Difference between revisions of "Manager 1July2015"

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(Report from C. elegans Meeting - UCLA 2015 (Kimberly))
(Agenda)
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===Minting DOIs for GO_REFs (Rama)===
 
===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.
 
Mike Cherry now has the power to mint (create) DOIs. We should create DOIs for GO_Refs so referring to them is easy etc.
 +
 +
===Evidence code for Inferences made from inter-ontology links===
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There will be a new ECO term for this inferencing pipeline. The GO ID will be in the with/from column. IEA will be used in regular GAFs and ECO in the GPAD. We need to let people know about the use of IEA for this inferencing.
  
 
===Obsoleting relationships (Rama)===
 
===Obsoleting relationships (Rama)===

Revision as of 20:25, 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.

Evidence code for Inferences made from inter-ontology links

There will be a new ECO term for this inferencing pipeline. The GO ID will be in the with/from column. IEA will be used in regular GAFs and ECO in the GPAD. We need to let people know about the use of IEA for this inferencing.

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.