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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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PAINT annotations to budding yeast GTT1 #48

Closed srengel closed 6 years ago

srengel commented 7 years ago

GTT1 is an ER-associated glutathione transferase.

it has PAINT annotations to nucleus and translation elongation factor activity. can someone please check these? they seem to be in error.

thanks, stacia

pgaudet commented 7 years ago

Hi Stacia,

This is odd. This protein was annotated as NOT nucleus, see http://pantree.org/node/annotationNode.jsp?id=PTN000136573

However in the yeast species specific file (http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/gene-associations/submission/paint/pre-submission/gene_association.paint_sgd.gz?revision=37505) the NOT seems to have been lost. @selewis @cmungall - who is responsible for the conversion script ?

Thanks, Pascale

selewis commented 7 years ago

Hi - would help a lot to include IDs (i.e. for family, go term, and protein). Maybe asking too much but it adds an extra step to figure out exactly what is being discussed. (e.g. PTHR11260, GO:0005634, and P29547)

Anyhoo - at this point in PANTHER v11, many of the experimental annotations are no longer found in this family. The original annotation was (in part) based on SGD:S000005969's annotation to nucleus http://amigo.geneontology.org/amigo/gene_product/SGD:S000005969. Same for translation elongation factor from SGD:S000001564 (it is in the same branch as GTT2, but very far removed from GTT1).

This is another very big family. Maybe it is me, but it seems like many (most?) of the issues we see are happening in big families

@pgaudet this really needs review because the trees have significantly changed since this was originally annotated.

I've yet to see anything lost in the conversion scripts. It would be almost impossible since the script merely copies an entire line from one file and puts it into another file.

pgaudet commented 6 years ago

@huaiyumi Dis you reannotate the tree ? (next time can you please make a comment when you close a ticket)

Thanks, Pascale