Merge pull request #95 from FlyBase/release_2024-06-13

release files 2024-06-13

.github/workflows/qc.yml

@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.1
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

fly_development.obo

@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: 2024-04-25
-date: 25:04:2024 05:20
+data-version: 2024-06-13
+date: 13:06:2024 09:02
 subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
 subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
 subsetdef: goslim_aspergillus "Aspergillus GO slim"

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for fbdv
 # Generated using ontology-development-kit
-# ODK Version: v1.5
+# ODK Version: v1.5.1
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use fbdv.Makefile instead
 
@@ -45,8 +45,8 @@ REPORT_LABEL =              -l true
 REPORT_PROFILE_OPTS =       
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties 
-SPARQL_EXPORTS =            basic-report edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.5
+SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
+ODK_VERSION_MAKEFILE =      v1.5.1
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')

src/ontology/reports/class-count-by-prefix.tsv

@@ -0,0 +1,4 @@
+?prefix	?numberOfClasses
+"FBdv"	222
+"BFO"	3
+"GO"	25

src/ontology/reports/obo_qc_fbdv.owl.txt

@@ -1,16 +1,10 @@
 Level	Rule Name	Subject	Property	Value
 WARN	annotation_whitespace	RO:0002093	rdfs:comment	X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). @en
-WARN	annotation_whitespace	RO:0002215	IAO:0000115	A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 
 WARN	duplicate_label	FBdv:00007009	rdfs:label	developmental process
 WARN	duplicate_label	GO:0032502	rdfs:label	developmental process
 WARN	duplicate_label_synonym	FBdv:00007024	oboInOwl:hasExactSynonym	biological process
-WARN	missing_definition	BFO:0000016	IAO:0000115	
-WARN	missing_definition	BFO:0000019	IAO:0000115	
-WARN	missing_definition	BFO:0000034	IAO:0000115	
 WARN	missing_definition	IAO:0000115	IAO:0000115	
 WARN	missing_definition	IAO:0100001	IAO:0000115	
-WARN	missing_definition	RO:0002017	IAO:0000115	
-WARN	missing_definition	RO:0002022	IAO:0000115	
 WARN	missing_definition	RO:0002084	IAO:0000115	
 WARN	missing_definition	RO:0002085	IAO:0000115	
 WARN	missing_definition	RO:0002086	IAO:0000115	
@@ -21,19 +15,6 @@ WARN	missing_definition	RO:0002091	IAO:0000115
 WARN	missing_definition	RO:0002092	IAO:0000115	
 WARN	missing_definition	RO:0002093	IAO:0000115	
 WARN	missing_definition	RO:0002222	IAO:0000115	
-WARN	missing_definition	RO:0002405	IAO:0000115	
-WARN	missing_definition	RO:0002447	IAO:0000115	
-WARN	missing_definition	RO:0002464	IAO:0000115	
-WARN	missing_definition	RO:0002481	IAO:0000115	
-WARN	missing_definition	RO:0002502	IAO:0000115	
-WARN	missing_definition	RO:0002506	IAO:0000115	
-WARN	missing_definition	RO:0002559	IAO:0000115	
-WARN	missing_definition	RO:0002563	IAO:0000115	
-WARN	missing_definition	RO:0002564	IAO:0000115	
-WARN	missing_definition	RO:0004032	IAO:0000115	
-WARN	missing_definition	RO:0004033	IAO:0000115	
-WARN	missing_definition	RO:0004046	IAO:0000115	
-WARN	missing_definition	RO:0004047	IAO:0000115	
 WARN	missing_definition	oboInOwl:NamespaceIdRule	IAO:0000115	
 WARN	missing_definition	oboInOwl:SubsetProperty	IAO:0000115	
 WARN	missing_definition	oboInOwl:hasAlternativeId	IAO:0000115	
@@ -45,73 +26,21 @@ WARN	missing_definition	oboInOwl:hasOBOFormatVersion	IAO:0000115
 WARN	missing_definition	oboInOwl:hasOBONamespace	IAO:0000115	
 WARN	missing_definition	oboInOwl:hasRelatedSynonym	IAO:0000115	
 WARN	missing_definition	oboInOwl:id	IAO:0000115	
-WARN	missing_superclass	GO:0003674	rdfs:subClassOf	
 WARN	missing_superclass	GO:0008150	rdfs:subClassOf	
-INFO	lowercase_definition	BFO:0000004	IAO:0000115	b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])@en
-INFO	lowercase_definition	BFO:0000015	IAO:0000115	p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])@en
-INFO	lowercase_definition	BFO:0000020	IAO:0000115	b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en
 INFO	lowercase_definition	BFO:0000050	IAO:0000115	a core relation that holds between a part and its whole@en
 INFO	lowercase_definition	BFO:0000051	IAO:0000115	a core relation that holds between a whole and its part@en
 INFO	lowercase_definition	BFO:0000062	IAO:0000115	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.@en
 INFO	lowercase_definition	BFO:0000063	IAO:0000115	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.@en
-INFO	lowercase_definition	RO:0000052	IAO:0000115	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.@en
-INFO	lowercase_definition	RO:0000056	IAO:0000115	a relation between a continuant and a process, in which the continuant is somehow involved in the process@en
-INFO	lowercase_definition	RO:0000057	IAO:0000115	a relation between a process and a continuant, in which the continuant is somehow involved in the process@en
-INFO	lowercase_definition	RO:0000079	IAO:0000115	a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence@en
-INFO	lowercase_definition	RO:0000080	IAO:0000115	a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence@en
-INFO	lowercase_definition	RO:0000081	IAO:0000115	a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence@en
-INFO	lowercase_definition	RO:0000085	IAO:0000115	a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence@en
-INFO	lowercase_definition	RO:0000086	IAO:0000115	a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence@en
-INFO	lowercase_definition	RO:0000087	IAO:0000115	a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence@en
