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geneontology / paint

This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
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column 2: DB Object ID in TAIR files #33

Closed tberardini closed 6 years ago

tberardini commented 7 years ago

http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/gene-associations/submission/paint/pre-submission/gene_association.paint_tair.gaf

In this most recent file, there are two variations on the information present in column 2. Here's one example of each: (AT3G51730 vs. locus:2014922)

TAIR AT3G51730 T18N14.110 GO:0008047 PAINT_REF:11480 IBA PANTHER:PTN001352635 F UniProtKB:Q9SCT5|PTN000159460 protein taxon:3702 20150818 GO_Central

TAIR locus:2014922 LSM3A GO:0000932 PAINT_REF:13110 IBA PANTHER:PTN000318821 C AT1G21190 UniProtKB:Q9LMN4|PTN000318877|TAIR:AT1G21190|F16F4.12|AT1G21190|SM-like 3A|F16F4_12 protein taxon:3702 20150709 GO_Central

Why are there some of this kind, AT3G51730? We expect everything to look like this, locus:2014922.

Thanks for your insight.

selewis commented 7 years ago

It is dependent on when the family-gaf files were produced, older ones used the ATxxxxxxx ID. Once touchup is finally run these should all be of the preferred form. I'll leave the issue open until touchup is run.

tberardini commented 7 years ago

Thanks for the update. I'll keep my eyes open for the notification about the touchup run.

tberardini commented 6 years ago

Has the touchup been run? If so, where are the resulting new files? I looked here:

http://geneontology.org/gene-associations/submission/paint/pre-submission/

and here

http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/gene-associations/submission/paint/pre-submission/

but those files are from May of 2017.

huaiyumi commented 6 years ago

@tberardini The location of updated gafs can be found in the yaml file below: https://github.com/geneontology/go-site/blob/master/metadata/datasets/paint.yaml

tberardini commented 6 years ago

Thanks for the pointer, @huaiyumi .