+), 19 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 3bfe78b..91a5833 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5324,7 +5324,7 @@ Environmental exposures include those imposed by natural environments, experimen - + International Classification of Diseases @@ -5561,7 +5561,7 @@ Environmental exposures include those imposed by natural environments, experimen - + Systematized Nomenclature of Medicine @@ -10266,23 +10266,10 @@ excludes emergency department encounters - - - - - - - - - - - - - - - - a set of non-lexical symbols with a conventionally agreed usage among a group for a particular purpose - code set + This class is superfluous, given the addition of PNO: code set. + DEPRECATED obsolete code set + + true From 36f28a0449af30f0efcb54842f973c3c36e68cb5 Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Mon, 27 Apr 2020 14:54:45 -0400 Subject: [PATCH 28/69] MIREOT'd from UBERON 'amniotic fluid', 'adrenal gland', 'bulb of aorta', 'bone marrow', 'bile', 'gas in respiratory system', 'arterial blood', 'umbilical cord blood', and 'venous blood'. --- PCORnetCDM.owl | 347 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 347 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 91a5833..baf11a2 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6606,6 +6606,38 @@ editor date: 2017-04-18 + + + + + Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + + BTO:0000068 + CALOHA:TS-0034 + EMAPA:36771 + ENVO:02000021 + EV:0100123 + FMA:305905 + GAID:1155 + MA:0002893 + MESH:D000653 + MP:MP + NCIT:C13188 + UMLS:C0002638 + VHOG:0001267 + uberon + acqua amnii + liquor amnii + + UBERON:0000173 + + ncithesaurus:Amniotic_Fluid + amniotic fluid + + + + @@ -8308,6 +8340,45 @@ editor date: 2017-04-18 + + + + + vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum. + aids the process of digestion of lipids in the small intestine + bile salts function to emulsify dietary fats and facilitate their intestinal absorption + elimination of cholesterol + major excretory route for potentially harmful exogenous lipophilic substances + many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates + protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine + + + + BTO:0000121 + CALOHA:TS-1172 + ENVO:02000023 + FMA:62971 + GAID:1157 + MA:0002513 + MESH:D001646 + NCIT:C13192 + UMLS:C0005388 + ZFA:0005857 + galen:Bile + uberon + fel + gall + UBERON:0001970 + + + ncithesaurus:Bile + bile + + + + @@ -8935,6 +9006,130 @@ editor date: 2017-04-18 + + + + + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole + suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. + 2012-06-20 + 2012-09-17 + AAO:0010551 + VHOG:0001141 + + + + AAO:0010551 + BTO:0000047 + CALOHA:TS-0016 + EFO:0000238 + EMAPA:18426 + EV:0100135 + FMA:9604 + GAID:446 + GO:0030325 + MA:0000116 + MAT:0000071 + MESH:D000311 + MIAA:0000071 + NCIT:C12666 + OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA + UMLS:C0001625 + VHOG:0001141 + XAO:0000164 + galen:AdrenalGland + glandula adrenalis + glandula suprarenalis + uberon + adrenal + adrenal capsule + adrenal medulla cell + atrabiliary capsule + epinephric gland + epinephros + glandula suprarenalis + interrenal gland + suprarenal capsule + suprarenal gland + + + UBERON:0002369 + + + + AAO + VHOG + + AAO:BJB + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 + ncithesaurus:Adrenal_Gland + adrenal gland + + + + + + + + + + + the soft tissue that fills the cavities of bones + TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs + consider placement of NCIT:C53466 medullary bone + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] + In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] + 2012-09-17 + VHOG:0001218 + + + + AAO:0011007 + BTO:0000141 + BTO:0000829 + CALOHA:TS-0087 + EFO:0000868 + EMAPA:32760 + EV:0100046 + FMA:9608 + GAID:1287 + MA:0000134 + MAT:0000084 + MESH:D001853 + MGI:cwg + MIAA:0000084 + MP:0002397 + NCIT:C12431 + OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA + UMLS:C0005953 + VHOG:0001218 + XAO:0000123 + galen:BoneMarrow + medulla ossea + medulla ossium + uberon + medulla of bone + medullary bone + + UBERON:0002371 + + + + VHOG + + DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) + ncithesaurus:Bone_Marrow + bone marrow + + + + + @@ -9325,6 +9520,34 @@ editor date: 2017-04-18 + + + + + This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] + keep this grouping class so long as it is required for GO + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + 2012-09-17 + VHOG:0001141 + GO:0030325 + VHOG:0001141 + adrenal gland - interrenal gland + adrenal gland/interrenal tissue + uberon + adrenal - interrenal gland + suprarenal gland - interrenal gland + UBERON:0006858 + + + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 + adrenal/interrenal gland + + + + @@ -9542,6 +9765,60 @@ editor date: 2017-04-18 + + + + + The portion of the left ventricular outflow tract delineated by the sinotubular ridge superiorly and the bases of the valve leaflets inferiorly; it comprises the aortic sinuses, the aortic valve leaflets, the commissures, and the interleaflet triangles + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + The dilated first part of the aorta containing the aortic semilunar valves and the aortic sinuses. + + BTO:0004695 + FMA:3740 + FMA:TA + MP:0011572 + MP:0011575 + aorta bulb + aortic bulb + aortic root + bulb of ascending aorta + bulbus aortae + root of aorta + supraaortic valve area + uberon + + UBERON:0010172 + + + bulb of aorta + + + + + + + + + blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + + BTO:0004053 + CALOHA:TS-1079 + EFO:0001942 + MESH:A12.207.152.200 + MESH:D005312 + uberon + cord blood + fetal blood + umbilical cord blood + UBERON:0012168 + + Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP] + umbilical cord blood + + + + @@ -9592,6 +9869,43 @@ editor date: 2017-04-18 + + + + + A blood that is part of a artery. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + FMA:83066 + OBOL:automatic + arterial blood + blood in artery + portion of arterial blood + uberon + UBERON:0013755 + + arterial blood + + + + + + + + + A blood that is part of a vein. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + FMA:83067 + OBOL:automatic + blood in vein + portion of venous blood + venous blood + uberon + UBERON:0013756 + venous blood + + + + @@ -9612,6 +9926,23 @@ editor date: 2017-04-18 + + + + + Any substance in the body or expelled from the body that is in a gaseous state. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + + FMA:84580 + gas in anatomical space + portion of gas in anatomical space + uberon + UBERON:0034873 + bodily gas + + + + @@ -9643,6 +9974,22 @@ editor date: 2017-04-18 + + + + + Any portion of gas located in a part of the respiratory system. + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + + respiratory gas + respiratory system gas + uberon + UBERON:0034947 + gas in respiratory system + + + + From 49e87e1d4a8aecf06d465f18de94e65a583276aa Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 12:11:04 -0400 Subject: [PATCH 29/69] Created 'PCORnet ethnic identity information content entity.' --- PCORnetCDM.