diff --git a/.gitignore b/.gitignore index 3bafc35..ac15987 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ *.properties catalog-v001.xml +.DS_Store diff --git a/PCORnetCDM.owl b/PCORnetCDM.owl old mode 100644 new mode 100755 index 395a50a..e3cdb3d --- a/PCORnetCDM.owl +++ b/PCORnetCDM.owl @@ -1,37 +1,39 @@ + 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#"> + - - - - - + + + Amanda Hicks - 2019-08-02 + Josh Hanna William R. Hogan + 2019-08-03 RDFized PCORnet CDM - Josh Hanna @@ -91,7 +93,6 @@ definition definition - definition textual definition @@ -102,32 +103,45 @@ editor note editor note - editor note - + + definition editor + definition editor + term editor + term editor + - + + alternative term + - + + definition source + definition source + - + + curator note + curator note + curator notes + @@ -240,32 +254,6 @@ 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 - - - - - - - - - S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] - ambiguous for taxon - - - - - - - - - - S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - https://orcid.org/0000-0002-6601-2165 - - This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost - dubious for taxon - - @@ -273,12 +261,7 @@ - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - https://orcid.org/0000-0002-6601-2165 - - present in taxon - - + present_in_taxon @@ -329,7 +312,6 @@ A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property - @@ -348,7 +330,6 @@ logical macro assertion on an annotation property - @@ -813,6 +794,70 @@ 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 + + + + @@ -821,10 +866,27 @@ Where we have an annotation assertion + + + + fma_set_term + + + + - PCORnet CDM Comments + A verbatim excerpt—such as a definition, comment, or description—from the PCORnet Common Data Model. + PCORnet CDM comment + + + + + + + + Unique Apollo Label @@ -838,6 +900,14 @@ Where we have an annotation assertion + + + + contributor + + + + @@ -876,6 +946,40 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + + has_alternative_id + + + + + + + + has_broad_synonym + + + + @@ -916,6 +1020,22 @@ Where we have an annotation assertion + + + + has_scope + + + + + + + + has_synonym_type + + + + @@ -930,6 +1050,24 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + @@ -960,6 +1098,38 @@ Where we have an annotation assertion + + + + + + + + + + + + + + + + + + + + + + + + + + + + depicted by + + + + @@ -1229,6 +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 + + + + @@ -1418,19 +1621,6 @@ 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 - - - - @@ -1483,10 +1673,6 @@ 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 @@ -1600,18 +1786,6 @@ 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 - - - - @@ -1742,14 +1916,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - - - - - @@ -1794,174 +1960,42 @@ 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) - )))))) + 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) - - fasciculates with + + overlaps - + - - - - - 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) + 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) - has plasma membrane part - - - - - - - - - - - - has neurotransmitter - releases neurotransmitter + continuous with + FMA:85972 - + - - - - 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 - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - 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 - - - - - - - - + + 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 @@ -2047,19 +2081,6 @@ 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 - - - - @@ -2072,18 +2093,6 @@ 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 - - - - @@ -2100,29 +2109,6 @@ 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 - - - - @@ -2138,44 +2124,6 @@ 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 - - - - @@ -2191,75 +2139,6 @@ 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 - - - - @@ -2492,61 +2371,6 @@ 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 - - - - @@ -2631,36 +2455,6 @@ 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 - - - - @@ -2765,96 +2559,6 @@ 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 - - - - @@ -2880,184 +2584,33 @@ 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 'is substance that treats' + cjm + + is treated by substance - + - - - - Inverse of developmentally preceded by - Chris Mungall - developmentally succeeded by + + + + + 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 - - - - - - - - - '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 - - - - - - - - - - Inverse of 'is substance that treats' - cjm - - is treated by substance - - - - - - - - - - - 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 - - - - - + @@ -3085,19 +2638,6 @@ 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 - - - - @@ -3130,22 +2670,6 @@ 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 - - - - @@ -3362,17 +2886,6 @@ 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 - - - - @@ -3396,18 +2909,6 @@ 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 - - - - @@ -3419,43 +2920,6 @@ 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 - - - - @@ -3506,42 +2970,6 @@ 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 - - - - @@ -3553,61 +2981,6 @@ 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 - - - - @@ -3763,67 +3136,6 @@ 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 - - - - @@ -4248,349 +3560,71 @@ 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 - - - - - - - - - - - - - - - - - - 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 - - - - - + @@ -4662,42 +3696,6 @@ 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 - - - - @@ -4729,41 +3727,6 @@ 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 - - - - @@ -4820,239 +3783,97 @@ 