Skip to content

Commit

Permalink
Merge pull request #45 from obophenotype/ODK-release-2023-09-26
Browse files Browse the repository at this point in the history
ODK Release 2023-09-26
  • Loading branch information
chris-grove authored Sep 26, 2023
2 parents bdcc48a + 97c8ab2 commit 99f006c
Showing 14 changed files with 51 additions and 199 deletions.
4 changes: 2 additions & 2 deletions src/ontology/Makefile
Original file line number Diff line number Diff line change
@@ -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')
30 changes: 6 additions & 24 deletions src/ontology/imports/ro_import.owl
Original file line number Diff line number Diff line change
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/wbls/imports/ro_import.owl>
<http://purl.obolibrary.org/obo/wbls/releases/2023-07-10/imports/ro_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2023-06-28/ro.owl>)
Annotation(owl:versionInfo "2023-07-10")
<http://purl.obolibrary.org/obo/wbls/releases/2023-09-26/imports/ro_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro.owl>)
Annotation(owl:versionInfo "2023-09-26")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
@@ -127,7 +127,6 @@ Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002596>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002597>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002598>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002608>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002610>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002629>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002630>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0004031>))
@@ -141,7 +140,6 @@ Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0011002>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0012011>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0012012>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0017001>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0017003>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0019000>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0019001>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0019002>))
@@ -417,7 +415,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/BFO_0000062> "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(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/BFO_0000062> "is preceded by"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/BFO_0000062> "preceded_by"@en)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/BFO_0000062> "http://www.obofoundry.org/ro/#OBO_REL:preceded_by")
AnnotationAssertion(<http://purl.org/dc/terms/source> <http://purl.obolibrary.org/obo/BFO_0000062> "http://www.obofoundry.org/ro/#OBO_REL:preceded_by")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/BFO_0000062> <http://purl.obolibrary.org/obo/ro/subsets#ro-eco>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000062> "preceded by"@en)
SubObjectPropertyOf(<http://purl.obolibrary.org/obo/BFO_0000062> <http://purl.obolibrary.org/obo/RO_0002086>)
@@ -487,7 +485,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.ob
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0000057> "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/RO_0000057> "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(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/RO_0000057> "has_participant"@en)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/RO_0000057> "http://www.obofoundry.org/ro/#OBO_REL:has_participant")
AnnotationAssertion(<http://purl.org/dc/terms/source> <http://purl.obolibrary.org/obo/RO_0000057> "http://www.obofoundry.org/ro/#OBO_REL:has_participant")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000057> "has participant"@en)
ObjectPropertyDomain(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/BFO_0000003>)
ObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/BFO_0000002>)
@@ -1459,12 +1457,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.ob
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002608> "process has causal agent")
SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0002608> <http://purl.obolibrary.org/obo/RO_0002410>)

# Object Property: <http://purl.obolibrary.org/obo/RO_0002610> (correlated with)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002610> "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(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/RO_0002610> "Groups both positive and negative correlation")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002610> "correlated with")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002629> (directly positively regulates)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0002629> "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.")
@@ -1597,20 +1589,10 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.ob
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/RO_0017001> <https://orcid.org/0000-0003-2620-0345>)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/RO_0017001> "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(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/RO_0017001> "See github ticket https://github.com/oborel/obo-relations/issues/497")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/RO_0017001> "2021-11-08T12:00:00Z")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/RO_0017001> "2021-11-08T12:00:00Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/RO_0017001> "utilizes")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0017001> "device utilizes material"@en)

# Object Property: <http://purl.obolibrary.org/obo/RO_0017003> (positively correlated with)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0017003> "A relation between entities in which one increases or decreases as the other does the same."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/RO_0017003> "directly correlated with"@en)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/RO_0017003> <https://orcid.org/0000-0003-1909-9269>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0017003> "positively correlated with"@en)
SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0017003> <http://purl.obolibrary.org/obo/RO_0002610>)
SymmetricObjectProperty(<http://purl.obolibrary.org/obo/RO_0017003>)
ReflexiveObjectProperty(<http://purl.obolibrary.org/obo/RO_0017003>)

# Object Property: <http://purl.obolibrary.org/obo/RO_0019000> (regulates characteristic)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0019000> "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.")
4 changes: 2 additions & 2 deletions wbls-base.json
Original file line number Diff line number Diff line change
@@ -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",
4 changes: 2 additions & 2 deletions wbls-base.obo
Original file line number Diff line number Diff line change
@@ -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
4 changes: 2 additions & 2 deletions wbls-base.owl
Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/wbls/wbls-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/wbls/releases/2023-07-10/wbls-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/wbls/releases/2023-09-26/wbls-base.owl"/>
<obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/WBls_0000075"/>
<dce:description>Ontology about the development and life stages of the C. elegans</dce:description>
<dce:title>C. elegans Development Ontology</dce:title>
@@ -25,7 +25,7 @@
<oboInOwl:saved-by>chris-grove</oboInOwl:saved-by>
<rdfs:comment>Editors: Wen J. Chen &amp; Daniela Raciti, Raymond Lee, Chris Grove, WormBase, Caltech. Jane Lomax, Wellcome Trust Sanger Institute.</rdfs:comment>
<rdfs:comment>Version: 1.04</rdfs:comment>
<owl:versionInfo>2023-07-10</owl:versionInfo>
<owl:versionInfo>2023-09-26</owl:versionInfo>
</owl:Ontology>


41 changes: 4 additions & 37 deletions wbls-full.json
Original file line number Diff line number Diff line change
@@ -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",
Loading

0 comments on commit 99f006c

Please sign in to comment.