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prefixcommons / prefixcommons-py

Prefix commons python utlities
BSD 3-Clause "New" or "Revised" License
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strategy for prefixcommons-py wrapping or otherwise aligning with bioregistry #24

Open sierra-moxon opened 2 years ago

sierra-moxon commented 2 years ago

Can we outline a strategy for prefixcommons in light of bioregistry? https://bioregistry.io/ Should contexts be generated from bioregistry?
Should we preserve this code base as a wrapper? @cmungall @cthoyt

cthoyt commented 2 years ago

The Bioregistry automatically generates some contexts https://github.com/biopragmatics/bioregistry/tree/main/exports/contexts. This includes ones based on curated prefix lists in https://bioregistry.io/collection/ as well as "prescriptive" contexts listed in https://bioregistry.io/context/ that I piloted with @matentzn. We took great care to enable specifying the domain-specific assumptions in the OBO community to automatically process the canonical Bioregistry prefixes and URIs. I think we'd face some difficulties doing this for the monarch context because it's the case that a lot of things in the monarch context can't be matched to anything in the Bioregistry (nor should it, given many of them have either questionable prefixes and or URIs).