-INFO	lowercase_definition	RO:0000091	IAO:0000115	a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence@en
-INFO	lowercase_definition	RO:0000092	IAO:0000115	inverse of has disposition
-INFO	lowercase_definition	RO:0002018	IAO:0000115	w 'has process component' p if p and w are processes,  w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
 INFO	lowercase_definition	RO:0002131	IAO:0000115	x overlaps y if and only if there exists some z such that x has part z and z part of y
-INFO	lowercase_definition	RO:0002180	IAO:0000115	w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
 INFO	lowercase_definition	RO:0002202	IAO:0000115	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
 INFO	lowercase_definition	RO:0002203	IAO:0000115	inverse of develops from
-INFO	lowercase_definition	RO:0002211	IAO:0000115	p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
-INFO	lowercase_definition	RO:0002212	IAO:0000115	p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
-INFO	lowercase_definition	RO:0002213	IAO:0000115	p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
-INFO	lowercase_definition	RO:0002216	IAO:0000115	c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
-INFO	lowercase_definition	RO:0002233	IAO:0000115	p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
 INFO	lowercase_definition	RO:0002254	IAO:0000115	x has developmental contribution from y iff x has some part z such that z develops from y@en
 INFO	lowercase_definition	RO:0002255	IAO:0000115	inverse of has developmental contribution from
-INFO	lowercase_definition	RO:0002263	IAO:0000115	c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
-INFO	lowercase_definition	RO:0002264	IAO:0000115	c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
-INFO	lowercase_definition	RO:0002304	IAO:0000115	p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
-INFO	lowercase_definition	RO:0002305	IAO:0000115	p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
-INFO	lowercase_definition	RO:0002314	IAO:0000115	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.
-INFO	lowercase_definition	RO:0002327	IAO:0000115	c enables p iff c is capable of p and c acts to execute p.
-INFO	lowercase_definition	RO:0002329	IAO:0000115	this relation holds between c and p when c is part of some c', and c' is capable of p.
-INFO	lowercase_definition	RO:0002331	IAO:0000115	c involved_in p if and only if c enables some process p', and p' is part of p
-INFO	lowercase_definition	RO:0002333	IAO:0000115	inverse of enables
-INFO	lowercase_definition	RO:0002334	IAO:0000115	inverse of regulates
-INFO	lowercase_definition	RO:0002335	IAO:0000115	inverse of negatively regulates
-INFO	lowercase_definition	RO:0002336	IAO:0000115	inverse of positively regulates
-INFO	lowercase_definition	RO:0002352	IAO:0000115	inverse of has input
 INFO	lowercase_definition	RO:0002384	IAO:0000115	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).@en
 INFO	lowercase_definition	RO:0002385	IAO:0000115	x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y@en
 INFO	lowercase_definition	RO:0002387	IAO:0000115	x has the potential to develop into y iff x develops into y or if x is capable of developing into y@en
 INFO	lowercase_definition	RO:0002388	IAO:0000115	x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y@en
-INFO	lowercase_definition	RO:0002404	IAO:0000115	inverse of upstream of
-INFO	lowercase_definition	RO:0002407	IAO:0000115	p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
-INFO	lowercase_definition	RO:0002409	IAO:0000115	p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
 INFO	lowercase_definition	RO:0002410	IAO:0000115	relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
-INFO	lowercase_definition	RO:0002411	IAO:0000115	p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
-INFO	lowercase_definition	RO:0002412	IAO:0000115	p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
 INFO	lowercase_definition	RO:0002418	IAO:0000115	p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
 INFO	lowercase_definition	RO:0002427	IAO:0000115	inverse of causally upstream of or within
-INFO	lowercase_definition	RO:0002428	IAO:0000115	c involved in regulation of p if c is involved in some p' and p' regulates some p
-INFO	lowercase_definition	RO:0002429	IAO:0000115	c involved in regulation of p if c is involved in some p' and p' positively regulates some p
-INFO	lowercase_definition	RO:0002430	IAO:0000115	c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
-INFO	lowercase_definition	RO:0002431	IAO:0000115	c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
 INFO	lowercase_definition	RO:0002501	IAO:0000115	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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
-INFO	lowercase_definition	RO:0002578	IAO:0000115	p directly regulates q iff p is immediately causally upstream of q and p regulates q.
-INFO	lowercase_definition	RO:0002584	IAO:0000115	s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
-INFO	lowercase_definition	RO:0002629	IAO:0000115	p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
-INFO	lowercase_definition	RO:0002630	IAO:0000115	p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
-INFO	lowercase_definition	RO:0004034	IAO:0000115	c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
-INFO	lowercase_definition	RO:0004035	IAO:0000115	c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
-INFO	lowercase_definition	RO:0012011	IAO:0000115	p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
-INFO	lowercase_definition	RO:0012012	IAO:0000115	p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.

src/ontology/reports/obsoletes.tsv

@@ -3,7 +3,7 @@
 <http://purl.obolibrary.org/obo/FBdv_00005310>		
 <http://purl.obolibrary.org/obo/FBdv_00005320>		
 <http://purl.obolibrary.org/obo/FBdv_00005326>		
-<http://purl.obolibrary.org/obo/FBdv_00005329>	"FBdv:00005330"	
+<http://purl.obolibrary.org/obo/FBdv_00005329>	<http://purl.obolibrary.org/obo/FBdv_00005330>	
 <http://purl.obolibrary.org/obo/FBdv_00005373>	<http://purl.obolibrary.org/obo/FBdv_00005370>	
 <http://purl.obolibrary.org/obo/FBdv_00005374>	<http://purl.obolibrary.org/obo/FBdv_00005371>	
 <http://purl.obolibrary.org/obo/FBdv_00005375>	<http://purl.obolibrary.org/obo/FBdv_00006012>	

src/ontology/reports/robot_simple_diff.txt

@@ -1,9 +1,9 @@
 3 axioms in left ontology but not in right ontology:
-- Annotation(<oboInOwl:date> "25:04:2024 05:20")
-- Annotation(<owl:versionInfo> "2024-04-25")
-- OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple/fbdv/releases/2024-04-25/fbdv-simple.owl/fbdv/fbdv-simple.owl>))
+- Annotation(<oboInOwl:date> "13:06:2024 09:02")
+- Annotation(<owl:versionInfo> "2024-06-13")
+- OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple/fbdv/releases/2024-06-13/fbdv-simple.owl/fbdv/fbdv-simple.owl>))
 
 3 axioms in right ontology but not in left ontology:
-+ Annotation(<oboInOwl:date> "18:04:2024 09:08")
-+ Annotation(<owl:versionInfo> "2024-04-18")
-+ OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple/fbdv/releases/2024-04-18/fbdv-simple.owl/fbdv/fbdv-simple.owl>))
++ Annotation(<oboInOwl:date> "25:04:2024 05:20")
++ Annotation(<owl:versionInfo> "2024-04-25")
++ OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple/fbdv/releases/2024-04-25/fbdv-simple.owl/fbdv/fbdv-simple.owl>))