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joergwajoergwa
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reorganized bfo import
1 parent 00d120f commit eb1f1e9

8 files changed

Lines changed: 108 additions & 1400 deletions

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‎src/ontology/Makefile‎

Lines changed: 1 addition & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@
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# More information: https://github.com/INCATools/ontology-development-kit/
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# Fingerprint of the configuration file when this Makefile was last generated
13-
CONFIG_HASH= 01c9d9a87b41663a3121104770d09ee7f07ec7b2300026f3150df43365e26c89
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CONFIG_HASH= c15fe6b540abdbd6bcdf9d76309e332b7b3185ad3826bf31bea48acef629eabd
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# ----------------------------------------
@@ -422,15 +422,6 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms.txt \
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.PRECIOUS: $(IMPORTDIR)/%_import.owl
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425-
## Module for ontology: bfo (mirror)
426-
$(IMPORTDIR)/bfo_import.owl: $(MIRRORDIR)/bfo.owl | all_robot_plugins
427-
$(ROBOT) annotate --input $< --remove-annotations \
428-
odk:normalize --base-iri https://w3id.org/lehrplan \
429-
--subset-decls true --synonym-decls true \
430-
--add-source true \
431-
repair --merge-axiom-annotations true \
432-
$(ANNOTATE_CONVERT_FILE)
433-
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## Module for ontology: qudt (slme)
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$(IMPORTDIR)/qudt_import.owl: $(MIRRORDIR)/qudt.owl $(IMPORTDIR)/qudt_terms.txt $(IMPORTSEED) | all_robot_plugins
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$(ROBOT) annotate --input $< --remove-annotations \

‎src/ontology/components/bfo-edit.owl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,7 @@ SubObjectPropertyOf(<https://w3id.org/lehrplan/ontology/LP_0000017> <http://purl
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# Object Property: <https://w3id.org/lehrplan/ontology/LP_0000021> (endet mit Abschluss)
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48-
SubObjectPropertyOf(<https://w3id.org/lehrplan/ontology/LP_0000021> <http://purl.obolibrary.org/obo/BFO_0000117>)
48+
SubObjectPropertyOf(<https://w3id.org/lehrplan/ontology/LP_0000021> <http://purl.obolibrary.org/obo/BFO_0000051>)
4949
ObjectPropertyRange(<https://w3id.org/lehrplan/ontology/LP_0000021> <https://w3id.org/lehrplan/ontology/LP_0000019>)
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# Object Property: <https://w3id.org/lehrplan/ontology/LP_0000024> (wird beschrieben von)

‎src/ontology/components/lehrplan-core.owl‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -818,19 +818,19 @@ Bsp:
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:schuleTreburSchulform1 a Schulartfunktion .
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:schuleTreburSchulform1 bfo:existsAt :someTimeIntervalUntilDateX .
821-
:schuleTreburSchulform1 :konkretisiertSchulform :Realschule .
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:schuleTreburSchulform1 :wirdBeschriebenVon :Realschule .
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:schuleTreburSchulform2 a Schulartfunktion .
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:schuleTreburSchulform2 bfo:existsAt :someTimeIntervalUntilDateX .
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:schuleTreburSchulform2 :konkretisiertSchulform :Hauptschule .
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:schuleTreburSchulform2 :wirdBeschriebenVon :Hauptschule .
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:schuleTreburSchulform3 a Schulartfunktion .
828-
:schuleTreburSchulform3 :konkretisiertSchulform :Gesamtschule
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:schuleTreburSchulform3 bfo:existsAt :someTimeIntervalFromDateY .
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:schuleTreburSchulform3 :wirdBeschriebenVon :Gesamtschule .
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:schuleTrebur :hatSchulformfunktion :schuleTreburSchulform1 .
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:schuleTrebur :hatSchulformfunktion :schuleTreburSchulform2 .
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:schuleTrebur :hatSchulformfunktion :schuleTreburSchulform3 .
831+
:schuleTrebur :hatFunktion :schuleTreburSchulform1 .
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:schuleTrebur :hatFunktion :schuleTreburSchulform2 .
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:schuleTrebur :hatFunktion :schuleTreburSchulform3 .
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:someTimeIntervalUntilDateX bfo:precedes :someTimeIntervalUntilDateY .")
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‎src/ontology/imports/bfo_import.owl‎

Lines changed: 62 additions & 599 deletions
Large diffs are not rendered by default.

