From 97c8ab28334d05ebb0cae8d423f4abc81ab78224 Mon Sep 17 00:00:00 2001 From: Chris Grove Date: Tue, 26 Sep 2023 13:20:51 -0400 Subject: [PATCH] ODK Release 2023-09-26 --- src/ontology/Makefile | 4 +-- src/ontology/imports/ro_import.owl | 30 +++++----------------- wbls-base.json | 4 +-- wbls-base.obo | 4 +-- wbls-base.owl | 4 +-- wbls-full.json | 41 +++--------------------------- wbls-full.obo | 24 +++-------------- wbls-full.owl | 34 ++++--------------------- wbls-simple.json | 6 ++--- wbls-simple.obo | 4 +-- wbls-simple.owl | 16 ++++++------ wbls.json | 41 +++--------------------------- wbls.obo | 4 +-- wbls.owl | 34 ++++--------------------- 14 files changed, 51 insertions(+), 199 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index bc684c4..6b35b9b 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for wbls # Generated using ontology-development-kit -# ODK Version: v1.4.1 +# ODK Version: v1.4.2 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use wbls.Makefile instead @@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.4.1 +ODK_VERSION_MAKEFILE = v1.4.2 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 3b9fe4a..3e5c1d4 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-07-10") + +Annotation( ) +Annotation(owl:versionInfo "2023-09-26") Declaration(Class()) Declaration(Class()) @@ -127,7 +127,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -141,7 +140,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -417,7 +415,7 @@ AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) AnnotationAssertion( "is preceded by"@en) AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "preceded by"@en) SubObjectPropertyOf( ) @@ -487,7 +485,7 @@ AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -1459,12 +1457,6 @@ AnnotationAssertion( "process has causal agent") SubObjectPropertyOf( ) -# Object Property: (correlated with) - -AnnotationAssertion( "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.") -AnnotationAssertion( "Groups both positive and negative correlation") -AnnotationAssertion(rdfs:label "correlated with") - # Object Property: (directly positively regulates) AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") @@ -1597,20 +1589,10 @@ AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z") +AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) -# Object Property: (positively correlated with) - -AnnotationAssertion( "A relation between entities in which one increases or decreases as the other does the same."@en) -AnnotationAssertion( "directly correlated with"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively correlated with"@en) -SubObjectPropertyOf( ) -SymmetricObjectProperty() -ReflexiveObjectProperty() - # Object Property: (regulates characteristic) AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") diff --git a/wbls-base.json b/wbls-base.json index 6aa79f2..f409cde 100644 --- a/wbls-base.json +++ b/wbls-base.json @@ -40,9 +40,9 @@ "val" : "Version: 1.04" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-07-10" + "val" : "2023-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/wbls/releases/2023-07-10/wbls-base.json" + "version" : "http://purl.obolibrary.org/obo/wbls/releases/2023-09-26/wbls-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", diff --git a/wbls-base.obo b/wbls-base.obo index 1dbaae6..28a4e37 100644 --- a/wbls-base.obo +++ b/wbls-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: wbls/releases/2023-07-10/wbls-base.owl +data-version: wbls/releases/2023-09-26/wbls-base.owl date: 15:11:2017 12:24 saved-by: chris-grove auto-generated-by: OBO-Edit 2.2-rc1 @@ -12,7 +12,7 @@ property_value: http://purl.org/dc/elements/1.1/title "C. elegans Development On property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/license "http://creativecommons.org/licenses/by/4.0/" xsd:string property_value: IAO:0000700 WBls:0000075 -property_value: owl:versionInfo "2023-07-10" xsd:string +property_value: owl:versionInfo "2023-09-26" xsd:string [Term] id: WBls:0000001 diff --git a/wbls-base.owl b/wbls-base.owl index 017878a..3e5a6c6 100644 --- a/wbls-base.owl +++ b/wbls-base.owl @@ -12,7 +12,7 @@ xmlns:dcterms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Ontology about the development and life stages of the C. elegans C. elegans Development Ontology @@ -25,7 +25,7 @@ chris-grove Editors: Wen J. Chen & Daniela Raciti, Raymond Lee, Chris Grove, WormBase, Caltech. Jane Lomax, Wellcome Trust Sanger Institute. Version: 1.04 - 2023-07-10 + 2023-09-26 diff --git a/wbls-full.json b/wbls-full.json index 771b584..371ad86 100644 --- a/wbls-full.json +++ b/wbls-full.json @@ -37,9 +37,9 @@ "val" : "Version: 1.04" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-07-10" + "val" : "2023-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/wbls/releases/2023-07-10/wbls-full.json" + "version" : "http://purl.obolibrary.org/obo/wbls/releases/2023-09-26/wbls-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -337,7 +337,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -710,7 +710,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } @@ -2440,19 +2440,6 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", - "lbl" : "correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Groups both positive and negative correlation" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", @@ -2716,22 +2703,6 @@ "val" : "2021-11-08T12:00:00Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0017003", - "lbl" : "positively correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between entities in which one increases or decreases as the other does the same." