2016 Los Angeles GOC Meeting Agenda

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Agenda

Follow-up on outstanding action items from previous GOC meeting in Geneva and Washington, DC

Informatics and Infrastructure 5 year plan

Can we have this on this first day? I will give up update on various changes Cjm (talk) 15:11, 5 October 2016 (UTC)

Annotation Metrics

  • Estimated time: 1 hour
  • What are the best metrics to assess progress in GO annotation?
    • Improved information content - how would that be measured?
    • Number of annotations
    • Number of references
    • Percentage of genome annotated vs percentage of genome with annotatable information?
  • How does LEGO modeling change our assessment of curator contributions?
  • Attribution of annotations to enable credit for:
    • Noctua annotations (This was discussed during LEGO call (http://wiki.geneontology.org/index.php/LEGO_September_19,_2016)
    • Multiple funding bodies (Ruth)
    • Distinguishing annotations that are created automatically, e.g. inference pipelines (Tony)
    • Individual curators attribution via Orcid IDs, it is important to establish if this wanted, and if it is wanted at what level of information? At an annotation by annotation level or just as a summation of contribution.

Protein Complexes

  • Estimated time: 1-2 hours
  • Overview of complex creation within Noctua https://vimeo.com/channels/noctua/148800722
  • What protein complexes should be in the Cellular Component branch of the ontology?
    • These were the action items from the 2015-09 Washington, D.C. meeting:
      • Action item: new evidence code for capturing complexes, child of IPI (ECO:0000353)
      • Action item: new evidence code for reconstituted biological system consisting of components of more than one species
      • Action item: Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included.

Regulation relations

Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. DOS: I would like to present progress on the development of the relevant relations along with a proposal for how to improve them. This would probably work best as a collaborative presentation with LEGO annotators where we can show application to LEGO models.

Genetic entities in GO annotation

  • What genetic entities do we need to refer to as the primary object of GO annotation and in extended forms of conventional or LEGO annotation?
  • What conventions should we enforce regarding which identifiers to use to refer to these genetic features and how?

Conference Calls and Communication

  • Estimated time: 15 minutes
  • Proposal to consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one GO call held weekly on Tuesdays at 8am PST
  • These areas of annotation, and ontology development, are, or have been, converging for some time now and we think it would be a better use of everyone's time to have one weekly call where we discuss any annotation- or ontology-related issues
  • Can we design new SOPS for mechanisms of communication
    • What is the best mechanism to alert annotation groups of changes to the ontology that will affect annotations? We have started a table of contacts, but is this how annotation groups would like to proceed?

Annotation Issues - Conventional Annotations

  • Modified protein binding: GO terms & annotations are very inconsistent.
    • Recent github issues:
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020
ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320
  • How are people capturing data where both direct assay AND protein motif/domains/sequence needs to be used by the curator to provide the annotation? [15 min Ruth, started by Rebecca] A system needs to be in place to enable the more specific annotations to be created for orthologous proteins (which cannot be done across all species with the IC evidence code)
    • eg transmembrane domain used as evidence to create the annotation 'integral to membrane' with IEA evidence; immunofluorescence localises protein to 'plasma membrane' (annotated with IDA evidence), ideal annotation to be created 'integral to plasma membrane'
    • 3 obvious options (any others?)
      • new evidence code IDD 'inferred by direct assay AND protein domain(sequence/motif?)' (would probably also want IMD, IGD, IED)
      • no new evidence code requires as this is implied by the 'inferred' aspect of the evidence code as well as 'author intent'
      • Create a GOC pipeline that creates the CC annotations based on the IDA annotation (eg plasma membrane) and the IEA information (eg integral to membrane) to create the more specific annotation (eg integral to plasma membrane).
  • Flowchart guidelines for transcription factor annotations [10 min Rachael/Ruth/Barbara]. To improve consistency UCL team have created an annotation flowchart which is being circulated to GOC members.
  • Protein families in terms
    • Currently the inclusion of protein family information in term names is leading to inconsistent annotation.
      • For now, the ontology editors have not been adding terms that specifically refer to protein families with the exception of signaling pathways. Should we make this a rule? If so, how will we capture the detail desired by annotators and how will we make this backward compatible?

Annotation Issues - LEGO Annotations (Sunday AM?)

  • How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?
  • Generating conventional annotations from Noctua models
    • Since Noctua models are a much more detailed and complete picture of the biology as a whole, we need to be able to process that Noctua information to generate gafs and gpad files from it. We should discuss progress about strategies to digest this information into the conventional annotation paradigms.
  • Are we going to allow Noctua to make annotations to the root nodes of the ontology?
    • This would be useful for contextual annotations that are to otherwise root nodes.
    • However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information.
    • Note that the evidence code for a root node annotation in Noctua would/could be different in that the curator might assert that a gene product has some molecular function due to the observation that, when mutated, there is a phenotypic outcome, e.g. apoptosis execution fails.
    • This is a different statement from no biological data (ND) in which there is no information at all to assert a role in any biological process.
  • MGI's experience roundtripping with Noctua Models (DPH)
  • Brainstorm about visualization of GO data.

Production

New data flow (Chris)