LEGO October 17, 2016

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

https://bluejeans.com/969313231

Agenda

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:
      • !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

• David presented Noctua to the PRO team last week.

Domain, Range Constraints for Relations in Noctua

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

Annotation

Tuesday Annotation Calls

• Next annotation call is a consistency exercise from RGD.

Templates

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

Minutes

• 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

GAF/GPAD Output

• 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

Annotation

Templates

• 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?