LEGO October 17, 2016

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Software Updates

Monday Morning Model Disappearance

  • We need to address the disappearing models on Monday mornings.

GAF/GPAD Updates

  • Still working on this with Wednesday group
  • Not all traditional GO annotations are being generated in the GAF/GPAD output

GPI Files

  • Specifications are decided; need to update documentation and share it with rest of GOC
  • 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

  • David presented Noctua to the PRO team last week.

Domain, Range Constraints for Relations in Noctua


Model Review

Tuesday Annotation Calls

  • Next annotation call is a consistency exercise from RGD.


  • Compile list of specific templates that would be useful to have.
  • Use github projects to manage creation of templates.


  • On call: David H, David OS, Giulia, Helen, Jim, Kimberly, Moni, Paul T., Sabrina, Seth, Stacia

Software Updates

Monday Morning Model Disappearance

  • A result of a fail in the AmiGO load - SOLR gets flushed periodically
  • Seth will manually fix this right now, but try to make Noctua model population independent of AmiGO build?
  • Models have not gone away, they just don't show up on the main Noctua landing page
  • Alternative way to get to models: open up Danger Zone link (this accesses minerva directly)
  • This will be permanently fixed by the GOC meeting


  • Still working on this on Wednesday calls
  • Not all traditional GO annotations are being generated
  • Only those annotations that are directly associated with an annoton are generated
    • AI: Check go-help question about GAF/GPAD - essentially when will GPAD annotations become available?

GPI Files

  • Specs are in place, just need to shore up documentation

Presentation to PRO

  • David presented Noctua/LEGO to PRO
  • Liked it but had two questions:
    • Are all annotations in LEGO?
    • How far across the property chains are annotations generated?

Importing Existing Biological Process and Cellular Component Annotations

  • See Paul's github ticket - detailed specs on how this might work
  • This is high priority

Domain and Range Constraints

  • Will be incorporated as part of Noctua
  • What will be the source for these?
  • Chris has implemented a client-side java reasoner - this affects what properties are available to the user



  • There are two templates to look at as examples
  • Specify templates and design patterns at the same time would be a good use of efforts
  • List of conserved processes that are good candidates for creating templates being put together by David and Kimberly

Presentation to AgBioData Consortium

  • Will present Noctua to this group

Model Review

  • Discussion of model on Rian lncRNA effects on transcription
  • Mechanism is not known, i.e. it's not known whether Rian activity is part_of transcription or regulates transcription
  • Therefore, the relation between Rian and transcription is causally_upstream_of_or_within
  • What is the effect on analysis if we do/do not include these kinds of annotations in GO?
  • These Rian-type models may be helpful for network analysis, but for detailed analysis of biology, maybe not so much
  • Should these annotations be included in the default annotation set?
    • Should less direct annotations be included in the default set?
  • Future iterations of AmiGO will allow users to more easily select different sets of annotations for their analyses
  • Additional causal relations will be included in GPAD, could also be included in the Qualifier column of the GAF
  • Another point about this model - the Rian molecular activity is connected to different transcriptional instances with multiple targets
    • Will we always need to clone the molecular activity for each instance when there is more than one input for the transcription?
    • What query use cases could address this question?