‎src/ontology/imports/bfo_terms.txt‎

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Original file line numberDiff line numberDiff line change
@@ -1 +1,11 @@
1+
http://purl.obolibrary.org/obo/BFO_0000031
2+
http://purl.obolibrary.org/obo/BFO_0000030
3+
http://purl.obolibrary.org/obo/BFO_0000040
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http://purl.obolibrary.org/obo/BFO_0000034
5+
http://purl.obolibrary.org/obo/BFO_0000023
6+
http://purl.obolibrary.org/obo/BFO_0000015
7+
http://purl.obolibrary.org/obo/BFO_0000035
18

9+
10+
http://purl.obolibrary.org/obo/BFO_0000051
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http://purl.obolibrary.org/obo/BFO_0000050

‎src/ontology/imports/ro_import.owl‎

Lines changed: 0 additions & 71 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,6 @@ Annotation(owl:versionInfo "2026-01-07")
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000004>))
17-
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000006>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
2019
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000017>))
@@ -24,13 +23,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000023>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000031>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000034>))
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Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
27-
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000141>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
30-
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000054>))
31-
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000055>))
32-
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000066>))
33-
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000067>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000052>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000056>))
@@ -53,7 +47,6 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000118>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000600>))
56-
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/license>))
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Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
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Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
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@@ -94,57 +87,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.ob
9487
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000051> "has part"@en)
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TransitiveObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>)
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# Object Property: <http://purl.obolibrary.org/obo/BFO_0000054> (realized in)
98-
99-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/BFO_0000054> "realized in"@en)
100-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000054> "this disease is realized in this disease course"@en)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000054> "this fragility is realized in this shattering"@en)
102-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000054> "this investigator role is realized in this investigation"@en)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/BFO_0000054> "is realized by"@en)
104-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/BFO_0000054> "realized_in"@en)
105-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000600> <http://purl.obolibrary.org/obo/BFO_0000054> "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en)
106-
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/BFO_0000054> "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process")
107-
AnnotationAssertion(rdfs:isDefinedBy <http://purl.obolibrary.org/obo/BFO_0000054> <http://purl.obolibrary.org/obo/bfo.owl>)
108-
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000054> "realized in"@en)
109-
InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000054> <http://purl.obolibrary.org/obo/BFO_0000055>)
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ObjectPropertyDomain(<http://purl.obolibrary.org/obo/BFO_0000054> <http://purl.obolibrary.org/obo/BFO_0000017>)
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ObjectPropertyRange(<http://purl.obolibrary.org/obo/BFO_0000054> <http://purl.obolibrary.org/obo/BFO_0000015>)
112-
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# Object Property: <http://purl.obolibrary.org/obo/BFO_0000055> (realizes)
114-
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/BFO_0000055> "realizes"@en)
116-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000055> "this disease course realizes this disease"@en)
117-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000055> "this investigation realizes this investigator role"@en)
118-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/BFO_0000055> "this shattering realizes this fragility"@en)
119-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000600> <http://purl.obolibrary.org/obo/BFO_0000055> "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en)
120-
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/BFO_0000055> "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process")
121-
AnnotationAssertion(rdfs:isDefinedBy <http://purl.obolibrary.org/obo/BFO_0000055> <http://purl.obolibrary.org/obo/iao.owl>)
122-
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000055> "realizes"@en)
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ObjectPropertyDomain(<http://purl.obolibrary.org/obo/BFO_0000055> <http://purl.obolibrary.org/obo/BFO_0000015>)
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ObjectPropertyRange(<http://purl.obolibrary.org/obo/BFO_0000055> <http://purl.obolibrary.org/obo/BFO_0000017>)
125-
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# Object Property: <http://purl.obolibrary.org/obo/BFO_0000066> (occurs in)
127-
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/BFO_0000066> "occurs in"@en)
129-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/BFO_0000066> "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en)
130-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/BFO_0000066> "occurs_in"@en)
131-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/BFO_0000066> "unfolds in"@en)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/BFO_0000066> "unfolds_in"@en)
133-
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/BFO_0000066> "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant")
134-
AnnotationAssertion(rdfs:isDefinedBy <http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/bfo.owl>)
135-
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000066> "occurs in"@en)
136-
InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000067>)
137-
ObjectPropertyDomain(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000003>)
138-
ObjectPropertyRange(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000004>)
139-
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# Object Property: <http://purl.obolibrary.org/obo/BFO_0000067> (contains process)
141-
142-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/BFO_0000067> "site of"@en)
143-
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/BFO_0000067> "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en)
144-
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/BFO_0000067> "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant")
145-
AnnotationAssertion(rdfs:isDefinedBy <http://purl.obolibrary.org/obo/BFO_0000067> <http://purl.obolibrary.org/obo/bfo.owl>)
146-
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000067> "contains process"@en)
147-
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# Object Property: <http://purl.obolibrary.org/obo/RO_0000052> (characteristic of)
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15092
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/RO_0000052> "inheres in"@en)
@@ -327,11 +269,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000004> <http://purl.obolibrary.
327269
DisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000004> <http://purl.obolibrary.org/obo/BFO_0000020>)
328270
DisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000004> <http://purl.obolibrary.org/obo/BFO_0000031>)
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# Class: <http://purl.obolibrary.org/obo/BFO_0000006> (spatial region)
331-
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000006> "spatial region"@en)
333-
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000006> <http://purl.obolibrary.org/obo/BFO_0000141>)
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# Class: <http://purl.obolibrary.org/obo/BFO_0000015> (process)
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <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)
@@ -388,16 +325,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000034> <http://purl.obolibrary.
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AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <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)
389326
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000040> "material entity"@en)
390327
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000040> <http://purl.obolibrary.org/obo/BFO_0000004>)
391-
DisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000040> <http://purl.obolibrary.org/obo/BFO_0000141>)
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# Class: <http://purl.obolibrary.org/obo/BFO_0000141> (immaterial entity)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000141> "immaterial entity"@en)
396-
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000141> <http://purl.obolibrary.org/obo/BFO_0000004>)
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SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000066>) <http://purl.obolibrary.org/obo/BFO_0000066>)
400-
SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000050>) <http://purl.obolibrary.org/obo/BFO_0000066>)
401330
DLSafeRule(Body(ClassAtom(<http://purl.obolibrary.org/obo/BFO_0000016> Variable(<urn:swrl:var#d>)) ObjectPropertyAtom(<http://purl.obolibrary.org/obo/RO_0000053> Variable(<urn:swrl:var#e>) Variable(<urn:swrl:var#d>)))Head(ObjectPropertyAtom(<http://purl.obolibrary.org/obo/RO_0000091> Variable(<urn:swrl:var#e>) Variable(<urn:swrl:var#d>))))
402331
DLSafeRule(Body(ClassAtom(<http://purl.obolibrary.org/obo/BFO_0000019> Variable(<urn:swrl:var#d>)) ObjectPropertyAtom(<http://purl.obolibrary.org/obo/RO_0000053> Variable(<urn:swrl:var#e>) Variable(<urn:swrl:var#d>)))Head(ObjectPropertyAtom(<http://purl.obolibrary.org/obo/RO_0000086> Variable(<urn:swrl:var#e>) Variable(<urn:swrl:var#d>))))
403332
DLSafeRule(Body(ClassAtom(<http://purl.obolibrary.org/obo/BFO_0000023> Variable(<urn:swrl:var#d>)) ObjectPropertyAtom(<http://purl.obolibrary.org/obo/RO_0000053> Variable(<urn:swrl:var#e>) Variable(<urn:swrl:var#d>)))Head(ObjectPropertyAtom(<http://purl.obolibrary.org/obo/RO_0000087> Variable(<urn:swrl:var#e>) Variable(<urn:swrl:var#d>))))