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly correlated with" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1909-9269" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0019000", "lbl" : "regulates characteristic", @@ -35101,10 +35072,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0017003", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002610" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0019000", "pred" : "subPropertyOf", diff --git a/wbls-full.obo b/wbls-full.obo index e12a65b..a82eb1d 100644 --- a/wbls-full.obo +++ b/wbls-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: wbls/releases/2023-07-10/wbls-full.owl +data-version: wbls/releases/2023-09-26/wbls-full.owl date: 15:11:2017 12:24 saved-by: chris-grove auto-generated-by: OBO-Edit 2.2-rc1 @@ -19,7 +19,7 @@ property_value: http://purl.org/dc/elements/1.1/description "Ontology about the property_value: http://purl.org/dc/elements/1.1/title "C. elegans Development Ontology" xsd:string property_value: http://purl.org/dc/terms/license "http://creativecommons.org/licenses/by/4.0/" xsd:string property_value: IAO:0000700 WBls:0000075 -property_value: owl:versionInfo "2023-07-10" xsd:string +property_value: owl:versionInfo "2023-09-26" xsd:string [Term] id: BFO:0000002 @@ -9663,7 +9663,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -10650,12 +10650,6 @@ def: "Inverse of 'causal agent in process'" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to -[Typedef] -id: RO:0002610 -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string - [Typedef] id: RO:0002629 name: directly positively regulates @@ -10798,16 +10792,6 @@ property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-rel holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z -[Typedef] -id: RO:0017003 -name: positively correlated with -def: "A relation between entities in which one increases or decreases as the other does the same." [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 -property_value: IAO:0000118 "directly correlated with" xsd:string -is_reflexive: true -is_symmetric: true -is_a: RO:0002610 ! correlated with - [Typedef] id: RO:0019000 name: regulates characteristic @@ -10876,7 +10860,7 @@ name: preceded_by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/wbls-full.owl b/wbls-full.owl index a9a55dc..d6925cd 100644 --- a/wbls-full.owl +++ b/wbls-full.owl @@ -19,7 +19,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Ontology about the development and life stages of the C. elegans C. elegans Development Ontology @@ -31,7 +31,7 @@ chris-grove Editors: Wen J. Chen & Daniela Raciti, Raymond Lee, Chris Grove, WormBase, Caltech. Jane Lomax, Wellcome Trust Sanger Institute. Version: 1.04 - 2023-07-10 + 2023-09-26 @@ -660,7 +660,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 worm_development preceded_by @@ -760,7 +760,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -2337,16 +2337,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - correlated with - - - - @@ -2552,27 +2542,13 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - directly correlated with - - positively correlated with - - - - diff --git a/wbls-simple.json b/wbls-simple.json index 5275611..723b127 100644 --- a/wbls-simple.json +++ b/wbls-simple.json @@ -37,9 +37,9 @@ "val" : "Version: 1.04" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-07-10" + "val" : "2023-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/wbls/releases/2023-07-10/wbls-simple.json" + "version" : "http://purl.obolibrary.org/obo/wbls/releases/2023-09-26/wbls-simple.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -143,7 +143,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", diff --git a/wbls-simple.obo b/wbls-simple.obo index 3593b0e..d6ad027 100644 --- a/wbls-simple.obo +++ b/wbls-simple.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: wbls/releases/2023-07-10/wbls-simple.owl +data-version: wbls/releases/2023-09-26/wbls-simple.owl date: 15:11:2017 12:24 saved-by: chris-grove auto-generated-by: OBO-Edit 2.2-rc1 @@ -8814,7 +8814,7 @@ name: preceded_by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/wbls-simple.owl b/wbls-simple.owl index b8a3cea..d127415 100644 --- a/wbls-simple.owl +++ b/wbls-simple.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Ontology about the development and life stages of the C. elegans C. elegans Development Ontology @@ -122,12 +122,6 @@ - - - - - - @@ -140,6 +134,12 @@ + + + + + + @@ -314,7 +314,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 worm_development preceded_by diff --git a/wbls.json b/wbls.json index 171a109..bf66dea 100644 --- a/wbls.json +++ b/wbls.json @@ -37,9 +37,9 @@ "val" : "Version: 1.04" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-07-10" + "val" : "2023-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/wbls/releases/2023-07-10/wbls.json" + "version" : "http://purl.obolibrary.org/obo/wbls/releases/2023-09-26/wbls.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -337,7 +337,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -710,7 +710,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } @@ -2440,19 +2440,6 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", - "lbl" : "correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Groups both positive and negative correlation" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", @@ -2716,22 +2703,6 @@ "val" : "2021-11-08T12:00:00Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0017003", - "lbl" : "positively correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between entities in which one increases or decreases as the other does the same." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly correlated with" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1909-9269" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0019000", "lbl" : "regulates characteristic", @@ -35101,10 +35072,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0017003", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002610" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0019000", "pred" : "subPropertyOf", diff --git a/wbls.obo b/wbls.obo index 3593b0e..d6ad027 100644 --- a/wbls.obo +++ b/wbls.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: wbls/releases/2023-07-10/wbls-simple.owl +data-version: wbls/releases/2023-09-26/wbls-simple.owl date: 15:11:2017 12:24 saved-by: chris-grove auto-generated-by: OBO-Edit 2.2-rc1 @@ -8814,7 +8814,7 @@ name: preceded_by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/wbls.owl b/wbls.owl index 7ececf5..ddc065e 100644 --- a/wbls.owl +++ b/wbls.owl @@ -19,7 +19,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Ontology about the development and life stages of the C. elegans C. elegans Development Ontology @@ -31,7 +31,7 @@ chris-grove Editors: Wen J. Chen & Daniela Raciti, Raymond Lee, Chris Grove, WormBase, Caltech. Jane Lomax, Wellcome Trust Sanger Institute. Version: 1.04 - 2023-07-10 + 2023-09-26 @@ -660,7 +660,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 worm_development preceded_by @@ -760,7 +760,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -2337,16 +2337,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - correlated with - - - - @@ -2552,27 +2542,13 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - directly correlated with - - positively correlated with - - - -