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index baf11a2..553a44e 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5910,6 +5910,21 @@ editor date: 2017-04-18 + + + + + An ethnic identity information content entity that uses PCORnet CDM terminology for ethnicity, where this terminology corresponds to values for the "Hispanic" field of the Demographic Table. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet ethnic identity information content entity + + + + From 8d1c2b04bd5dd6e3a08680a555f2aa685f01c010 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 12:25:13 -0400 Subject: [PATCH 30/69] Created 'PCORnet ethnic identity information content entity.' --- PCORnetCDM.owl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 553a44e..700a25d 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5910,16 +5910,16 @@ editor date: 2017-04-18 - + - + An ethnic identity information content entity that uses PCORnet CDM terminology for ethnicity, where this terminology corresponds to values for the "Hispanic" field of the Demographic Table. - S. Clint Dowland - Mathias Brochhausen - Matthew Diller - Sarah Bost - William R. Hogan + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan PCORnet ethnic identity information content entity From 5b9de38d1abfc94cbcf1c604c4ced2f47f72e9ef Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 12:33:52 -0400 Subject: [PATCH 31/69] Created PCORnet non-Hispanic identity information content entity.' --- PCORnetCDM.owl | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 700a25d..e5e1395 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5925,6 +5925,37 @@ editor date: 2017-04-18 + + + + + A PCORnet ethnic identity information content entity that is about some person's identifying as Hispanic, which is intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. + S. Clint Dowland + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet Hispanic identity information content entity + + + + + + + + + A PCORnet ethnic identity information content entity that is about some person's identifying as not Hispanic, where "Hispanic" is intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet non-Hispanic identity information content entity + + + + From 46ffd54516445e16057d820af6e8472152c32a66 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 12:41:20 -0400 Subject: [PATCH 32/69] Created 'PCORnet gender identity information content entity.' --- PCORnetCDM.owl | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index e5e1395..2fab8b1 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5956,6 +5956,23 @@ editor date: 2017-04-18 + + + + + A gender identity information content entity that uses the PCORnet CDM terminology for gender, where this terminology corresponds to values for the "gender identity" field of the Demographic Table. + S. Clint Dowland + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The PCORnet CDM cites the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services as the source for its terminology, but the two differ in that the PCORnet CDM allows one to select only one value for gender and includes 'multiple gender' as an option, while the other lacks a 'multiple gender' option and allows multiple options to be selected. For that source used by PCORnet, see here: https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base + PCORnet gender identity information content entity + + + + From 67d5193e5729aae11804b9500fd4073ac302d80f Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 12:44:29 -0400 Subject: [PATCH 33/69] Created 'PCORnet genderqueer/non-binary identity information content entity.' --- PCORnetCDM.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 2fab8b1..a8775e0 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5973,6 +5973,21 @@ editor date: 2017-04-18 + + + + + A PCORnet gender identity information content entity that is about some person's identifying as neither exclusively male nor exclusively female in gender. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet genderqueer/non-binary identity information content entity + + + + From 820b9ffe9e3e2fe0f73698154bc62af9a80009de Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 12:57:15 -0400 Subject: [PATCH 34/69] Created 'PCORnet something else gender identity information content entity.' --- PCORnetCDM.owl | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index a8775e0..f676c01 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5988,6 +5988,51 @@ editor date: 2017-04-18 + + + + + A PCORnet gender identity information content entity that is about some person's identifying as a man. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet man identity information content entity + + + + + + + + + A PCORnet gender identity information content entity that is about some person's identifying as more than one gender. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet multiple gender categories identity information content entity + + + + + + + + + A PCORnet gender identity information content entity that is about some person's identifying as some gender that is not referred to or described by the other value options for the "gender identity" field of the PCORnet Demographic Table. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet something else gender identity information content entity + + + + From 7def78253cca9bf39e61c24792f57481bd9cd3b0 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:09:51 -0400 Subject: [PATCH 35/69] Created 'PCORnet transgender female/trans woman/male-to-female identity information content entity.' --- PCORnetCDM.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index f676c01..67dbf72 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6033,6 +6033,21 @@ editor date: 2017-04-18 + + + + + A PCORnet gender identity information content entity that is about some person's identifying as transgender female, a trans woman, or male-to-female. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet transgender female/trans woman/male-to-female identity information content entity + + + + From 4910757234cb7ae1075a36fb62411872bd80a493 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:16:35 -0400 Subject: [PATCH 36/69] Created 'PCORnet woman identity information content entity.' --- PCORnetCDM.owl | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 67dbf72..107dd08 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6048,6 +6048,36 @@ editor date: 2017-04-18 + + + + + A PCORnet gender identity information content entity that is about some person's identifying as transgender male, a trans man, or female-to-male. + Mathias Brochhausen + Matthew Diller + S. Clint Dowland + William R. Hogan + Sarah Bost + PCORnet transgender male/trans man/female-to-male identity information content entity + + + + + + + + + A PCORnet gender identity information content entity that is about some person's identifying as a woman. