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Some FamPlex equivalences have missing namespace

Open bgyori opened this issue 4 years ago • 2 comments

Some of the target name spaces in the FamPlex equivalences file are not recognized and are replaced by None when processing the xrefs df. Example: MEDSCAN urn:agi-aopfc:0000458 is picked up as None:urn:agi-aopfc:0000458. Similarly IP (InterPro) entries are picked up as None:IPR008349. Where should the mapping of these be fixed? In get_famplex_xrefs_df or normalize_prefix, or some other place?

bgyori avatar Apr 22 '20 15:04 bgyori

Just found that there is already an entry in the metaregistry that should handle this but that doesn't appear to apply here:

https://github.com/pyobo/pyobo/blob/ba0db6df0b3f622b1d2dba8bf4a51a6a8bee31e1/src/pyobo/registries/metaregistry.json#L421-L424

bgyori avatar Apr 22 '20 16:04 bgyori

The interpro problem was solved with #42, now all we need to do is add MEDSCAN to the metaregistry and should also be solved.

cthoyt avatar Apr 22 '20 21:04 cthoyt