Manager 1July2015

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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)
    • Clarification request from Chris: I think you mean relations/ObjectProperties (e.g. 'part of') rather than actual relationships (nucleus part_of cell)?
  • 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.


DOIs for GO_REFs:

  • cjm:
  • ID mapping issue
  • we will investigate better ways to manage GO_REFs [cjm]
  • suzi: make sure we take PAINT REFs into consideration


  • For now we will keep IEA
  • cjm: people use IEA as proxy for quality
  • pascale: IEA is most accurate description
  • mc: Marcus has the ECO ticket, he has a few questions
  • After this
  • Moni: remember to update documentation
  • Rama: first Marcus, then switch the scripts, make the announcement, change docs


  • Rama: we are moving drupal machine in amazon cloud, don't edit the site today

Obsoleting relationships

  • we are a bit confused
  • mc: P2GO loads on a daily basis
  • suzi: Tony should take snapshot
  • rama: P2GO may be loading a different file?
  • kimberley: need to clarify what happens with Tony on the P2GO end
  • mc: will follow-up
  • mc: DOS has code to keep wiki in sync with ontology
  • cjm: sounds like DOS and MC are on top of this
  • suzi: what about replacements
  • mc: if 1:1 replacement will happen automatically
  • rama: how is the file maintained
  • action: obsoletions should be announced in advance

Worm GAFs

  • WB will be authority
  • Action: change Mikes script
  • Suzi: we will migrate Mikes script to Jenkins
  • cjm: are all these in QfO?
  • paulT: no, but this OK, so long as representative in larger ref proteome set
  • Kimberley: Jane in convo with UniProt, get the remaining two in
  • Kimberley will check with cjm when ready to make the new GAFs
  • Kimberley: will be many more nematode genomes. Automate svn? cjm: split files into wb (elegans) and wb_other?
  • Suzi: worm specific PAINT
  • Paul: building tool to make inferences for species not in the tree
  • Judy: new genomes, not just nematodes, need to be sure we can manage this data
  • need to think about files

transcript files

  • Provide on main GO site, but in directory that clearly denotes that this may not be provided forever. WB would be responsible for generating.
  • Redundancy