GO-CAM August 23, 2017

Zoom URL

https://stanford.zoom.us/j/679970729

Agenda

github Trackers

• Clarification about which one(s) to use
  • noctua - client and middleware code
  • noctua-models - annotation (may be merged with go-annotation)
  • minerva

Table Editor Workbench

• Chris and Seth will demo the new 'Simple annoton editor' workbench now available in Noctua
• The table editor allows curators to add, and edit, simple annotons in a table format
• Annotations entered in the table are automatically added to the Noctua graph editor

Annotation Provenance

• Review of how attribution is assigned for Noctua annotations
  • de novo annotations
  • imported annotations using function and component companions

Annotating with any UniProtID

• Use add individual functionality

Minutes

• On call: Chris, Harold, Karen, Kevin, Kimberly, Pascale, Paul T., Rob, Sabrina, Sage, Seth, Stacia, Suzi

New Noctua Features

• Curators can submit an issue to the github tracker from the Issues menu
  • Model will be automatically referenced in the github ticket and the github ticket number will be listed in the models menu
• Simple annoton editor
  • Curators are prompted to add an annoton, but can add distinct parts of the annoton, if needed
  • Will be prompted to add evidence and a reference
    • References are fairly neutral right now - can add PMIDs, GO_REFs - just need to have them be properly formatted (e.g., PMID:nnnnnnnn or GO_REF:nnnnnnnn)
  • Save annoton button adds the annoton to the graphical view, but curators still need to add a title and save their models in the graph view
• ACTION: Curators need to test the editor and give feedback.

Modeling in Noctua

• We discussed what the current modeling statements in Noctua actually mean
• For example, the model currently requires that a molecular_function is associated with a cellular component
• Is it possible to make a different type of statement in Noctua, or GO in general?
  • For example, a TF is observed in the cytoplasm, but it does not execute its MF there
• Curators should read Paul T.'s chapter about representation of function in the GO Handbook
• Can different localizations be annotated using different CC qualifiers?
• Counter-argument
  • Shouldn't GO just be focused on capturing where activities occur?
  • Adding more relations to CC could potentially generate another point for annotation inconsistency and noise
• One question: when would curators make an annotation to a CC and when not?
  • If you don't know anything about a protein but its localization, curators would typically make that CC
• There is a distinction between saying a protein localizes to a CC and likely functions there vs a protein localizes to a CC and we don't know if it actually has a function there
• This is a very fundamental question for GO - what information do we want to capture and why?
  • There are fundamental differences between the annotations that might result, say, from an HTP localization screen vs a well-studied gene for which we know exactly where and how it functions
• Should we use different qualifiers for CC?
• Should the GO supply different files with different qualifiers for our users?
• In terms of Noctua, what should the behavior be for simply adding a conventional CC annotation?
• ACTION ITEM: Draft different proposals for how to handle GO annotation statements going forward
  • Annotation of well-studied genes vs annotation of isolated observations and GO-CAM models vs conventional annotation
  • These proposals should be in place by the October GO meeting so we can discuss and make a decision
  • Stakeholders and considerations:
    • Developers
      • Tool development and maintenance
        • Changes to existing UI
      • Impacts on data storage
      • Impacts on annotation file generation
      • Impacts on data display
    • Curators
      • Efficiency of annotation
        • Capturing all data when reading a paper vs capturing only a defined subset of data
      • Consistency of annotation
        • Adding more relations increases the number of decision points during curation which could lead to more inconsistency, and could, at least temporarily, reduce efficiency
      • Dealing with legacy annotation
        • Individual groups could decide what is best for their annotation set
      • Need for clear curation guidelines
    • Users
      • Clarity in semantics of GO annotation
        • Precision of results in building genes sets (eliminating false positive and false negatives)
        • Informativeness of enrichment results and other summary analyses
      • Ease of use of GO data, i.e. would GO users effectively use different slices of GO annotation
      • Opportunities to use GO for different types of analyses
      • Communication and outreach if changes are made to current practice

Different annotation scenarios for Cellular Component

• • DPY-19 mannosyltransferase
    • endoplasmic reticulum - functional
  • ENU-3.6 - novel
    • cytoplasm - functional?? (not known, but no compelling reason to think it's not)
  • DAF-16 Forkhead TF
    • cytoplasm - sequestered, not functional
    • nucleus - functional
  • WNT3a - receptor agonist activity
    • endoplasmic reticulum lumen - trafficking, not functional
    • extracellular exosome - functional
  • HIST2H2AC - this is actually manually annotated to root MF, but has IBA and IEA for DNA binding
    • nucleus - functional
    • extracellular exosome - functional?? (not known, but no compelling reason to think it is)
  • NRAS - GTPase
    • Golgi apparatus - functional and trafficking, depending on context
    • membrane - functional
    • extracellular exosome - functional?? (not known, no compelling reason for either functional or non-functional)