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet woman identity information content entity + + + + From 7453e81f051b7c86c27f671490c1984f1d99ffaf Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:20:39 -0400 Subject: [PATCH 37/69] Created 'PCORnet racial identity information content entity.' --- PCORnetCDM.owl | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 107dd08..65759eb 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6078,6 +6078,23 @@ editor date: 2017-04-18 + + + + + A racial identity information content entity that uses the PCORnet CDM terminology for race, where this terminology corresponds to the values for the "race" field of the Demographic Table. + S. Clint Dowland + Amanda Hicks + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The PCORnet CDM's values for the race field are based on the OMB racial classification, but differ in that the PCORnet CDM allows one to select only one value for race and includes "multiple race" as an option, while OMB lacks a 'multiple race' option and allows multiple options to be selected. + PCORnet racial identity information content entity + + + + From 3cdfde8073f72744dc19afbadab2e05184ace2ef Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:26:11 -0400 Subject: [PATCH 38/69] Created 'PCORnet American Indian or Alaska Native identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 65759eb..ef8ceda 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6095,6 +6095,22 @@ editor date: 2017-04-18 + + + + + A PCORnet racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + This definition corresponds to that used by OMB, which is PCORnet's source for the terminology used for the value options of the 'race' field. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment. + PCORnet American Indian or Alaska Native identity information content entity + + + + From 5c87d7bccec57155fee186e9e19c914d57798246 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:29:57 -0400 Subject: [PATCH 39/69] Created 'PCORnet Asian identity information content entity.' --- PCORnetCDM.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index ef8ceda..63a4162 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6111,6 +6111,21 @@ editor date: 2017-04-18 + + + + + A PCORnet racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet Asian identity information content entity + + + + From 11fa49afe4258b654dac16da166de3dd6dc9b436 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:32:39 -0400 Subject: [PATCH 40/69] Created 'PCORnet black or African American identity information content entity.' --- PCORnetCDM.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 63a4162..0608f48 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6126,6 +6126,21 @@ editor date: 2017-04-18 + + + + + A PCORnet racial identity information content entity that is about some person's identifying as black or African American, which is intended to mean having origins in any of the black racial groups of Africa. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet black or African American identity information content entity + + + + From 2677d6e7854c7c4b10c3130471916d7297a3e752 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:34:53 -0400 Subject: [PATCH 41/69] Created 'PCORnet multiple race identity information content entity.' --- PCORnetCDM.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 0608f48..9958654 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6141,6 +6141,21 @@ editor date: 2017-04-18 + + + + + A PCORnet racial identity information content entity that is about some person's identifying as more than one race. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet multiple race identity information content entity + + + + From 5055321bc337c28093f71435981e58752a876561 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:36:38 -0400 Subject: [PATCH 42/69] Created 'PCORnet Native Hawaiian or other Pacific Islander identity information content entity.' --- PCORnetCDM.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 9958654..e1d28c8 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6156,6 +6156,21 @@ editor date: 2017-04-18 + + + + + A PCORnet racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet Native Hawaiian or other Pacific Islander identity information content entity + + + + From e1b9893fd972fc8e5eb23d560f2de591c79958de Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:38:02 -0400 Subject: [PATCH 43/69] Created 'PCORnet white identity information content entity.' --- PCORnetCDM.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index e1d28c8..1da9679 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6171,6 +6171,21 @@ editor date: 2017-04-18 + + + + + A PCORnet racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + PCORnet white identity information content entity + + + + From 3537788ae1b99568d8d3d39365de7b7f8dea9331 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:42:30 -0400 Subject: [PATCH 44/69] Created 'PCORnet sexual orientation identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 1da9679..6eb6d76 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6186,6 +6186,22 @@ editor date: 2017-04-18 + + + + + A sexual orientation identity information content entity that uses the PCORnet terminology for sexual orientation, where this terminology corresponds to the permitted values for the "sexual orientation" field of the Demographic Table. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet sexual orientation identity information content entity + + + + From 83593f2c34d162d3d9c6049246f233d602d10571 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:46:35 -0400 Subject: [PATCH 45/69] Created 'PCORnet asexual identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 6eb6d76..f54668f 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6202,6 +6202,22 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "asexual." + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet asexual identity information content entity + + + + From 34c2d14f1db7a8d4c3ef9b4f5c0a99148c6b6207 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:48:07 -0400 Subject: [PATCH 46/69] Created 'PCORnet bisexual identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index f54668f..f323a89 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6218,6 +6218,22 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "bisexual." + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet bisexual identity information content entity + + + + From 1b5da2fb6e23fea40aaa08e80b47639440925aec Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:49:55 -0400 Subject: [PATCH 47/69] Created 'PCORnet gay identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index f323a89..7c116ad 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6234,6 +6234,22 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "gay." + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet gay identity information content entity + + + + From 0a7bf088827efa18f5e5ee54af64af7b9631ff30 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:51:01 -0400 Subject: [PATCH 48/69] Created 'PCORnet lesbian identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 7c116ad..282279d 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6250,6 +6250,22 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "lesbian." + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet lesbian identity information content entity + + + + From 5e798a5450113bc00d8458e15f12b09880eccfb9 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:52:39 -0400 Subject: [PATCH 49/69] Created 'PCORnet multiple sexual orientations identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 282279d..f5ab0e8 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6266,6 +6266,22 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as having multiple sexual orientations. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet multiple sexual orientations identity information content entity + + + + From e246baded90864c7662bc95a34d7cb2fd1e6043b Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:53:44 -0400 Subject: [PATCH 50/69] Created 'PCORnet queer identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index f5ab0e8..2306103 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6282,6 +6282,22 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "queer." + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet queer identity information content entity + + + + From 8545a9ddc616021952769e90a28f12b7a5434a48 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:55:45 -0400 Subject: [PATCH 51/69] Created 'PCORnet questioning sexual orientation identity information content entity.' --- PCORnetCDM.owl | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 2306103..fb00569 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6298,6 +6298,23 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "queer." + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + While this is not about one's identifying as having or not having some sexual orientation, we regard it as a 'sexual orientation identity information content entity,' which is defined as being about "whether one identifies as having some sexual orientation." For example, if one is uncertain whether one is bisexual or heterosexual, one might be in a state of questioning one's sexuality, and an information content entity about that would seem to qualify as being about whether one identifies as having some sexual orientations. Indeed, there would be two sexual orientations in that example, and the information content entity could be both about whether one identifies as bisexual and about whether one identifies as heterosexual. + PCORnet questioning sexual orientation identity information content entity + + + + From 152e6d8ac0b960ae526099ca602eecf72ebb4554 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:57:19 -0400 Subject: [PATCH 52/69] Created 'PCORnet something else sexual orientation identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index fb00569..d88400f 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6315,6 +6315,22 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as some sexual orientation that is not represented by the other value set options for the "sexual orientation" field of the PCORnet Demographic Table. + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet something else sexual orientation identity information content entity + + + + From e0fa3aca0c9ab579573c29ee7ff6f6e5bc0bde62 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 14:58:45 -0400 Subject: [PATCH 53/69] Created 'PCORnet straight identity information content entity.' --- PCORnetCDM.owl | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index d88400f..38a0428 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6331,6 +6331,22 @@ editor date: 2017-04-18 + + + + + A PCORnet sexual orientation identity information content entity that is about some person's identifying as having a sexual orientation referred to by the PCORnet CDM with the term "straight." + S. Clint Dowland + Mathias Brochhausen + Matthew Diller + Sarah Bost + William R. Hogan + The labels and definitions used for the subclasses of 'PCORnet sexual orientation identity information content entity' are based on the terminology used for the value set options for the PCORnet Common Data Model's 'sexual orientation' field, which is a modifed version of the terms for, and categories of, sexual orientation that are found in the "2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications" of the US Department of Health and Human Services (https://www.federalregister.gov/documents/2015/10/16/2015-25597/2015-edition-health-information-technology-health-it-certification-criteria-2015-edition-base). Neither the PCORnet CDM nor the other source provide definitions of their terms for sexual orientations. Our definitions for the corresponding classes thus point to the terms, rather than explain what they mean, as it is unclear how PCORnet intends them to be understood. Furthermore, these terms may be understood differently by different patients who select them as self-descriptions, as some may understand them to be defined in terms of phenotypic sex, others in terms of gender, and others in terms of some combination of the two. + PCORnet straight identity information content entity + + + + From dce12d8f458e96cdace81eaa65003873a7ae287c Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 24 Jun 2020 16:02:31 -0400 Subject: [PATCH 54/69] Deprecated and obsoleted all PCOR subclasses of OMRSE 'identity datum,' and used the 'term replaced by' annotation to point from each to the corresponding social identity information content entity. --- PCORnetCDM.owl | 118 +++++++++++++++++++++++++++++++++++-------------- 1 file changed, 86 insertions(+), 32 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 38a0428..1e96cbb 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -10544,8 +10544,10 @@ editor date: 2017-04-18 Amanda Hicks + 'PCORnet racial identity information content entity' A racial identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the OMB racial classification, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the OMB allows for multiple racial identities as outputs of an identification process. - PCORnet racial identity datum + obsolete PCORnet racial identity datum + true @@ -10555,7 +10557,9 @@ editor date: 2017-04-18 Amanda Hicks - PCORnet American Indian or Alaska Native identity datum + 'PCORnet American Indian or Alaska Native identity information content entity' + obsolete PCORnet American Indian or Alaska Native identity datum + true @@ -10565,7 +10569,9 @@ editor date: 2017-04-18 Amanda Hicks - PCORnet Asian identity datum + 'PCORnet Asian identity information content entity' + obsolete PCORnet Asian identity datum + true @@ -10575,8 +10581,10 @@ editor date: 2017-04-18 Amanda Hicks - PCORnet black or African American identity datum - PCORnet item + 'PCORnet black or African American identity information content entity' + obsolete PCORnet black or African American identity datum + obsolete PCORnet item + true @@ -10606,7 +10614,9 @@ editor date: 2017-04-18 Amanda Hicks - PCORnet Native Hawaiian or other Pacific Islander identity datum + 'PCORnet Native