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 + + + + 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 - + - - - - 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). + + + + + 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 - existence starts during + + 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 - + - - - 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 + depends on + - + - - - 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)) + + + 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 - 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 + + towards - + - - - - 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) + + + '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 - 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 + has intermediate product + + has intermediate - + - - - - 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 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 - 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 + + 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 - + - - - 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 - - - - - - - - - - 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 - - - - - - - - - - - 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 - - - - - - - - Chris Mungall - depends on - - - - - - - - - - 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 - - towards - - - - - - - - - '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 - 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 - - - - - - - - - - - - - - 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 + + + + + + + + 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 Chris Mungall determined by (system to material entity) @@ -5392,122 +4213,6 @@ 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 - - - - @@ -5558,18 +4263,6 @@ 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 - - - - @@ -5654,34 +4347,6 @@ 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 - - - - @@ -5697,16 +4362,6 @@ 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 - - - - @@ -5724,17 +4379,6 @@ the a supports either the existence of b, or the truth value of b. - - - - - 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 - - - - @@ -5745,25 +4389,6 @@ the a supports either the existence of b, or the truth value of b. - - - - results in synthesis of - - - - - - - - - - results in assembly of - - - - @@ -5774,46 +4399,6 @@ the a supports either the existence of b, or the truth value of b. - - - - - 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 - - - - - - - - - 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 - - - - @@ -5984,101 +4569,21 @@ the a supports either the existence of b, or the truth value of b. + - - - - visits - https://github.com/oborel/obo-relations/issues/74 + + + + 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 - - - - - 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 - - - - - - - - - - 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 - - - - - + @@ -6092,119 +4597,6 @@ 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 - - - - @@ -6667,20 +5059,6 @@ 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 - - - - @@ -6695,74 +5073,6 @@ 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 - - - - @@ -6793,19 +5103,6 @@ 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 - - - - @@ -6901,73 +5198,6 @@ 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 - - - - @@ -7093,36 +5323,6 @@ 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 - - - - - - - - TODO: Add homeomorphy axiom - - - - - - @@ -7183,44 +5383,82 @@ Environmental exposures include those imposed by natural environments, experimen - + - + + + obsolete International Classification of Diseases + true + - + - - - - - - - - - - - - - - + + + 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 + + + + + + + + + + + + @@ -7235,14 +5473,7 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - - - + @@ -7282,64 +5513,114 @@ 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 + - + - - - - - - - + + + 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 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 + - + - + + + 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 + @@ -7423,12 +5704,154 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + obsolete Systematized Nomenclature of Medicine + true + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + @@ -7459,6 +5882,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -7509,6 +5938,21 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + 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 + + + + @@ -7539,6 +5983,34 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + 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 + + + + + + + + + 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 + + + + @@ -7565,1856 +6037,6208 @@ Environmental exposures include those imposed by natural environments, experimen - + - - - 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 - http://www.jbiomedsem.com/content/4/1/43 - system + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 - + + + 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 - + - - - 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 + + + 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 - + - - - 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 - + + + 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 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 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 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 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 - + - - - 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 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - a diagnosis about some patient that occurs before or during