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
• AmiGO build? If so, could there be a message displayed on the tool?

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
      • !Date: 2016-10-10
    • Other possible tag value-pairs:
      • !Project_name: WB
      • !Contact_email: help@wormbase.org
      • !URL: http://www.wormbase.org
      • !Release: WS256
    • Other possible content:
      • Explanation of gpi file fields
      • Explanation of entities represented, e.g. Reference Proteome
      • Explanation of specific DB_xrefs included
  • 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? - YES
      • 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

Use of PRO Identifiers for Modified Forms of Proteins

• The dictyBase annotation consistency exercise model was a good example of where we might like to be able to annotate to modified forms of proteins, e.g. GTP-bound Ras
• For consistency, do we want to make this required? What/How would that be indicated in a template?
• What work needs to be done with PRO to prepare for this if we decide to go that route?

Domain, Range Constraints for Relations in Noctua

• Updates?
• https://github.com/geneontology/noctua/issues/358

Annotation

Tuesday Annotation Calls

• We will discuss the latest version of the dictyBase annotation consistency exercise on tomorrow's (2016-10-11) annotation call.
• Will try to incorporate more LEGO discussion into Tuesday annotation calls.

Templates

• Compile list of specific templates that would be useful to have.

Minutes

• On call: Chris, David, Giulia, Helen, Jim, Kimberly VA, Moni, Ruth, Sabrina, Seth, Stacia, Suzi

AmiGO build fails and Noctua

• When an AmiGO build fails, no models are visible on Noctua
• Seth may be able to set up a 'Don't worry' message to explain what happened for tool users

Software Updates

GAF/GPAD Updates

• Reasoner can show all inferred relations in the graphical editor
  • These relations are not wrong, but we wouldn't normally have made them
• Not all relations need to be shown, though
• Next step is to work on the GAF output with the select relations
• Models and desired GAF/GPAD output are being collected in the minerva repository on github
• Some of our traditional annotation rules are violated with LEGO models
  • We will need to re-visit some of these rules to see if we need to change them
    • TAS for protein binding
    • IEP for cellular component

GPI File Specifications

• Different specs available depending upon where you look
• Just need to keep this as a markdown in github
• website specs could be simplified with the more detailed specs available for developers
• Required gpi fields:
  • !gpi-version: 1.2
  • !Date: 2016-10-10