Hawaiian or other Pacific Islander identity information content entity' + obsolete PCORnet Native Hawaiian or other Pacific Islander identity datum + true @@ -10616,7 +10626,9 @@ editor date: 2017-04-18 Amanda Hicks - PCORnet white identity datum + 'PCORnet white identity information content entity' + obsolete PCORnet white identity datum + true @@ -10626,7 +10638,9 @@ editor date: 2017-04-18 Amanda Hicks - PCORnet multiple race identity datum + 'PCORnet multiple race identity information content entity' + obsolete PCORnet multiple race identity datum + true @@ -10636,8 +10650,10 @@ editor date: 2017-04-18 Amanda Hicks + 'PCORnet Hispanic identity information content entity' From PCORnet CDM "A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." - PCORnet Hispanic identity datum + obsolete PCORnet Hispanic identity datum + true @@ -10647,7 +10663,9 @@ editor date: 2017-04-18 Amanda Hicks - PCORnet not Hispanic identity datum + 'PCORnet non-Hispanic identity information content entity' + obsolete PCORnet not Hispanic identity datum + true @@ -10657,7 +10675,8 @@ editor date: 2017-04-18 Amanda Hicks - PCORnet ethnic identity datum + 'PCORnet ethnic identity information content entity' + obsolete PCORnet ethnic identity datum true @@ -10814,7 +10833,9 @@ editor date: 2017-04-18 - PCORnet sexual orientation identity datum + 'PCORnet sexual orientation identity information content entity' + obsolete PCORnet sexual orientation identity datum + true @@ -10882,10 +10903,12 @@ excludes emergency department encounters A healthcare encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay Amanda Hicks PCORnet CDM 4.1 + 'sexual orientation identity information content entity' Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished. A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person. Unlike data items they are not necessilary contributed or acquired by a reliable method. - emergency department admit to inpatient hospital stay - sexual orientation identity datum + obsolete emergency department admit to inpatient hospital stay + obsolete sexual orientation identity datum + true @@ -10894,9 +10917,10 @@ excludes emergency department encounters - - PCORnet asexual identity datum - inpatient hospital encounter + 'PCORnet asexual identity information content entity' + obsolete PCORnet asexual identity datum + obsolete inpatient hospital encounter + true @@ -10905,7 +10929,9 @@ excludes emergency department encounters - PCORnet gay identity datum + 'PCORnet gay identity information content entity' + obsolete PCORnet gay identity datum + true @@ -10914,7 +10940,9 @@ excludes emergency department encounters - PCORnet lesbian identity datum + 'PCORnet lesbian identity information content entity' + obsolete PCORnet lesbian identity datum + true @@ -10923,7 +10951,9 @@ excludes emergency department encounters - PCORnet multiple sexual orientations identity datum + 'PCORnet multiple sexual orientations identity information content entity' + obsolete PCORnet multiple sexual orientations identity datum + true @@ -10932,7 +10962,9 @@ excludes emergency department encounters - PCORnet queer identity datum + 'PCORnet queer identity information content entity' + obsolete PCORnet queer identity datum + true @@ -10941,7 +10973,9 @@ excludes emergency department encounters - PCORnet questioning identity datum + 'PCORnet questioning sexual orientation identity information content entity' + obsolete PCORnet questioning identity datum + true @@ -10950,7 +10984,9 @@ excludes emergency department encounters - PCORnet something else identity datum + 'PCORnet something else sexual orientation identity information content entity' + obsolete PCORnet something else identity datum + true @@ -10959,7 +10995,9 @@ excludes emergency department encounters - PCORnet straight identity datum + 'PCORnet straight identity information content entity' + obsolete PCORnet straight identity datum + true @@ -10968,8 +11006,10 @@ excludes emergency department encounters + 'PCORnet gender identity information content entity' A gender identity that is the output of a racial identification process that uses the PCORnet CDM race or terminology. PCORnet CDM claims to use the 2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, but the crucial difference is that PCORnet CDM requires persons to identify with only one category whereas the other does not have a multiple gender option, which changes the meaning of the values in the value set. - PCORnet gender identity datum + obsolete PCORnet gender identity datum + true @@ -10978,7 +11018,9 @@ excludes emergency department encounters - PCORnet genderqueer identity datum + 'PCORnet genderqueer/non-binary identity information content entity' + obsolete PCORnet genderqueer identity datum + true @@ -10987,7 +11029,9 @@ excludes emergency department encounters - PCORnet man identity datum + 'PCORnet man identity information content entity' + obsolete PCORnet man identity datum + true @@ -10996,7 +11040,9 @@ excludes emergency department encounters - PCORnet multiple genders datum + 'PCORnet multiple gender categories identity information content entity' + obsolete PCORnet multiple genders datum + true @@ -11005,7 +11051,9 @@ excludes emergency department encounters - PCORnet something else identity datum + 'PCORnet something else gender identity information content entity' + obsolete PCORnet something else identity datum + true @@ -11014,7 +11062,9 @@ excludes emergency department encounters - PCORnet transgenderfemale/transwoman/male-to-female identity datum + 'PCORnet transgender female/trans woman/male-to-female identity information content entity' + obsolete PCORnet transgenderfemale/transwoman/male-to-female identity datum + true @@ -11023,7 +11073,9 @@ excludes emergency department encounters - PCORnet transgendermale/transman/female-to-male identity datum + 'PCORnet transgender male/trans man/female-to-male identity information content entity' + obsolete PCORnet transgendermale/transman/female-to-male identity datum + true @@ -11032,7 +11084,9 @@ excludes emergency department encounters - PCORnet woman identity datum + 'PCORnet woman identity information content entity' + obsolete PCORnet woman identity datum + true From 93804996571580811eee1d5f3f556452fbc5ffac Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Fri, 17 Jul 2020 13:34:50 -0400 Subject: [PATCH 55/69] Close #13: Created 'PCORnet specimen source value name', as well as classes for specimen_source value names that contain disjunctions. --- PCORnetCDM.owl | 70 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 1e96cbb..7550550 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6347,6 +6347,76 @@ editor date: 2017-04-18 + + + + + An identifier that denotes a LOINC information content entity that itself is about some material entity that is the bearer of a specimen role. + Matthew Diller + PCORnet Common Data Model Specification v5.1 + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + PCORnet specimen source value name + + + + + + + + + A PCORnet specimen source value name that is about some blood serum, blood plasma, or urine samples. