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PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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Use namespaces instead of preferred names when normalizing Xref.db values #307

Closed IgorRodchenkov closed 3 months ago

IgorRodchenkov commented 5 years ago

I now think that using Identifiers.org namespaces bioregistry.io prefix instead of the preferred name when normalizing Xrefs would be a better approach (Although BioPAX L3 docs recommend using standard names from MIRIAM or MI "database citation", that was before identifiers.org bioregistry.io registry emerged.)

For example, xref.db will contain "uniprot.isoform" instead "Uniprot Isoform" and "uniprot" instead "uniprot protein", which is usually shorter and also makes creating bio entity/resource URLs from Xrefs straightforward: https://identifiers.org/<xref.db>/<xref.id>, not requiring extra steps to resolve a name to namespace.

IgorRodchenkov commented 3 months ago

Done that - will be in PC v14 release.