‎src/ontology/lp.Makefile‎

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Original file line numberDiff line numberDiff line change
@@ -15,6 +15,22 @@ $(IMPORTDIR)/iao_import.owl: $(MIRRORDIR)/iao.owl $(IMPORTDIR)/iao_terms.txt
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$(ANNOTATE_CONVERT_FILE); fi
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$(IMPORTDIR)/bfo_import.owl: $(MIRRORDIR)/bfo.owl $(IMPORTDIR)/bfo_terms.txt \
19+
$(IMPORTSEED) | all_robot_plugins
20+
$(ROBOT) annotate --input $< --remove-annotations \
21+
odk:normalize --add-source true \
22+
extract --term-file $(IMPORTDIR)/bfo_terms.txt \
23+
--force true --copy-ontology-annotations true \
24+
--individuals include \
25+
--method BOT \
26+
remove $(foreach p, $(ANNOTATION_PROPERTIES), --term $(p)) \
27+
--term-file $(IMPORTDIR)/bfo_terms.txt $(T_IMPORTSEED) \
28+
--select complement --select annotation-properties \
29+
odk:normalize --base-iri https://w3id.org/lehrplan \
30+
--subset-decls true --synonym-decls true \
31+
repair --merge-axiom-annotations true \
32+
$(ANNOTATE_CONVERT_FILE)
33+
1834
CITATION="'Lehrplan Ontology. Version $(VERSION), https://w3id.org/lehrplan/ontology'"
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ALL_ANNOTATIONS=--annotate-defined-by false \

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