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OBI with workshop-revised COB demo #1834

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OBI with workshop-revised COB demo #1834

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9c7986c
Replace OMO import with versioned OMO import
sebastianduesing Oct 25, 2024
ced9b9a
Add OntoFox RO import and drop external-byhand
sebastianduesing Oct 25, 2024
04389c2
Prepare IAO import file
sebastianduesing Oct 25, 2024
07bf569
Remove BFO import
sebastianduesing Oct 25, 2024
972064d
Add import of revised COB
sebastianduesing Oct 25, 2024
5245b12
Relabel alternative term to alternative label in all templates
sebastianduesing Oct 28, 2024
eb9e87f
Replace inheres in and bearer of with characteristic of and has chara…
sebastianduesing Oct 28, 2024
5d7da15
Redirect CHEBI:atom references to COB:atom
sebastianduesing Oct 28, 2024
b03f544
Redirect CHEBI:molecular entity references to COB:molecule
sebastianduesing Oct 28, 2024
b79d55c
Obsolete OBI:device and redirect to COB:device
sebastianduesing Oct 31, 2024
97f0623
Obsolete OBI:organism and redirect to COB:organism
sebastianduesing Nov 1, 2024
13238a7
Obsolete OBI:planned process and redirect to COB:CEPP
sebastianduesing Nov 1, 2024
e83988f
Obsolete OBI:material processing and redirect to COB:material processing
sebastianduesing Nov 1, 2024
30c60b3
Line order update to obi-edit by Protege
sebastianduesing Nov 1, 2024
a850a9a
Remove BFO:0000001
sebastianduesing Nov 1, 2024
fb3c0f0
Remove BFO:0000002
sebastianduesing Nov 1, 2024
0bae0fd
Remove BFO:0000003
sebastianduesing Nov 1, 2024
082607d
Remove BFO:0000004
sebastianduesing Nov 1, 2024
4f065ec
Remove BFO:0000019
sebastianduesing Nov 1, 2024
40478c2
Remove BFO:0000020
sebastianduesing Nov 1, 2024
ad9bb8a
Remove BFO:0000028
sebastianduesing Nov 1, 2024
72981f0
Remove one usage of BFO:0000031
sebastianduesing Nov 1, 2024
2850a17
Line order update by Protege
sebastianduesing Nov 1, 2024
738995c
Remove BFO:0000035
sebastianduesing Nov 1, 2024
e840aac
Fix duplicate labels
sebastianduesing Nov 1, 2024
c9c6973
Obsolete OBI:processed material and redirect to COB:processed materia…
sebastianduesing Nov 1, 2024
e42f22b
Update version of COB
sebastianduesing Nov 6, 2024
547fbc8
Remove unused BFO_0000066
sebastianduesing Nov 6, 2024
e4b218a
Relabel terms in templates
sebastianduesing Nov 6, 2024
fb84f84
Import 'realized in'
sebastianduesing Nov 6, 2024
1a4ee1b
Fix weird quoting in assays.tsv
sebastianduesing Nov 6, 2024
ae0fc5b
Run make modules
sebastianduesing Nov 6, 2024
24558f1
Update OMO version
sebastianduesing Nov 13, 2024
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1 change: 1 addition & 0 deletions src/ontology/catalog-v001.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/cob/releases/2024-10-24/cob.owl" uri="https://raw.githubusercontent.com/OBOFoundry/COB/f2782d893faa87a2a9de41a1884e849d8bf628b9/cob.owl"/>
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@sebastianduesing Please try this again with my updates to OBOFoundry/COB#288

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Done; looks a lot better now.

<uri name="http://purl.obolibrary.org/obo/dev/obi_edit.owl" uri="obi-edit.owl"/>
<uri name="http://purl.obolibrary.org/obo/obi/dev/import/ChEBI_imports.owl" uri="OntoFox_outputs/ChEBI_imports.owl"/>
<uri name="http://purl.obolibrary.org/obo/obi/dev/import/CL_imports.owl" uri="OntoFox_outputs/CL_imports.owl"/>
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3 changes: 2 additions & 1 deletion src/ontology/obi-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/obi/dev/obi-edit.owl">
<owl:imports rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2024-10-24/cob.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/import/CLO_imports.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/import/CL_imports.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/import/COB_imports.owl"/>
Expand Down Expand Up @@ -58,6 +58,7 @@
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/specimen-assay-data.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/study-designs.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/modules/value-specifications.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.owl"/>
<protege:defaultLanguage>en</protege:defaultLanguage>
<obo:IAO_0000589 xml:lang="en">Ontology for Biomedical Investigations</obo:IAO_0000589>
<dc:contributor xml:lang="en">Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester</dc:contributor>
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