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’). + serum, plasma, or urine PCORnet specimen source value name + + + + + + + + + A PCORnet specimen source value name that is about some blood serum or blood plasma samples. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’). + serum or plasma PCORnet specimen source value name + + + + + + + + + A PCORnet specimen source value name that is about some blood serum, blood plasma, or whole blood samples. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’). + serum, plasma, or blood PCORnet specimen source value name + + + + + + + + + A PCORnet specimen source value name that is about some blood plasma or tissue samples. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + This class, while not ideal in that it doesn’t refer to an actual universal, is a consequence of LOINC system identifiers that consist of disjunctions (e.g., ‘Serum or plasma’). + blood or tissue PCORnet specimen source value name + + + + From e79062e86a8cd8134929658157303c067b0ba535 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Thu, 23 Jul 2020 11:53:28 -0400 Subject: [PATCH 56/69] The term 'patient discharge' is an OMRSE term. However, the definition and some other annotations were added to this term in PCORnetCDM.owl instead of its home ontology. Since the term is soon to be updated in its home ontology to include such annotations, I removed them from PCORnetCDM.owl. The term will still be imported here via OMRSE, and will have any annotations that OMRSE has for it. --- PCORnetCDM.owl | 22 +--------------------- 1 file changed, 1 insertion(+), 21 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 7550550..6eeb644 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5737,27 +5737,7 @@ editor date: 2017-04-18 - - - - - - - - - - - - - - - - - - Amanda Hicks - a document act that concludes an inpatient encounter - discharge process - + From a4b9a445ea21c5fe744e07a0302fad9ded083952 Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Fri, 24 Jul 2020 14:05:38 -0400 Subject: [PATCH 57/69] Close #16: Added 'blood plasma PCORnet specimen source value name', 'cerebrospinal fluid PCORnet specimen source value name', 'vagina PCORnet specimen source value name', 'cervix PCORnet specimen source value name', and 'pericardial fluid PCORnet specimen source value name'. --- PCORnetCDM.owl | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 6eeb644..e8c6969 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6397,6 +6397,71 @@ editor date: 2017-04-18 + + + + + A PCORnet specimen source value name that is about some specimen of blood plasma. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + blood plasma PCORnet specimen source value name + + + + + + + + + A PCORnet specimen source value name that is about some specimen of cerebrospinal fluid. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + cerebrospinal fluid PCORnet specimen source value name + + + + + + + + + A PCORnet specimen source value name that is about some vaginal specimen. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + vagina PCORnet specimen source value name + + + + + + + + + A PCORnet specimen source value name that is about some cervical specimen. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + cervix PCORnet specimen source value name + + + + + + + + + A PCORnet specimen source value name that is about some specimen of pericardial fluid. + Matthew Diller + William R. Hogan + The use of 'value name' in the label is a product of PCORnet calling these identifiers "value names." + pericardial fluid PCORnet specimen source value name + + + + From a009670498e566e5b853fcb75f577262f57de9e6 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Fri, 24 Jul 2020 15:28:05 -0400 Subject: [PATCH 58/69] =?UTF-8?q?Deprecated/obsoleted=20the=20PCORowl=20ve?= =?UTF-8?q?rsion=20of=20=E2=80=98admission=20process,=E2=80=99=20a=20new?= =?UTF-8?q?=20version=20of=20which=20is=20now=20imported=20from=20OMRSE.?= =?UTF-8?q?=20Updated=20axioms=20for=20=E2=80=98ambulatory=20visit?= =?UTF-8?q?=E2=80=99=20and=20=E2=80=98admitting=20diagnosis=E2=80=99=20so?= =?UTF-8?q?=20they=20now=20use=20the=20OMRSE=20version=20of=20=E2=80=98adm?= =?UTF-8?q?ission=20process=E2=80=99=20instead=20of=20the=20PCORowl=20vers?= =?UTF-8?q?ion.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- PCORnetCDM.owl | 32 +++++++++----------------------- 1 file changed, 9 insertions(+), 23 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index e8c6969..bc68b29 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1846,14 +1846,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - @@ -10621,7 +10613,7 @@ editor date: 2017-04-18 - + @@ -10812,21 +10804,12 @@ editor date: 2017-04-18 - - - - - - - - - - - - a social act in which a patient is registered with a health care provider for the purposes of recieving care in an inpatient encounter Amanda Hicks - admission process + 'admission process' +http://purl.obolibrary.org/obo/OMRSE_00000201 + obsolete admission process + true @@ -10974,7 +10957,7 @@ editor date: 2017-04-18 - + @@ -11969,6 +11952,9 @@ excludes emergency department encounters David Osumi-Sutherland + + + From efa13caa481e322c87760288d901abe7958dd94a Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Thu, 6 Aug 2020 15:28:51 -0400 Subject: [PATCH 59/69] Created term 'patient PCORnet specimen source value name'. --- PCORnetCDM.owl | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index bc68b29..40db426 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6319,6 +6319,20 @@ editor date: 2017-04-18 + + + + + A PCORnet specimen source value name that is about a patient. + Matthew Diller + William R. Hogan + The LOINC codes that this value name applies to are 59768-2 (Procedure indications [Interpretation] Narrative), 32624-9 (Race), 56850-1 (Interpretation and review of laboratory results), and 56794-1 (Internal identifier). + This value name is not about an actual specimen. + patient PCORnet specimen source value name + + + + From 7bf1ddbdbebbdc692c5eea4e2a7ac44ff338af47 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Thu, 6 Aug 2020 15:33:17 -0400 Subject: [PATCH 60/69] Created term 'provider PCORnet specimen source value name'. --- PCORnetCDM.owl | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 40db426..8077e29 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6333,6 +6333,20 @@ editor date: 2017-04-18 + + + + + A PCORnet specimen source value name that is about some identifier that denotes a physician. + Matthew Diller + William R. Hogan + The PROVIDER value name might denote something other than a physician identifier, like a telephone number, depending on the data source. We limit it to being about an identifier that denotes a physician because this is what our data sources apply the value name to. + This value name is not about an actual specimen. + provider PCORnet specimen source value name + + + + From c3c113a87ee172c4ece2c01a1e6717a830ae4192 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Fri, 4 Sep 2020 12:43:59 -0400 Subject: [PATCH 61/69] =?UTF-8?q?The=20term=20'emergency=20department=20ad?