Curate remaining entries to the Bioregistry

[cthoyt]

After lots of careful curation, there are only four resources listed in this repository that I can't quite figure out

datasource_name	system_code	website_url	linkout_pattern	example_identifier	entity_identified	single_species	identifier_type	uri	regex	official_name	wikidata_property	bioregistry
Gramene Arabidopsis	EnAt	http://www.gramene.org/	http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id	ATMG01360-TAIR-G	gene	Arabidopsis thaliana	1	EnAt	AT[\dCM]G\d{5}-TAIR-G	Gramene Arabidopsis	nan	nan
Gramene Maize	EnZm	http://www.ensembl.org	http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id	GRMZM2G174107	gene	nan	1	EnZm	nan	Gramene Maize	nan	nan
Gramene Rice	EnOj	http://www.gramene.org/	http://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=$id	osa-MIR171a	gene	nan	1	EnOj	nan	Gramene Rice	nan	nan
Rice Ensembl Gene	Os	http://www.gramene.org/Oryza_sativa	http://www.gramene.org/Oryza_sativa/geneview?gene=$id	LOC_Os04g54800	gene	Oryza sativa	1	Os	nan	Rice Ensembl Gene	nan	nan

Example URLs:

• http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=ATMG01360-TAIR-G (works, but should just be ATMG01360)
• http://www.maizesequence.org/Zea_mays/Gene/Summary?g=GRMZM2G174107 (redirects to https://ensembl.gramene.org/Zea_mays/Gene/Summary?g=GRMZM2G174107)
• http://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=osa-MIR171a (dead)
• http://www.gramene.org/Oryza_sativa/geneview?gene=LOC_Os04g54800 (dead)

So the question is for the first two, what should we call these in Bioregistry? should they really get their own prefixes or is there a more general Gramene resolver for all of these IDs?

For the last two, can these be fixed? Maybe just need a new example from the same pattern.

[cthoyt]

@egonw these are the ones that aren’t complete

[DeniseSl22]

@mkutmon @Finterly : could you please check these databases, if they're used in any GPML?

[DeniseSl22]

And @tabbassidaloii : could you check if the databases above are part of our new BridgeDb mapping files?

[tabbassidaloii]

We have mapping files for Arabidopsis thaliana (At), Zea mays (Zm), Oryza sativa japonica (Oj), and Oryza sativa indica (Oi).

[egonw]

We have mapping files for Arabidopsis thaliana (At), Zea mays (Zm), Oryza sativa japonica (Oj), and Oryza sativa indica (Oi).

@tabbassidaloii, but do we have mappings on those to Gramene?

[Chris-Evelo]

FWIW I think these pathways were created by the Gramene team at the time.

[tabbassidaloii]

Gramene

@egonw No, we don't. Not sure if BioMart provides it.