Manager 1July2015: Difference between revisions

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Kimberly and Rama talked about the next steps (make a GAF file, a config file, gp2protein file etc). Once they are ready with the files those taxons will be filtered out of the GOA file.
Kimberly and Rama talked about the next steps (make a GAF file, a config file, gp2protein file etc). Once they are ready with the files those taxons will be filtered out of the GOA file.


===Report from C. elegans Meeting - UCLA 2015 (Kimberly)===
===Report from 2015 ''C. elegans'' Meeting - UCLA (Kimberly)===
*We were asked to provide transcript-centric GAFs.  It would be nice to offer up different versions of the GAF on the GO site.
*We were asked to provide transcript-centric GAFs.  It would be nice to offer up different versions of the GAF on the GO site.
*We also got feedback on the redundancy of annotation in our GAFs wrt annotations to both parent and child (often because of overlapping automated vs manual annotations).  Explore ways to provide select set of granular annotations in yet additional versions of the GAF?  Pros? Cons? What do other groups do wrt this issue?
*We also got feedback on the redundancy of annotation in our GAFs wrt annotations to both parent and child (often because of overlapping automated vs manual annotations).  Explore ways to provide select set of granular annotations in yet additional versions of the GAF?  Pros? Cons? What do other groups do wrt this issue?
*Users would like to perform Term Enrichment with Phenotypes and the Worm Phenotype Ontology - a possible extension to PANTHER tools?  Phenotype term enrichment would be a great complement to GO term enrichment.
*Users would like to perform Term Enrichment with Phenotypes and the Worm Phenotype Ontology - a possible extension to PANTHER tools?  Phenotype term enrichment would be a great complement to GO term enrichment.

Revision as of 12:55, 30 June 2015

Agenda

Minting DOIs for GO_REFs (Rama)

Mike Cherry now has the power to mint (create) DOIs. We should create DOIs for GO_Refs so referring to them is easy etc.

Obsoleting relationships (Rama)

  • We need to have a process in place to obsolete relationships (like we do for GO terms)
  • There should be one master file and all other tools/files should be in sync with that file (should the master file be gorel.obo?)

GAF for New worm species (Rama)

WormBase will be submitting annotation files for some additional species, namely:

Onchocerca volvulus
Brugia malayi
Strongyloides ratti
C. briggsae

Kimberly and Rama talked about the next steps (make a GAF file, a config file, gp2protein file etc). Once they are ready with the files those taxons will be filtered out of the GOA file.

Report from 2015 C. elegans Meeting - UCLA (Kimberly)

  • We were asked to provide transcript-centric GAFs. It would be nice to offer up different versions of the GAF on the GO site.
  • We also got feedback on the redundancy of annotation in our GAFs wrt annotations to both parent and child (often because of overlapping automated vs manual annotations). Explore ways to provide select set of granular annotations in yet additional versions of the GAF? Pros? Cons? What do other groups do wrt this issue?
  • Users would like to perform Term Enrichment with Phenotypes and the Worm Phenotype Ontology - a possible extension to PANTHER tools? Phenotype term enrichment would be a great complement to GO term enrichment.