LEGO October 10, 2016

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Software Updates

  • Monday morning - no existing models visible after login
  • AmiGO build? If so, could there be a message displayed on the tool?

GAF/GPAD Updates

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:
      • 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


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.


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


  • 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