Merge pull request #179 from FlyBase/release_2024-04-25

release files 2024-04-25

dpo.obo

@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: dpo/releases/2024-02-23
-date: 23:02:2024 08:54
+data-version: dpo/releases/2024-04-25
+date: 25:04:2024 13:28
 subsetdef: abnormal_slim "Abnormal/normal slim"
 subsetdef: absent_slim "Absent/present slim"
 subsetdef: attribute_slim "Attribute slim"
@@ -44,7 +44,7 @@ property_value: http://purl.org/dc/elements/1.1/description "An ontology for the
 property_value: http://purl.org/dc/elements/1.1/title "Drosophila Phenotype Ontology (DPO)" xsd:string
 property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string
 property_value: IAO:0000700 FBcv:0000347
-property_value: owl:versionInfo "2024-02-23" xsd:string
+property_value: owl:versionInfo "2024-04-25" xsd:string
 
 [Term]
 id: FBcv:0000002
@@ -2377,26 +2377,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
-property_value: IAO:0000111 "is part of" xsd:string
-property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
-property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
-property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
-property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
-property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
-property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
-property_value: IAO:0000118 "part_of" xsd:string
-property_value: RO:0001900 RO:0001901
-property_value: RO:0040042 BFO:0000002
-property_value: RO:0040042 BFO:0000003
-property_value: RO:0040042 BFO:0000004
-property_value: RO:0040042 BFO:0000017
-property_value: RO:0040042 BFO:0000019
-property_value: RO:0040042 BFO:0000020
-property_value: RO:0040042 BFO:0000031
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
-property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
-property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string
-property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI
 is_transitive: true
 inverse_of: BFO:0000051 ! has part
 
@@ -2407,23 +2387,13 @@ def: "a core relation that holds between a whole and its part" []
 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
-property_value: IAO:0000111 "has part" xsd:string
-property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
-property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
-property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
-property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string
-property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
-property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string
-property_value: IAO:0000118 "has_part" xsd:string
-property_value: RO:0001900 RO:0001901
 is_transitive: true
 
 [Typedef]
 id: BFO:0000063
 name: precedes
 def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), 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
-property_value: IAO:0000111 "precedes" xsd:string
 holds_over_chain: BFO:0000050 BFO:0000063
 is_transitive: true
 
@@ -2446,11 +2416,6 @@ id: RO:0000052
 name: characteristic of
 def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
 comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
-property_value: IAO:0000111 "inheres in" xsd:string
-property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string
-property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string
-property_value: IAO:0000118 "inheres_in" xsd:string
-property_value: RO:0001900 RO:0001901
 is_functional: true
 is_a: RO:0002314 ! characteristic of part of
 
@@ -2459,44 +2424,29 @@ id: RO:0002083
 name: before
 comment: t1 before t2 iff:=  t1 before_or_simulataneous_with t2  and not (t1 simultaeous_with t2)
 subset: ro-eco
-property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
 is_transitive: true
 
 [Typedef]
 id: RO:0002314
 name: characteristic of part of
 def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." []
-property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string
-property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: IAO:0000118 "inheres in part of" xsd:string
-property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
-property_value: RO:0001900 RO:0001901
-property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
 holds_over_chain: RO:0000052 BFO:0000050
 transitive_over: BFO:0000050 ! part of
 
 [Typedef]
 id: RO:0002351
 name: has member
 def: "has member is a mereological relation between a collection and an item." []
-property_value: IAO:0000119 "SIO" xsd:string
-property_value: RO:0001900 RO:0001901
 is_a: BFO:0000051 ! has part
 
 [Typedef]
 id: RO:0002503
 name: towards
 def: "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" []
-property_value: IAO:0000116 "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." xsd:string
-property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
 
 [Typedef]
 id: RO:0002573
 name: has modifier
 def: "A relation that holds between an attribute or a qualifier and another attribute." []
 subset: ro-eco
-property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
-property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
-property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string