LEGO October 10, 2016

Bluejeans URL - NOTE NEW MEETING TIME: 8:00am PST

https://bluejeans.com/969313231

Agenda

Software Updates

• Monday morning - no existing models visible after login

GPI Files

• Review specifications
  • Groups will need to start submitting these files routinely, but there are still a few aspects of the specifications that need to be clarified and then documented on github, website
  • Chris' gpad-gpi docs on github
  • Kimberly's Google doc on gpi specs for website
  • Contents of header - what's required, what's optional, format for tag value-pairs, format for free text
    • Required:
      • !gpi-version: 1.2
    • Other possible tag value-pairs:
      • !Date: 20161010
      • !Project_name: WB
      • !Contact_email: help@wormbase.org
      • !URL: http://www.wormbase.org
      • !WB_release: WS256
    • Other possible content:
      • Explanation of gpi file fields
      • Explanation of entities represented, e.g. Reference Proteome
  • Contents of file - what's required, what's optional, format
    • Required fields are indicated in github doc, website
    • Entities needed for curation should be included in gpi file
    • Clarification needed on:
      • Entity namespace in Column 1?
      • DB Object Type - use SO terms (and IDs?) here?
      • Taxon prefix, i.e. 6239 or taxon:6239?
      • Parent IDs - always a gene? canonical protein and a gene?
      • DB_xrefs - are any DB_xrefs required?
        • MODs should include xrefs from genes to UniProtKB GCRP (Gene-Centric Reference Proteome) accessions? Reciprocal?
        • RNAcentral accessions for ncRNAs when possible
        • Protein/macromolecular complexes?
      • Gene Product Properties - anything required?
        • UniProtKB includes information on Swiss_Prot vs TrEMBL subset