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New composite pipeline #3129

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merged 20 commits into from
Dec 1, 2023
+515,756 −265,956
Merged

New composite pipeline #3129

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c51c93d
Remove UBERON-modifying axiom in local copy of CEPH.
gouttegd Nov 28, 2023
d9e0a7f
Factor conditional test in the LOCAL section.
gouttegd Nov 28, 2023
4153ddb
Treat the Allen ontologies as "local imports".
gouttegd Nov 28, 2023
7f57fb9
Treat CL, SSSO, and ZFA as "local imports".
gouttegd Nov 28, 2023
2c625f0
Fix the custom rules for downloading mirrors.
gouttegd Nov 29, 2023
1c22eee
Add a mirror for the "SSSO" ontology.
gouttegd Nov 29, 2023
b6bacf7
Simplify treatment of "local imports".
gouttegd Nov 29, 2023
9250d1e
Simplify treatment of EMAPA local import.
gouttegd Nov 29, 2023
1727ffe
Store local imports in OFN format.
gouttegd Nov 29, 2023
56e7d9d
Properly import MmusDv and HsapDv.
gouttegd Nov 29, 2023
ec4c753
Allow quickly refreshing all "local" imports.
gouttegd Nov 29, 2023
2a828ff
Fix more old-style properties.
gouttegd Nov 29, 2023
273299e
Overhaul the composite pipeline.
gouttegd Nov 29, 2023
7bdaf40
Update the XML catalog.
gouttegd Nov 29, 2023
d35e419
Add title and description to the composite- products.
gouttegd Nov 30, 2023
ad1eadb
Turn collected-metazoan.owl into a release artefact.
gouttegd Nov 30, 2023
8064a50
Remove old "collected" files.
gouttegd Nov 30, 2023
13517a8
Cleaning up Makefile.
gouttegd Nov 30, 2023
441fb39
Commit "local" imports.
gouttegd Nov 30, 2023
6849142
Ignore top-level collected-metazoan.
gouttegd Nov 30, 2023
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -194,6 +194,7 @@ composite-metazoan.*
composite-metazoan-basic.*
composite-vertebrate.*
composite-vertebrate-basic.*
collected-metazoan.*
ext.json
ext.obo
ext.owl
Expand All @@ -215,4 +216,4 @@ src/ontology/subsets/*.json
src/ontology/subsets/*.obo
src/ontology/subsets/*.owl
src/ontology/subsets/*.tsv
src/ontology/imports/*_import.owl
src/ontology/imports/*_import.owl
11 changes: 10 additions & 1 deletion src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.

FORMATS = $(sort owl obo json owl)
FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )

# ----------------------------------------
# Top-level targets
Expand Down Expand Up @@ -706,6 +706,12 @@ basic.json: basic.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
mv [email protected] $@
collected-metazoan.obo: collected-metazoan.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
collected-metazoan.json: collected-metazoan.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
mv [email protected] $@
composite-metazoan.obo: composite-metazoan.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
composite-metazoan.json: composite-metazoan.owl
Expand Down Expand Up @@ -810,6 +816,9 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION
basic.owl:
echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false

collected-metazoan.owl:
echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false

composite-metazoan.owl:
echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false

Expand Down
75 changes: 0 additions & 75 deletions src/ontology/bridge/catalog-v001.xml
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51 changes: 51 additions & 0 deletions src/ontology/bridge/collected-adult-mammal-hdr.owl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/uberon/bridge/collected-adult-mammal.owl#"
xml:base="http://purl.obolibrary.org/obo/uberon/bridge/collected-adult-mammal.owl"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/collected-adult-mammal.owl">
<terms:creator>Uberon editors</terms:creator>
<terms:description>This is an ontology that collects all of the core Uberon, plus the adult anatomy ontology for mouse (MA). Note that it does no longer include the adult anatomy ontology for human (FMA).</terms:description>
<terms:title>Collected anatomy ontology for post-natal mammals</terms:title>
<rdfs:comment>Uberon ontologies with the prefix ‘collected’ are ontologies that import the core Uberon ontology together with one or more external, typically species-centric, ontologies plus bridging axioms that connect Uberon to those external ontologies. Uberon ontologies with the prefix ‘composite’ are variations of the corresponding ‘collected’ ontologies with additional reasoning performed.</rdfs:comment>
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://genomebiology.com/2012/13/1/R5</rdfs:seeAlso>
</owl:Ontology>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://purl.org/dc/terms/creator -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/creator"/>



<!-- http://purl.org/dc/terms/description -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description"/>



<!-- http://purl.org/dc/terms/title -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title"/>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

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