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prefixcommons / biocontext

JSON-LD Contexts for Bioinformatics Data
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identifiers.org breaking change in IRIs (WB, FB, Panther and probably other don't resolve correctly) #34

Open lpalbou opened 3 years ago

lpalbou commented 3 years ago

This relates to the jsonld file (eg https://github.com/prefixcommons/biocontext/blob/master/registry/go_context.jsonld) used for CURIE <-> IRI conversions.

WB:WBGene00006575 is translated in http://identifiers.org/wormbase/WBGene00006575 which used to redirect to the real WB page https://wormbase.org/species/c_elegans/gene/WBGene00006575#0-9f-10.

But this IRI (http://identifiers.org/wormbase/WBGene00006575) doesn't resolve anymore to a valid identifiers.org pattern. After double checking, the correct IRI would now be https://identifiers.org/WB:WBGene00006575.

For uniquely identifying resources, it doesn't change anything (our past IRIs haven't changed), but for resources that were relying on identifiers.org IRI to resolve and link out to actual websites, this is a breaking change and side effects would have to be investigated.

cmungall commented 3 years ago

identifiers.org accepts both slash and colon forms http://identifiers.org/wb/WBGene00006575

but yes, it;'s unfortunate id.org and go use different prefixes wb/wormbase

cmungall commented 3 years ago

I think this is resolved by fixing upstream

https://github.com/geneontology/go-site/blob/09eb2dbdc4c71565528a2802d0591ba6b8f45fcc/metadata/db-xrefs.yaml#L2713

should be http://identifiers.org/wb/

cmungall commented 3 years ago

a lot of these are wrong

https://github.com/geneontology/go-site/blob/09eb2dbdc4c71565528a2802d0591ba6b8f45fcc/metadata/db-xrefs.yaml#L2852

should be http://identifiers.org/zfin/

lpalbou commented 3 years ago

Independent, but also noticed a missing "/" for NCBIGene. Fixed here: https://github.com/geneontology/go-site/commit/12f2a3850473d901a7112d3b7ce8c5b2316be83e