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obophenotype / brain_data_standards_ontologies

A repository for co-ordinating work on ontologies for the Brain Data Standards Project
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Automated obsoletion of old pCL terms #216

Closed shawntanzk closed 2 years ago

shawntanzk commented 2 years ago

Steps needed for obsoletion: 1) add owl:deprecated "true" assertion using this pattern: AnnotationAssertion(owl:deprecated obo:pCL_XXXXXX "true"^^xsd:boolean) 2) Remove all equivalence axioms 3) Remove all subclass axioms 4) add "obsolete" in front of the rdfs:label (eg "obsolete gamma-glutamyltransferase activity") <- Note: case-sensitive 5) add "OBSOLETE." in front of defintion (eg "OBSOLETE. Catalysis of the reaction: (5-L-glutamyl)-peptide + an amino acid = peptide + 5-L-glutamyl-amino acid.") 6) add rdfs:comment "this term has been obsoleted and replaced by an updated term from the Brain Data Standards ontology, please see 'term replaced by' axiom to for new term" 7) add 'term replaced by' axiom that maps to new term following this pattern - the first pCL ID being the one to be obsoleted, the second being the term it is being replaced by: AnnotationAssertion(obo:IAO_0100001 obo:pCL_XXXXXX "pCL_XXXXXX"^^xsd:string)

shawntanzk commented 2 years ago

For mappings (step 7): 1) Create a spreadsheet with the following columns by trying to automatically map synonym (pCL to be deprecated) to prefLabel (in BDSO)

deprecated pCL ID synonym preferred_name ID mapped to
pCL_0000370 Astro FGFR3 NWD1 CCDC129-expressing marmoset primary motor cortex astrocyte pCL_XXXXXXX

2) @shawntanzk will then fill up the rest that cannot be mapped automatically

hkir-dev commented 2 years ago

PCL legacy ontology released: https://github.com/obophenotype/brain_data_standards_ontologies/blob/pcl_migration/pcl-legacy.owl

shawntanzk commented 2 years ago

merge legacy into main file -> we need the obsoletion in base file when we export it as a component

hkir-dev commented 2 years ago

legacy merged to main (and all_templates.owl) https://github.com/obophenotype/brain_data_standards_ontologies/blob/pcl_migration/bdso-base.owl plc-legacy.owl is now a component: https://github.com/obophenotype/brain_data_standards_ontologies/blob/pcl_migration/src/ontology/components/pcl-legacy.owl