Fix the Allen ontologies used in composite-metazoan #3134
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Instead of generating the Allen ontologies (DHBA, DMBA, HBA, MBA, and PBA) locally using the JSON data obtained from the brain-map.org API, we use directly the ontologies pre-built by the Allen institute. This allows to treat those ontologies as any other "local imports". We also avoid storing them in OBO format, so that their non-OBO PURLs dont' get misinterpreted as OBO PURLs when reading the files with ROBOT.
All the Allen ontologies now use PURLs of the form "https://purl.brain-bican.org/ontology/xxxo/XXX_", so we must take care of using that prefix when 1) extracting the cross-references from the Uberon edit file and generating the mapping set, 2) generating the bridging axioms from the mappings.
Commit the new Allen imports (now in OFN format) and the re-generated bridge files (using the new purl.brain-bican.org PURLs).
matentzn
approved these changes
Dec 5, 2023
For reference, the apparent problems noted on that PR with unstable IDs are resolved by ensuring that the correct mappings between allen 'ontologies' and atlases. I think we can close. |
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This PR:
composite-*products: instead of generating the ontologies locally by processing JSON data obtained frombrain-map.org, we use the pre-built ontologies made available on https://github.com/brain-bican, as proposed in Revisit how the Allen ontologies are imported intocomposite-metazoan#3133;https://purl.brain-bican.org/ontology/dhbao/DHBA_XXXinstead ofhttp://purl.obolibrary.org/obo/DHBA_XXX).