= =?UTF-8?q?mit=20to=20inpatient=20hospital=20stay=E2=80=99=20had=20the=20s?= =?UTF-8?q?ame=20IRI=20as=20=E2=80=98sexual=20orientation=20identity=20dat?= =?UTF-8?q?um.=E2=80=99=20I=20created=20a=20new=20version=20of=20the=20for?= =?UTF-8?q?mer,=20and=20removed=20from=20each=20the=20annotations=20intend?= =?UTF-8?q?ed=20to=20go=20with=20the=20other.=20I=20also=20corrected=20an?= =?UTF-8?q?=20annotation=20error=20for=20the=20definition=20of=20'emergenc?= =?UTF-8?q?y=20department=20admit=20to=20inpatient=20hospital=20stay'=20an?= =?UTF-8?q?d=20replaced=20=E2=80=9Chealthcare=E2=80=9D=20with=20=E2=80=9Ch?= =?UTF-8?q?ealth=20care=E2=80=9D=20in=20that=20definition,=E2=80=9D=20and?= =?UTF-8?q?=20placed=20the=20term=20under=20the=20correct=20parent=20class?= =?UTF-8?q?=20(=E2=80=98health=20care=20encounter=E2=80=99).?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- PCORnetCDM.owl | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 8077e29..a29f977 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6347,6 +6347,19 @@ editor date: 2017-04-18 + + + + + A health care encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay + Amanda Hicks + PCORnet CDM 4.1 + Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished. + emergency department admit to inpatient hospital stay + + + + @@ -11026,13 +11039,9 @@ excludes emergency department encounters - A healthcare encounter that first occurs as an emergency department visit and then becomes an inpatient hospital stay Amanda Hicks - PCORnet CDM 4.1 'sexual orientation identity information content entity' - Permissible substitution for preferred state of separate ED and IP records. Only for use with data sources where the individual records for ED and IP cannot be distinguished. A sexual orientation identity datum sis an information content entity that is the output of some sexual orientation identitification process and is intended to be a truthful statement about the subjective feelings of sexual attration, emotional attraction, and romantic attatchments of the person. Unlike data items they are not necessilary contributed or acquired by a reliable method. - obsolete emergency department admit to inpatient hospital stay obsolete sexual orientation identity datum true From d9e8bc46d9ff90ff2eb16beee9ca3ae7ccd24c5f Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 16 Sep 2020 16:03:22 -0400 Subject: [PATCH 62/69] Imported 'temporal interval' and 'temporal instant' via MIREOT. --- PCORnetCDM.owl | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index a29f977..f94ea9e 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -11,6 +11,7 @@ xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:obda="https://w3id.org/obda/vocabulary#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" @@ -1085,6 +1086,30 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + + + + @@ -5388,6 +5413,35 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + http://purl.obolibrary.org/obo/bfo/2020/bfo.owl + 155-BFO + temporal interval + (Elucidation) a temporal interval is a one-dimensional temporal region that is continuous, thus without gaps or breaks + The year 2018. + temporal interval + A one-dimensional temporal region can include as parts not only temporal intervals but also temporal instants separated from other parts by gaps. + + + + + + + + + http://purl.obolibrary.org/obo/bfo/2020/bfo.owl + 209-BFO + temporal instant + (Elucidation) a temporal instant is a zero-dimensional temporal region that has no proper temporal part + The millennium. + temporal instant + + + + From e7de9097d6e970b2fbe74b2990e80988d35c6a1c Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Fri, 2 Oct 2020 12:09:17 -0400 Subject: [PATCH 63/69] =?UTF-8?q?Created=20the=20following=20individuals,?= =?UTF-8?q?=20which=20are=20instances=20of=20=E2=80=98code=20set=E2=80=99:?= =?UTF-8?q?=20=E2=80=98International=20Classification=20of=20Diseases,=20T?= =?UTF-8?q?enth=20Revision=E2=80=99;=20=E2=80=98Current=20Procedural=20Ter?= =?UTF-8?q?minology=E2=80=99;=20=E2=80=98Healthcare=20Common=20Procedural?= =?UTF-8?q?=20Coding=20System=E2=80=99;=20and=20=E2=80=98Uniform=20Billing?= =?UTF-8?q?=2004=20Form=20Locator=2042=20Revenue=20Codes.=E2=80=99=20Also?= =?UTF-8?q?=20changed=20=E2=80=98International=20Classification=20of=20Dis?= =?UTF-8?q?eases,=20Ninth=20Revision,=20Clinical=20Modification=E2=80=99?= =?UTF-8?q?=20to=20an=20instance=20of=20=E2=80=98code=20set=E2=80=99=20and?= =?UTF-8?q?=20gave=20it=20the=20alternative=20term=20=E2=80=98ICD-9-CM.?= =?UTF-8?q?=E2=80=99=20Also=20changed=20=E2=80=98International=20Classific?= =?UTF-8?q?ation=20of=20Diseases,=20Tenth=20Revision,=20Clinical=20Modific?= =?UTF-8?q?ation=E2=80=99=20to=20an=20instance=20of=20=E2=80=98code=20set?= =?UTF-8?q?=E2=80=99=20and=20gave=20it=20the=20alternative=20term=20?= =?UTF-8?q?=E2=80=98ICD-10-CM.=E2=80=99?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- PCORnetCDM.owl | 46 ++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 44 insertions(+), 2 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index f94ea9e..e3e6011 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -11635,8 +11635,9 @@ excludes emergency department encounters - + An extension of the ICD-10 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. + ICD-10-CM NCI International Classification of Diseases, Tenth Revision, Clinical Modification @@ -11657,8 +11658,9 @@ excludes emergency department encounters - + An extension of the ICD-9 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. + ICD-9-CM NCI International Classification of Diseases, Ninth Revision, Clinical Modification @@ -11683,6 +11685,46 @@ excludes emergency department encounters + + + + + ICD-10-PCS + International Classification of Diseases, Tenth Revision, Procedure Coding System + + + + + + + + + CPT + Current Procedural Terminology + + + + + + + + + HCPCS + Healthcare Common Procedural Coding System + + + + + + + + + UB-04 FL 42 Revenue Codes + Uniform Billing 04 Form Locator 42 Revenue Codes + + + + From 58fa846667f317bf57c005a274c32a72a118b499 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Fri, 2 Oct 2020 12:55:29 -0400 Subject: [PATCH 64/69] =?UTF-8?q?Changed=20'Systematized=20Nomenclature=20?= =?UTF-8?q?of=20Medicine=20Clinical=20Terms'=20to=20an=20instance=20of=20?= =?UTF-8?q?=E2=80=98code=20set=E2=80=99=20and=20gave=20it=20the=20alternat?= =?UTF-8?q?ive=20term=20=E2=80=98SNOMED=20CT.=E2=80=99=20Obsoleted=20?= =?UTF-8?q?=E2=80=98Systematized=20Nomenclature=20of=20Medicine=E2=80=99?= =?UTF-8?q?=20and=20gave=20it=20owl:deprecated=20status=20of=20=E2=80=98tr?= =?UTF-8?q?ue.=E2=80=99=20Obsoleted=20'International=20Classification=20of?= =?UTF-8?q?=20Diseases'=20and=20gave=20it=20owl:deprecated=20status=20of?= =?UTF-8?q?=20=E2=80=98true.=E2=80=99?