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strategy for prefixcommons-py wrapping or otherwise aligning with bioregistry #24

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sierra-moxon opened this issue Aug 11, 2022 · 1 comment

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@sierra-moxon
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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

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cthoyt commented Aug 12, 2022

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).

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