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linkml / prefixmaps

Semantic prefix map registry
https://linkml.io/prefixmaps/
Apache License 2.0
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Upgrade Bioregistry import #33

Closed cthoyt closed 1 year ago

cthoyt commented 1 year ago

This PR updates the Bioregistry import to handle Bioregistry v0.6.0 and above. This new version makes it possible to specify a priority order for prefixes. It also implements better functionality for switching between modern and legacy Identifiers.org URIs.

This PR does not yet take advantage of prefix synonyms, since that would make the diff much larger and more complicated.

sierra-moxon commented 1 year ago

Thanks @cthoyt! I was just wandering down this path myself in trying to debug the "gro" test failure on my PR. :) Maybe my PR where the deprecated prefixes are excluded would help the tests pass here as well. https://github.com/linkml/prefixmaps/pull/32

sierra-moxon commented 1 year ago

Hi Charlie - I also thought about adding "gro/GRO" to a skip list, but I didn't want to hard-code something here. Is the "deprecated" flag meant differently in bioregistry? It seems like we don't want to promote the use of a deprecated prefix?

cthoyt commented 1 year ago

@sierra-moxon I think maintaining a short manual skip list is a better stop-gap than excluding all deprecated resources. It's surprising how many deprecated resources are still in wide use.

I'll take another look after this on why this prefix is having so many problems and hopefully eliminate the need for a skip list after merge of this PR.