Merge pull request #20 from VirtualFlyBrain/release_2024-09-19

Release 2024-09-19

.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:v1.5.2
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for vfbext
 # Generated using ontology-development-kit
-# ODK Version: v1.5
+# ODK Version: v1.5.2
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vfbext.Makefile instead
 
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                11643cc79293c3aa48319672aa04a650c744220372aba01fe8124783bf56a725
+CONFIG_HASH=                f536379bcd203347d28185a6c0c3abdac1af3338ef70a92870fa1c31ea32920f
 
 
 # ----------------------------------------
@@ -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 =      v1.5.2
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -159,7 +159,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro caro fbbt obi
+IMPORTS =  bfo ro caro fbbt obi
 
 IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -416,6 +416,14 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports
 ifeq ($(strip $(MIR)),true)
 
 
+## ONTOLOGY: bfo
+.PHONY: mirror-bfo
+.PRECIOUS: $(MIRRORDIR)/bfo.owl
+mirror-bfo: | $(TMPDIR)
+	curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(TMPDIR)/bfo-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) remove -i $(TMPDIR)/bfo-download.owl --base-iri http://purl.obolibrary.org/obo/BFO_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
+
+
 ## ONTOLOGY: ro
 .PHONY: mirror-ro
 .PRECIOUS: $(MIRRORDIR)/ro.owl

src/ontology/imports/bfo_terms.txt

@@ -0,0 +1 @@
+

src/ontology/reports/basic-report.tsv

@@ -1,14 +1,13 @@
 ?cls	?def	?xrefs
 <http://purl.obolibrary.org/obo/CARO_0030002>	"The mereological sum of all cells in a single organism in which expression of some specified gene occurs."	
 <http://purl.obolibrary.org/obo/CARO_0000042>	"A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis."	
-<http://purl.obolibrary.org/obo/BFO_0000017>	"A specifically dependent continuant  that inheres in continuant  entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en	
 <http://purl.obolibrary.org/obo/OBI_0000684>	"A objective specification to obtain a material entity for potential use as an input during an investigation."	
 <http://purl.obolibrary.org/obo/CARO_0010004>	"An individual member of a clade of cellular organisms."	
 <http://purl.obolibrary.org/obo/CARO_0010000>	"An anatomical structure that has more than one cell as a part."	
 <http://purl.obolibrary.org/obo/CARO_0000007>	"Anatomical entity that has no mass."	
 <http://purl.obolibrary.org/obo/CARO_0001008>	"Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell.  Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. "	
+<http://purl.obolibrary.org/obo/BFO_0000002>		
 <http://purl.obolibrary.org/obo/CARO_0001000>	"A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part."	
-<http://purl.obolibrary.org/obo/BFO_0000034>		
 <http://purl.obolibrary.org/obo/SO_0000110>		
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004>		
 <http://purl.obolibrary.org/obo/OBI_0000112>	"a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en	
@@ -19,47 +18,42 @@
 <http://purl.obolibrary.org/obo/IAO_0000005>		
 <http://purl.obolibrary.org/obo/CARO_0000003>	"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/CARO_0000040>	"An anatomical structure that has no cells or cell parts as a part."	
+<http://purl.obolibrary.org/obo/BFO_0000017>		
 <http://purl.obolibrary.org/obo/CARO_0000006>	"An anatomical entity that has mass."	
-<http://purl.obolibrary.org/obo/BFO_0000003>	"An entity that has temporal parts and that happens, unfolds or develops through time."@en	
+<http://purl.obolibrary.org/obo/BFO_0000001>		
 <http://purl.obolibrary.org/obo/CARO_0000013>	"An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane."	"CL:0000000 GO:0005623"
-<http://purl.obolibrary.org/obo/BFO_0000015>	"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	
-<http://purl.obolibrary.org/obo/BFO_0000031>	"b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en	
 <http://purl.obolibrary.org/obo/CARO_0030000>	"Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them."	
 <http://purl.obolibrary.org/obo/NCBITaxon_7227>		
 <http://purl.obolibrary.org/obo/CARO_0020000>	"Material anatomical entity consisting of multiple anatomical structures that are not connected to each other."	
-<http://purl.obolibrary.org/obo/BFO_0000002>	"An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en	
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010>		
-<http://purl.obolibrary.org/obo/BFO_0000016>		
 <http://purl.obolibrary.org/obo/FBbt_10000000>	"Anatomical entity which is part_of Drosophila melanogaster."	"UBERON:0001062"
 <http://purl.obolibrary.org/obo/OBI_0002076>	"A material entity that has two or more specimens as its parts."@en	
+<http://purl.obolibrary.org/obo/BFO_0000004>		
+<http://purl.obolibrary.org/obo/BFO_0000020>		
 <http://purl.obolibrary.org/obo/CARO_0001010>	"Material anatomical entity that is a member of an individual species or is a viral or viroid particle."	
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000006>		
 <http://purl.obolibrary.org/obo/BFO_0000141>		
 <http://purl.obolibrary.org/obo/PATO_0002266>		
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014>		
 <http://purl.obolibrary.org/obo/PATO_0000125>		
-<http://purl.obolibrary.org/obo/GO_0008150>		
+<http://purl.obolibrary.org/obo/BFO_0000040>		
 <http://purl.obolibrary.org/obo/PATO_0001993>		
 <http://purl.obolibrary.org/obo/CARO_0000012>	"Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell."	
 <http://purl.obolibrary.org/obo/OBI_0000659>	"A planned process with the objective of collecting a specimen."	
 <http://purl.obolibrary.org/obo/CARO_0020003>	"An anatomical structure consisting of one or more cells."	
-<http://purl.obolibrary.org/obo/BFO_0000023>	"A realizable entity  the manifestation of which brings about some result or end that is not essential to a continuant  in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant  in some kinds of natural, social or institutional contexts."@en	
 <http://purl.obolibrary.org/obo/CARO_0000004>	"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 and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome."	
-<http://purl.obolibrary.org/obo/BFO_0000020>	"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	
 <http://purl.obolibrary.org/obo/FBbt_00100313>	"Anatomical structure that has multiple cells as parts."	"UBERON:0010000"
 <http://purl.obolibrary.org/obo/CARO_0000014>	"Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher."	
 <http://purl.obolibrary.org/obo/IAO_0000104>		
-<http://purl.obolibrary.org/obo/BFO_0000004>	"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	
-<http://purl.obolibrary.org/obo/PATO_0000001>		
 <http://purl.obolibrary.org/obo/FBbt_00007001>	"Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome."	"UBERON:0000061 CARO:0000003"
-<http://purl.obolibrary.org/obo/BFO_0000019>		
 <http://purl.obolibrary.org/obo/UBERON_0000465>		
+<http://purl.obolibrary.org/obo/BFO_0000023>		
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007>		
-<http://purl.obolibrary.org/obo/GO_0003674>		
+<http://purl.obolibrary.org/obo/BFO_0000015>		
+<http://purl.obolibrary.org/obo/BFO_0000003>		
+<http://purl.obolibrary.org/obo/BFO_0000031>		
 <http://purl.obolibrary.org/obo/OBI_0100051>	"A material entity that has the specimen role."@en	
 <http://purl.obolibrary.org/obo/CARO_0000000>	"A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex.  Or, a substance produced by a cellular organism with granularity above the level of a protein complex."	
-<http://purl.obolibrary.org/obo/BFO_0000040>	"An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en	
 <http://xmlns.com/foaf/0.1/image>		
 <http://purl.obolibrary.org/obo/FBbt_00007016>		"UBERON:0000465 CARO:0000006"
-<http://purl.obolibrary.org/obo/GO_0016301>		
 <http://purl.obolibrary.org/obo/PATO_0010001>		

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

@@ -0,0 +1,13 @@
+?prefix	?numberOfClasses
+"OBI"	6
+"CARO"	20
+"FBbt"	4
+"IAO"	2
+"BFO"	11
+"fbbt/vfb/VFBext"	5
+"NCBITaxon"	1
+"fbbt/vfb/VFB"	1
+"SO"	1
+"UBERON"	1
+"PATO"	5
+""	1

src/ontology/reports/edges.tsv

@@ -1,29 +1,28 @@
 ?x	?p	?y
-<http://purl.obolibrary.org/obo/CARO_0020000>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0010001>
-<http://purl.obolibrary.org/obo/CARO_0010000>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0001993>
-<http://purl.obolibrary.org/obo/CARO_0000006>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0000125>
-<http://purl.obolibrary.org/obo/CARO_0000003>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0010000>
 <http://purl.obolibrary.org/obo/CARO_0001008>	<http://purl.obolibrary.org/obo/BFO_0000050>	<http://purl.obolibrary.org/obo/CARO_0000012>
-<http://purl.obolibrary.org/obo/FBbt_10000000>	<http://purl.obolibrary.org/obo/BFO_0000050>	<http://purl.obolibrary.org/obo/NCBITaxon_7227>
 <http://purl.obolibrary.org/obo/CARO_0020000>	<http://purl.obolibrary.org/obo/RO_0002180>	<http://purl.obolibrary.org/obo/CARO_0000003>
+<http://purl.obolibrary.org/obo/FBbt_10000000>	<http://purl.obolibrary.org/obo/BFO_0000050>	<http://purl.obolibrary.org/obo/NCBITaxon_7227>
+<http://purl.obolibrary.org/obo/OBI_0000659>	<http://purl.obolibrary.org/obo/OBI_0000299>	<http://purl.obolibrary.org/obo/OBI_0100051>
+<http://purl.obolibrary.org/obo/CARO_0000003>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0010000>
 <http://purl.obolibrary.org/obo/OBI_0000659>	<http://purl.obolibrary.org/obo/OBI_0000293>	<http://purl.obolibrary.org/obo/BFO_0000040>
-<http://purl.obolibrary.org/obo/CARO_0030002>	<http://purl.obolibrary.org/obo/BFO_0000051>	<http://purl.obolibrary.org/obo/CARO_0000013>
+<http://purl.obolibrary.org/obo/OBI_0000112>	<http://purl.obolibrary.org/obo/RO_0000052>	_:Bdc27f7d2X2D59cfX2D47b2X2Db233X2De06e1623c4a4genid103
+<http://purl.obolibrary.org/obo/CARO_0010000>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0001993>
 <http://purl.obolibrary.org/obo/CARO_0000014>	<http://purl.obolibrary.org/obo/BFO_0000050>	<http://purl.obolibrary.org/obo/CARO_0000013>
-<http://purl.obolibrary.org/obo/OBI_0000659>	<http://purl.obolibrary.org/obo/OBI_0000299>	<http://purl.obolibrary.org/obo/OBI_0100051>
-<http://purl.obolibrary.org/obo/OBI_0000112>	<http://purl.obolibrary.org/obo/RO_0000052>	_:Bb1c3f966X2D3bfaX2D40deX2Da782X2Df38093fb7481genid218
+<http://purl.obolibrary.org/obo/CARO_0030002>	<http://purl.obolibrary.org/obo/BFO_0000051>	<http://purl.obolibrary.org/obo/CARO_0000013>
 <http://purl.obolibrary.org/obo/CARO_0000003>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0002266>
+<http://purl.obolibrary.org/obo/CARO_0000006>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0000125>
+<http://purl.obolibrary.org/obo/CARO_0020000>	<http://purl.obolibrary.org/obo/RO_0000053>	<http://purl.obolibrary.org/obo/PATO_0010001>
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://xmlns.com/foaf/0.1/image>
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000010>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/FBbt_10000000>
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014>
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000006>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://xmlns.com/foaf/0.1/image>
 <http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000004>
 <http://purl.obolibrary.org/obo/SO_0000110>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000040>
-<http://purl.obolibrary.org/obo/CARO_0001000>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	_:Bb1c3f966X2D3bfaX2D40deX2Da782X2Df38093fb7481genid176
+<http://purl.obolibrary.org/obo/BFO_0000002>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000001>
 <http://purl.obolibrary.org/obo/CARO_0000032>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0010000>
 <http://purl.obolibrary.org/obo/CARO_0000006>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0000000>
 <http://purl.obolibrary.org/obo/CARO_0020000>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0000006>
 <http://purl.obolibrary.org/obo/OBI_0000011>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000015>
-<http://purl.obolibrary.org/obo/BFO_0000019>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000020>
 <http://purl.obolibrary.org/obo/CARO_0000012>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0010004>
 <http://purl.obolibrary.org/obo/CARO_0000042>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0001008>
 <http://purl.obolibrary.org/obo/CARO_0000042>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0000003>
@@ -35,9 +34,7 @@
 <http://purl.obolibrary.org/obo/CARO_0000040>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0001008>
 <http://purl.obolibrary.org/obo/CARO_0020003>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0000006>
 <http://purl.obolibrary.org/obo/CARO_0000000>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0030000>
-<http://purl.obolibrary.org/obo/BFO_0000034>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000016>
 <http://purl.obolibrary.org/obo/CARO_0000007>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0000000>
-<http://purl.obolibrary.org/obo/BFO_0000016>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000017>
 <http://purl.obolibrary.org/obo/FBbt_00007016>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/FBbt_10000000>
 <http://purl.obolibrary.org/obo/CARO_0000004>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0001008>
 <http://purl.obolibrary.org/obo/CARO_0030002>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0020003>
@@ -51,9 +48,11 @@
 <http://purl.obolibrary.org/obo/BFO_0000015>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000003>
 <http://purl.obolibrary.org/obo/CARO_0000013>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0020003>
 <http://purl.obolibrary.org/obo/CARO_0010004>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0001010>
+<http://purl.obolibrary.org/obo/CARO_0001000>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	_:Bdc27f7d2X2D59cfX2D47b2X2Db233X2De06e1623c4a4genid62
 <http://purl.obolibrary.org/obo/CARO_0001000>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0001008>
 <http://purl.obolibrary.org/obo/CARO_0000040>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0000003>
 <http://purl.obolibrary.org/obo/BFO_0000031>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000002>
+<http://purl.obolibrary.org/obo/BFO_0000003>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000001>
 <http://purl.obolibrary.org/obo/OBI_0000659>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/OBI_0000011>
 <http://purl.obolibrary.org/obo/CARO_0000003>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/CARO_0000006>
 <http://purl.obolibrary.org/obo/BFO_0000004>	<http://www.w3.org/2000/01/rdf-schema#subClassOf>	<http://purl.obolibrary.org/obo/BFO_0000002>