QC: syntax for DB xrefs

[pombase-admin]

Putting this at low priority, but it might be worth doing at some point. It seems we will still need to use artemis for a while for some annotations (GO ISO) and community curations which can contain IDs

The GO DB -xrefs file has some syntax description see local_id_syntax: ^[0-9]{9}$ which could be used to identify any problem ones and report in the logs (I manually fixed a load of SGD IDs in the "with" field last week where I had typed too many zeros, or truncated the last digit....)

abbreviation: PR database: Protein Ontology object: Identifer synonym: PRO example_id: PR:000025380 local_id_syntax: ^[0-9]{9}$ generic_url: http://www.proconsortium.org/pro/pro.shtml url_syntax: http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:[example_id] url_example: http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:000025380 entity_type: PR:000000001 ! protein

HTML access to list: http://geneontology.org/doc/GO.xrf_abbs

Original comment by: ValWood

[ValWood]

Action here is to check that any IDs we use match the syntax defined in GO DB -xrefs file

eg. abbreviation: PR cal_id_syntax: ^[0-9]{9}$

this would find some malformed IDs that might have been cut and pasted incorrectly.... I don't think there will be many so it isn't high priority, but it is is quick it is a nice QC check to have.

[ValWood]

seems to overlap with https://github.com/pombase/pombase-chado/issues/614 ?

[ValWood]

is this done? 614 now closed...

[kimrutherford]

It's not done. We're not using the GO xrefs file yet.

[ValWood]

http://curation.pombase.org/pombe/view/list/db?model=chado

[ValWood]

Is this still pending?

[kimrutherford]

This is not done yet.