the admission of that patient - Amanda Hicks - PCORnet CDM 4.1 - admitting diagnosis + + + 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 - + - - - 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 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 - + - - - question text + + + 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 - + - - - Amanda Hicks - PCORnet American Indian or Alaska Native identity datum + + + 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 - + - - - Amanda Hicks - PCORnet Asian identity datum + + + 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 - + - - - - - - - - - - - - - - - - - - - material information bearer of question text plus answer set + + + 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 - + - - - Amanda Hicks - PCORnet black or African American identity datum + + + 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 - + - - - - - - - - - PCORnet CDM item identifier + + + 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 - + - - - - - - - - - PCORnet item + + + 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 - + - - - option as memeber of answer set + + + 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 - + - - - Amanda Hicks - PCORnet Native Hawaiian or other Pacific Islander identity datum + + + 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 - + - - - Amanda Hicks - PCORnet white identity datum + + + 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 - + - - - Amanda Hicks - PCORnet multiple race identity datum + + + 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 - + - - - - 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 + + + 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 - + - - - - Amanda Hicks - PCORnet not Hispanic identity datum + + + 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 - + - - - Amanda Hicks - PCORnet ethnic identity datum + + + 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 - + - - - 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 + + + 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 - + - - - - - - - - - - - - - - - admission process + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - a diagnosis that occurs before or simultaneously with the discharge of the patient whom the diagnosis is about - discharge diagnosis + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 - + - + - - - - - - - - - - - - + + - discharge process + A planned process that realizes a patient role. + William R. Hogan + Matthew Diller + S. Clint Dowland + Sarah Bost + PCORnet medical procedure - + - - - - - - - - - - - - - - - - - - - a diagnosis about a patient that is the specified output of a diagnostic process that occurs during an outpatient encounter - final diagnosis + + + 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 - + - - - - - - - - - - - - - - - - - - - interim diagnosis + + + 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 - + - - - PCORnet racial identification process + + + 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 - + - - - PCORnet sexual orientationidentity datum + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 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 - + - - - - 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 - 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 + + + 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 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 + + + 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 - + - - - - PCORnet asexual identity datum - inpatient hospital encounter + + + 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 - + - - - 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 + + + 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 - + - - - PCORnet lesbian identity datum + + + 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 - + - - - PCORnet multiple sexual orientations identity datum + + + 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 + http://www.jbiomedsem.com/content/4/1/43 + system - - - - - PCORnet queer identity datum + + + + + 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 - - - - - PCORnet questioning identity datum + + + + + 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 + + + + - - - PCORnet something else identity datum + + + + + + 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 + - + - - - PCORnet straight identity datum + + + 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 - + - - - 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 + + + 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 + + + + - - - PCORnet genderqueer identity datum + + + + + + 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 + + - - - PCORnet man identity datum + + + + + + 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 - + - - - PCORnet multiple genders datum + + + 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 - + - - - PCORnet something else identity datum + + + 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 - - - - - PCORnet transgenderfemale/transwoman/male-to-female identity datum + + + + + 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 - + - - - PCORnet transgendermale/transman/female-to-male identity datum + + + 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 + - + - - - PCORnet woman identity datum + + + 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 - - + + + + + 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 + + + - + - - - - John Doe - + + + 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 + + UBERON:0000172 + vomit + - + + + + + 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 + + - - - - - John Doe's birth - + + + + + + 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 + - + - - - - - 23:59 - + + + 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 + purulent exudate + UBERON:0000177 + pus + + - - - - - - John Doe's neonate stage - + + + + + 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 + - + - - - 1D temporal interval occuped by John Doe's neonate stage - + + + 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 + blood or blood analog + circulating fluid + UBERON:0000179 + haemolymphatic fluid + - - - - - 2000-02-02 - + + + + + 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 + + - - - - - - rta1 - + + + + + 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 + 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 + - - - - - eiqap1 - + + + + + 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 + - - - - - - Jane Doe - + + + + + 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 + - - - - - - g - + + + + + 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 + + - - - - - p4 - + + + + + 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 + - - - - - - f1 - + + + + + 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 + - - - - - p5 - + + + + + 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 + + - - - - - - - - John Doe's patient role - m1 - + + + + + 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 + - - - - - ridqap1 - + + + + + 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 + - - - - - Jane Doe's American Indian or Alaska Native identity datum - + + + + + 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 + + - - - - - - p6 - + + + + + 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 + + - - - - - - rta2 - + + + + + 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 + - - - - - Jane Doe's racial identification process - + + + + + 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 + + + - - - - - ETL process of Jane Doe’s racial identity datum - + + + + + 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 + + + - - - - - - - - John Doe's Hispanic or Latino identity datum - + + + + + 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 + + + - + + + + + 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 + + + - - - John Doe’s ethnic identification process - + + + + + + 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 + + - - - - - John Doe’s PCORnet Hispanic identity datum - + + + + + + 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 + + - - - ETL process of John Doe’s ethnic identity datum - + + + + + + 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 + + + - - - - - - Jane Doe's not Hispanic or Latino identity datum - + + + + + + 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 + - + - - - Jane Doe’s ethnic identification process - + + + http://purl.obolibrary.org/obo/uberon/releases/2019-11-22/uberon.owl + FMA:45733 + organ neck + uberon + UBERON:0001560 + + neck of organ + - - - - - - - Jane Doe’s PCORnet not Hispanic identity datum - + + + + + 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 + + - - - ETL process of John Doe’s ethnic identity datum - + + + + + + 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 + + - - - ETL process of Jane Doe’s ethnic identity datum - + + + + + + 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 + + + - - - 1234 - - - - + + + + + + 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 + - + + + + + 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 + + - - true - - - 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 - - - - - - - - - - - - - - - - + + + + + + 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 + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + 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 + + + + + + + + + + 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 + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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. + obsolete PCORnet racial identity datum + true + + + + + + + + + Amanda Hicks + 'PCORnet American Indian or Alaska Native identity information content entity' + obsolete PCORnet American Indian or Alaska Native identity datum + true + + + + + + + + + Amanda Hicks + 'PCORnet Asian identity information content entity' + obsolete PCORnet Asian identity datum + true + + + + + + + + + Amanda Hicks + 'PCORnet black or African American identity information content entity' + obsolete PCORnet black or African American identity datum + obsolete PCORnet item + true + + + + + + + + + obsolete PCORnet CDM item identifier + true + + + + + + + + + obsolete PCORnet item + true + + + + + + + + + Amanda Hicks + 'PCORnet Native Hawaiian or other Pacific Islander identity information content entity' + obsolete PCORnet Native Hawaiian or other Pacific Islander identity datum + true + + + + + + + + + Amanda Hicks + 'PCORnet white identity information content entity' + obsolete PCORnet white identity datum + true + + + + + + + + + Amanda Hicks + 'PCORnet multiple race identity information content entity' + obsolete PCORnet multiple race identity datum + true + + + + + + + + + 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." + obsolete PCORnet Hispanic identity datum + true + + + + + + + + + Amanda Hicks + 'PCORnet non-Hispanic identity information content entity' + obsolete PCORnet not Hispanic identity datum + true + + + + + + + + + Amanda Hicks + 'PCORnet ethnic identity information content entity' + obsolete PCORnet ethnic identity datum + true + + + + + + + + + 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 + + + + + + + + + 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' +http://purl.obolibrary.org/obo/OMRSE_00000201 + obsolete admission process + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + PCORnet racial identification process + + + + + + + + + 'PCORnet sexual orientation identity information content entity' + obsolete PCORnet sexual orientation identity datum + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + 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. + deprecated emergency department encounter + true + + + + + + + + + Amanda Hicks + 'sexual orientation identity information content entity' + 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 sexual orientation identity datum + true + + + + + + + + + 'PCORnet asexual identity information content entity' + obsolete PCORnet asexual identity datum + obsolete inpatient hospital encounter + true + + + + + + + + + 'PCORnet gay identity information content entity' + obsolete PCORnet gay identity datum + true + + + + + + + + + 'PCORnet lesbian identity information content entity' + obsolete PCORnet lesbian identity datum + true + + + + + + + + + 'PCORnet multiple sexual orientations identity information content entity' + obsolete PCORnet multiple sexual orientations identity datum + true + + + + + + + + + 'PCORnet queer identity information content entity' + obsolete PCORnet queer identity datum + true + + + + + + + + + 'PCORnet questioning sexual orientation identity information content entity' + obsolete PCORnet questioning identity datum + true + + + + + + + + + 'PCORnet something else sexual orientation identity information content entity' + obsolete PCORnet something else identity datum + true + + + + + + + + + 'PCORnet straight identity information content entity' + obsolete PCORnet straight identity datum + true + + + + + + + + + '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. + obsolete PCORnet gender identity datum + true + + + + + + + + + 'PCORnet genderqueer/non-binary identity information content entity' + obsolete PCORnet genderqueer identity datum + true + + + + + + + + + 'PCORnet man identity information content entity' + obsolete PCORnet man identity datum + true + + + + + + + + + 'PCORnet multiple gender categories identity information content entity' + obsolete PCORnet multiple genders datum + true + + + + + + + + + 'PCORnet something else gender identity information content entity' + obsolete PCORnet something else identity datum + true + + + + + + + + + 'PCORnet transgender female/trans woman/male-to-female identity information content entity' + obsolete PCORnet transgenderfemale/transwoman/male-to-female identity datum + true + + + + + + + + + 'PCORnet transgender male/trans man/female-to-male identity information content entity' + obsolete PCORnet transgendermale/transman/female-to-male identity datum + true + + + + + + + + + 'PCORnet woman identity information content entity' + obsolete PCORnet woman identity datum + true + + + + + + + + + An identifier that denotes a diagnosis. + PCORnet diagnosis identifier + + + + + + + + This class is superfluous, given the addition of PNO: code set. + DEPRECATED obsolete code set + + true + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + PCORnet other acute inpatient hospital discharge status data item + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 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 + + + + + + + + + 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 + + + + + + + + + An identifier that denotes a health care encounter and has part some symbol. + Matthew Diller + S. Clint Dowland + PCORnet health care encounter identifier + + + + + + + + + An identifier 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 + + + + + + + + + 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 + Matthew Diller + S. Clint Dowland + William R. Hogan + PCORnet absent without leave discharge status data item + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + John Doe + + + + + + + + + + + John Doe's birth + + + + + + + + + + + 23:59 + + + + + + + + + + John Doe's neonate stage + + + + + + + + + 1D temporal interval occuped by John Doe's neonate stage + + + + + + + + + 2000-02-02 + + + + + + + + + + rta1 + + + + + + + + + eiqap1 + + + + + + + + + + Jane Doe + + + + + + + + + + g + + + + + + + + + p4 + + + + + + + + + + f1 + + + + + + + + + p5 + + + + + + + + + + John Doe's patient role + m1 + + + + + + + + + ridqap1 + + + + + + + + + Jane Doe's American Indian or Alaska Native identity datum + + + + + + + + + + p6 + + + + + + + + + + rta2 + + + + + + + + + Jane Doe's racial identification process + + + + + + + + + ETL process of Jane Doe’s racial identity datum + + + + + + + + + + + + John Doe's Hispanic or Latino identity datum + + + + + + + + + John Doe’s ethnic identification process + + + + + + + + + + + John Doe’s PCORnet Hispanic identity datum + + + + + + + + + ETL process of John Doe’s ethnic identity datum + + + + + + + + + + + + Jane Doe's not Hispanic or Latino identity datum + + + + + + + + + Jane Doe’s ethnic identification process + + + + + + + + + + + Jane Doe’s PCORnet not Hispanic identity datum + + + + + + + + + ETL process of John Doe’s ethnic identity datum + + + + + + + + + ETL process of Jane Doe’s ethnic identity datum + + + + + + + + + + John Doe's patient role + + + + + + + + + 1234 + + + + + + + + + + + + + + + + + + + - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + true - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + 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. + + + + + + + David Osumi-Sutherland + + + - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + @@ -9424,9 +12248,9 @@ excludes emergency department encounters - - - + + + @@ -9434,57 +12258,24 @@ excludes emergency department encounters - - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - + + + + + + + + + - - + @@ -9495,9 +12286,9 @@ excludes emergency department encounters - - - + + + @@ -9508,5 +12299,5 @@ excludes emergency department encounters - + diff --git a/catalog-v001.xml b/catalog-v001.xml deleted file mode 100644 index 3aeb476..0000000 --- a/catalog-v001.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - -