Fixed some typos in the gaz_xrefs file and updated Makefile to deal w…

…ith artificat in GEO import
EBISPOT · May 12, 2022 · 029b4f8 · 029b4f8
1 parent 640b92c
commit 029b4f8
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Showing 10 changed files with 6,376 additions and 3,764 deletions.
diff --git a/hancestro.owl b/hancestro.owl
diff --git a/hancestro_bfo.owl b/hancestro_bfo.owl
diff --git a/hancestro_inferred.owl b/hancestro_inferred.owl
diff --git a/imports/geo_import.owl b/imports/geo_import.owl
diff --git a/imports/obi_import.owl b/imports/obi_import.owl
@@ -8,7 +8,7 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:obo="http://purl.obolibrary.org/obo/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/obi.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/obi/2020-08-24/obi.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/obi/2022-01-03/obi.owl"/>
     </owl:Ontology>
 
 
@@ -48,13 +48,21 @@
     <!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+        <obo:IAO_0000111>editor preferred label</obo:IAO_0000111>
+        <obo:IAO_0000111 xml:lang="en">editor preferred label</obo:IAO_0000111>
+        <obo:IAO_0000111>editor preferred term</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">editor preferred term</obo:IAO_0000111>
+        <obo:IAO_0000111>editor preferred term~editor preferred label</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
         <obo:IAO_0000115 xml:lang="en">The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)</obo:IAO_0000115>
         <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <rdfs:label>editor preferred label</rdfs:label>
+        <rdfs:label xml:lang="en">editor preferred label</rdfs:label>
+        <rdfs:label>editor preferred term</rdfs:label>
         <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+        <rdfs:label>editor preferred term~editor preferred label</rdfs:label>
     </owl:AnnotationProperty>
 
 
@@ -88,9 +96,11 @@
     <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+        <obo:IAO_0000111>definition</obo:IAO_0000111>
         <obo:IAO_0000111 xml:lang="en">definition</obo:IAO_0000111>
-        <obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</obo:IAO_0000111>
+        <obo:IAO_0000111>textual definition</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <obo:IAO_0000115 xml:lang="en">The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
         <obo:IAO_0000115 xml:lang="en">The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
         <obo:IAO_0000116 xml:lang="en">2012-04-05: 
 Barry Smith
@@ -115,8 +125,9 @@ We also have the outstanding issue of how to aim different definitions to differ
         <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <rdfs:label>definition</rdfs:label>
         <rdfs:label xml:lang="en">definition</rdfs:label>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label>
+        <rdfs:label>textual definition</rdfs:label>
     </owl:AnnotationProperty>
 
 
@@ -178,6 +189,21 @@ We also have the outstanding issue of how to aim different definitions to differ
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+        <obo:IAO_0000111 xml:lang="en">imported from</obo:IAO_0000111>
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+        <obo:IAO_0000115 xml:lang="en">For external terms/classes, the ontology from which the term was imported</obo:IAO_0000115>
+        <obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
+        <obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
+        <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
+        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+        <rdfs:label xml:lang="en">imported from</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
     <!-- http://purl.obolibrary.org/obo/IAO_0000600 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000600">
@@ -232,6 +258,7 @@ We also have the outstanding issue of how to aim different definitions to differ
     <!-- http://www.w3.org/2000/01/rdf-schema#label -->
 
     <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label">
+        <obo:IAO_0000111>label</obo:IAO_0000111>
         <rdfs:label>label</rdfs:label>
     </owl:AnnotationProperty>
 
@@ -253,6 +280,7 @@ We also have the outstanding issue of how to aim different definitions to differ
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040">
         <obo:BFO_0000179>material</obo:BFO_0000179>
         <obo:BFO_0000180>MaterialEntity</obo:BFO_0000180>
+        <obo:IAO_0000111 xml:lang="en">material entity</obo:IAO_0000111>
         <obo:IAO_0000112 xml:lang="en">a flame</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">a forest fire</obo:IAO_0000112>
         <obo:IAO_0000112 xml:lang="en">a human being</obo:IAO_0000112>
@@ -269,6 +297,7 @@ We also have the outstanding issue of how to aim different definitions to differ
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60</obo:IAO_0000116>
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.</obo:IAO_0000116>
         <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.</obo:IAO_0000116>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ido.owl"/>
         <obo:IAO_0000600 xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</obo:IAO_0000600>
         <obo:IAO_0000601 xml:lang="en">Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])</obo:IAO_0000601>
         <obo:IAO_0000601 xml:lang="en">every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])</obo:IAO_0000601>

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -58,7 +58,7 @@ $(ONT_INF).owl: $(ONT).owl
 
 IMPORTS = bfo geo obi
 # IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS)) $(patsubst %, imports/%_import.obo,$(IMPORTS))
-IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS))  imports/obi_import.owl
+IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS))  imports/geo_import.owl imports/obi_import.owl
 
 # Make this target to regenerate ALL
 all_imports: $(IMPORTS_OWL)
@@ -68,6 +68,10 @@ imports/%_import.owl: mirror/%.owl imports/%_terms.txt
 	$(ROBOT) extract -i $< -T imports/$*_terms.txt --method BOT -O $(BASE)/$@ -o $@
 .PRECIOUS: imports/%_import.owl
 
+imports/geo_import.owl: mirror/geo.owl imports/geo_terms.txt
+	$(ROBOT) extract -i $< -T imports/geo_terms.txt --method BOT -O $(BASE)/$@ remove --term IAO:0000030 -o $@
+.PRECIOUS: imports/geo_import.owl
+
 imports/obi_import.owl: mirror/obi.owl imports/obi_terms.txt
 	$(ROBOT) extract -i mirror/obi.owl -T imports/obi_terms.txt --method MIREOT --upper-term "obo:BFO_0000040" --lower-term "obo:OBI_0000181" -O $(BASE)/$@ -o $@
 .PRECIOUS: imports/obi_import.owl