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Planteome / planteome-annotation-data

This is a place to discuss issues around the Planteome annotation data and store useful scripts etc.
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MaizeGDB GO annotations for Jan 2017 Release #1

Closed austinmeier closed 7 years ago

austinmeier commented 7 years ago

"We are looking at making a release in December that's before PAG. Therefore please seek MaizeGDB GO annotations especially manual ones now that will go in in this release. This subset should also be deposited by us in GO repositories and thus become a beta tester for GO services."

-PJ

jaiswalp commented 7 years ago

@cmungall do you have these GO annotation file.

cmungall commented 7 years ago

See https://github.com/geneontology/go-site/issues/233

monicacecilia commented 7 years ago

@jaiswalp and @cmungall I just sent the GAFs from MaizeGDB to both of you.

cmungall commented 7 years ago

Yes. Recall we identified syntactic errors with these and proposed a script that would tidy this up and feed back to source.

@elserj this is the script for validation http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/software/utilities/filter-gene-association.pl?view=log

cooperl09 commented 7 years ago

Both files are currently on the SVN (http://palea.cgrb.oregonstate.edu/viewsvn/associations/go-associations/) and loaded on dev.

I think it's a bit odd as the 'go_genemodel_MaizeGDB.assoc' file are all listed as proteins not gene_models- I think this is incorrect Compare with 'po_anatomy_gene_model_zea_MaizeGDB.assoc' or 'po_gene_model_li_Zea_POC.assoc'

cooperl09 commented 7 years ago

In the 'go_gene_MaizeGDB.assoc' the links out to MaizeGDB reference page is incorrectly formatted: MGDB_REF:3133112 It should be: MaizeGDB_REF:3133112

Also 'object name" is missing from column 10. This leaves it blank on the webpage: for example: http://dev.planteome.org/amigo/gene_product/MaizeGDB:GRMZM2G300066

Fixed

elserj commented 7 years ago

In the 'go_gene_MaizeGDB.assoc' the links out to MaizeGDB reference page is incorrectly formatted: MGDB_REF:3133112 It should be: MaizeGDB_REF:3133112

Fixed in svn.

cooperl09 commented 7 years ago

In the 'go_gene_model_MaizeGDB.assoc' file, the links out to MaizeGDB reference page are incorrectly formatted: example: MaizeGDB:13376 should be MaizeGDB_REF:13376 See: http://dev.planteome.org/amigo/gene_product/MaizeGDB:12359

Fixed

elserj commented 7 years ago

These seem to be all fixed up and loading without issues.