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DO NOT MERGE remove or modify usages of non redundant relation graph output #33

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DO NOT MERGE remove or modify usages of non redundant relation graph output #33

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c2e9db1
DO NOT MERGE relation-graph 2.3 without non-dedundant
turbomam Feb 16, 2024
6e32478
Merge branch '30-use-semsql-download-to-download-released-envodb-inst…
turbomam Feb 16, 2024
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12 changes: 8 additions & 4 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -136,20 +136,24 @@ $(ONT)-relation-graph.owl: $(ONT).owl $(ONT)-merged-labels.ttl
# build relation-graph from nmdc-merged.ttl file
# for relation-graph see https://github.com/balhoff/relation-graph
# note, you may need to increase Java memory: export JAVA_OPTS=-Xmx16G

# --non-redundant-output-file $(ONT)-nonredundant.ttl \
# --redundant-output-file $(ONT)-redundant.ttl

@echo "\n** building $@ **"
relation-graph --ontology-file $< \
--reflexive-subclasses false \
--equivalence-as-subclass false \
--non-redundant-output-file $(ONT)-nonredundant.ttl \
--redundant-output-file $(ONT)-redundant.ttl \
--mode rdf
--mode rdf \
--output-file $(ONT)-relation-graph-raw.ttl
# merge in nmdco-merged for annotations
$(ROBOT) merge \
--input $(word 2, $^) \
--input $(ONT)-nonredundant.ttl \
--input $(ONT)-relation-graph-raw.ttl \
annotate --ontology-iri $(ONTBASE)/$@ \
$(ANNOTATE_ONTOLOGY_VERSION) \
--output $@
rm -f $(ONT)-relation-graph-raw.ttl

$(ONT).json: $(ONT)-relation-graph.owl
# convert ontology to json
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4 changes: 2 additions & 2 deletions src/ontology/imports/envo_import.owl
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Expand Up @@ -23,8 +23,8 @@
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:process_attribute="http://purl.obolibrary.org/obo/envo-p/patterns/process_attribute/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmdco/imports/envo_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2024-02-15/imports/envo_import.owl"/>
<owl:versionInfo>2024-02-15</owl:versionInfo>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2024-02-16/imports/envo_import.owl"/>
<owl:versionInfo>2024-02-16</owl:versionInfo>
</owl:Ontology>


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4 changes: 2 additions & 2 deletions src/ontology/imports/po_import.owl
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Expand Up @@ -15,8 +15,8 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmdco/imports/po_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2024-02-15/imports/po_import.owl"/>
<owl:versionInfo>2024-02-15</owl:versionInfo>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2024-02-16/imports/po_import.owl"/>
<owl:versionInfo>2024-02-16</owl:versionInfo>
</owl:Ontology>


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4 changes: 2 additions & 2 deletions src/ontology/imports/ro_import.owl
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Expand Up @@ -20,8 +20,8 @@
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmdco/imports/ro_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2024-02-15/imports/ro_import.owl"/>
<owl:versionInfo>2024-02-15</owl:versionInfo>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmdco/releases/2024-02-16/imports/ro_import.owl"/>
<owl:versionInfo>2024-02-16</owl:versionInfo>
</owl:Ontology>


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