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- PCORnetCDM.owl | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index e3e6011..9cb30f5 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -5342,7 +5342,8 @@ Environmental exposures include those imposed by natural environments, experimen - International Classification of Diseases + obsolete International Classification of Diseases + true @@ -5608,7 +5609,8 @@ Environmental exposures include those imposed by natural environments, experimen - Systematized Nomenclature of Medicine + obsolete Systematized Nomenclature of Medicine + true @@ -11647,8 +11649,9 @@ excludes emergency department encounters - + Published by the College of American Pathologists, the Systematized Nomenclature of Medicine Clinical Terms is a combination of content of SNOMED Reference Terminology and READ codes. + SNOMED CT NCI Systematized Nomenclature of Medicine Clinical Terms From ac67d52933ef1138ac0a2c5bffcea04309026e00 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Fri, 2 Oct 2020 13:00:13 -0400 Subject: [PATCH 65/69] Created term 'PCORnet medical procedure.' --- PCORnetCDM.owl | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 9cb30f5..cdf9553 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -6416,6 +6416,26 @@ editor date: 2017-04-18 + + + + + + + + + + + A planned process that realizes a patient role. + William R. Hogan + Matthew Diller + S. Clint Dowland + Sarah Bost + PCORnet medical procedure + + + + From 479a191271247e8ef0ca539fab3847ee30807996 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Tue, 27 Oct 2020 12:47:52 -0400 Subject: [PATCH 66/69] Changed the label of 'PCORnet CDM Comments' to 'PCORnet CDM comment' and gave it a definition. --- PCORnetCDM.owl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index cdf9553..933af30 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -874,7 +874,8 @@ Where we have an annotation assertion - PCORnet CDM Comments + A verbatim excerpt—such as a definition, comment, or description—from the PCORnet Common Data Model. + PCORnet CDM comment From 4432e7a35d8ad91562db0ee04f346da2f03e799d Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Tue, 10 Nov 2020 23:53:12 -0500 Subject: [PATCH 67/69] =?UTF-8?q?Removed=20an=20inconsistency=20found=20in?= =?UTF-8?q?=20the=20individual=20'John=20Doe's=20patient=20role.'=20It=20h?= =?UTF-8?q?ad=20been=20assigned=20the=20type=20'male'=20in=20addition=20to?= =?UTF-8?q?=20the=20type=20'patient=20role.'=20This=20is=20inconsistent,?= =?UTF-8?q?=20as=20it=20implies=20the=20individual=20is=20both=20a=20quali?= =?UTF-8?q?ty=20and=20a=20realizable=20entity.=20It=20is=20also=20incorrec?= =?UTF-8?q?t=20to=20make=20a=20patient=20role=20an=20instance=20of=20the?= =?UTF-8?q?=20quality=20'male,'=20since=20roles=20do=20not=20have=20sexes.?= =?UTF-8?q?=20This=20individual=20also=20had=20an=20=E2=80=98inheres=20in?= =?UTF-8?q?=E2=80=99=20annotation=20with=20the=20value=20=E2=80=98PCORnet?= =?UTF-8?q?=20white=20identity=20information=20content=20entity.=E2=80=99?= =?UTF-8?q?=20I=20went=20ahead=20and=20removed=20that,=20too,=20since=20pa?= =?UTF-8?q?tient=20roles=20do=20not=20inhere=20in=20ICEs.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- PCORnetCDM.owl | 2 -- 1 file changed, 2 deletions(-) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 933af30..6fef944 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -11880,9 +11880,7 @@ excludes emergency department encounters - - John Doe's patient role m1 From f0d4802c71c4a196adbb0aacdca692b48f5f7170 Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Mon, 23 Nov 2020 13:16:27 -0500 Subject: [PATCH 68/69] =?UTF-8?q?Via=20MIREOT,=20added=20=E2=80=98date?= =?UTF-8?q?=E2=80=99=20to=20be=20used=20as=20the=20class=20for=20the=20LV?= =?UTF-8?q?=20of=20date=20fields.=20Also=20added=20=E2=80=98name=20of=20te?= =?UTF-8?q?mporal=20region=E2=80=99=20because=20it=20goes=20between=20?= =?UTF-8?q?=E2=80=98identifier=E2=80=99=20and=20=E2=80=98date=E2=80=99=20i?= =?UTF-8?q?n=20the=20=E2=80=98is=20a=E2=80=99=20hierarchy.=20Also=20added?= =?UTF-8?q?=20the=20other=20two=20child=20classes=20of=20=E2=80=98name=20o?= =?UTF-8?q?f=20temporal=20region,=E2=80=99=20which=20are=20=E2=80=98name?= =?UTF-8?q?=20of=20a=20temporal=20boundary=E2=80=99=20and=20=E2=80=98name?= =?UTF-8?q?=20of=20temporal=20intervals,=E2=80=99=20as=20I=20suspect=20one?= =?UTF-8?q?=20of=20the=20two=20might=20be=20used=20for=20the=20LV=20of=20t?= =?UTF-8?q?ime=20fields=20(such=20as=20ADMIT=5FTIME).=20All=20of=20the=20c?= =?UTF-8?q?lasses=20added=20are=20from=20APOLLO=5FSV.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- PCORnetCDM.owl | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 6fef944..564de56 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -19,6 +19,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:apollo_sv="http://purl.obolibrary.org/obo/apollo_sv.owl/" xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> @@ -110,6 +111,8 @@ definition editor + definition editor + term editor term editor @@ -880,6 +883,14 @@ Where we have an annotation assertion + + + + Unique Apollo Label + + + + @@ -5349,6 +5360,60 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + A name of temporal region that specifies a time span on a specified time scale by giving a start time and a duration. + Mathias Brochhausen + http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl + An information content entity that specifies a time span on a specified time scale by giving a start time and a duration. + TimeSpanCategoryDefinition + name of temporal interval + + + + + + + + + A name of temporal region that designates a temporal boundary + Matthew Diller + William R. Hogan + http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl + An information content entity that designates a temporal boundary + RealTimePointCategoryDefinition + name of a temporal boundary + + + + + + + + + http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl + name of temporal region + + + + + + + + + A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar. + Matthew Diller + William R. Hogan + http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl + A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar. + date + date + + + + From 471e5e887050ef62fdc25ebd6226a713ac95ed4b Mon Sep 17 00:00:00 2001 From: Clint Dowland Date: Wed, 23 Dec 2020 11:46:19 -0500 Subject: [PATCH 69/69] Used MIREOT to import BFO's 'has history,' along with its inverse, 'history of.' Then, added that they are inverses of one another and set their domains and ranges. These additions capture aspects of the terms that MIREOT does not import with them. --- PCORnetCDM.owl | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl index 564de56..e3cdb3d 100755 --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1399,6 +1399,39 @@ Where we have an annotation assertion + + + + + + + + http://purl.obolibrary.org/obo/bfo/2020/bfo.owl + 144-BFO + history of + (Elucidation) b history of c if c is a material entity and b is a history that is the unique history of c + This life is the history of this organism. + history of + + + + + + + + + + + http://purl.obolibrary.org/obo/bfo/2020/bfo.owl + 145-BFO + has history + b has history c =Def c history of b + This organism has history this life. + has history + + + +