GO-CAM Working Group Call 2018-06-26

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Meeting URL

https://stanford.zoom.us/j/976175422

Agenda

Logistics

Noctua

  • Landing Page (under development)
    • Browsing GO-CAMs
    • User and Group Pages
    • Curators should look around the landing page, provide feedback
      • Can now search using a PMID
      • Green paper icons beneath model titles; mouse over shows paper data
      • One question about presentation of author name(s) - first? last?

Documentation

Proposal for this group

  • Focus on specific, commonly used curation modules
    • For example, transcription, signaling pathways, metabolic pathways
  • Groups will annotate papers of their own choosing
  • We will discuss representation of the data in GO-CAMs, and any questions or issues that arise
    • Choosing the appropriate relation
    • Assigning evidence
  • Give feedback to tool developers, ontology editors based on our discussions
  • Develop additional documentation

Curation Project(s) for this Group

  • Will try creating models for papers that describe transcriptional regulation
  • A caveat to this is that right now the MF branch for transcription factors is still under review, so we may have to make some changes to annotations in the future
    • However, it would still be good to work out the relations between the MFs and the BPs wrt transcription and upstream and downstream activities and processes
  • Google doc for entering papers and curation questions
    • Sabrina - PMID:28687631 'Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.'
    • Kimberly - PMID: 28578929 'Morphological Diversity of C. elegans Sensory Cilia Instructed by the Differential Expression of an Immunoglobulin Domain Protein.'

Minutes

  • On call: Chris G, Chris M, Dave F, David H, Dustin, Edith, Giulia, Harold, Jim, Kevin, Kimberly, Laurent-Philippe, Li, Pascale, Paul T., Penelope, Rob, Sabrina, Sandy, Seth, Stacia, Stan, Suzi A

Logistics

  • Need to follow up about what the pipeline is for adding new users
  • Need to discuss how to manage occasional updates to groups, both from a policy POV and a technical POV

Noctua

  • Landing page - please test using link above
  • Provide feedback to Laurent-Philippe, if needed
  • For displaying author names, curators would prefer First Name, et al., since that is what people are most used to seeing in citations in papers

Annotation Discussion

References

  • Order of preference for reference IDs:
    • PMID
    • doi
    • GO_REF
    • MOD- or group-specific IDs
  • Why?
    • Using PMIDs wherever possible allows for easier display of papers associated with a model as the software can readily retrieve paper data using the PubMed API, as opposed to retrieving paper data from many different sources

Transcription

New Models vs Updating Older Models

  • In general, when there is new information about a process modeled as a GO-CAM, curators should try to update an existing model rather than create a new one
  • This allows us to build on existing knowledge to create the most comprehensive picture of a biological process rather than having multiple, distinct models that represent a snapshot of knowledge at the time a paper was published

Annotation Relations

  • 'directly activates ' vs 'directly positively regulates'
  • Are these two relations equivalent?
  • Right now, in RO, 'directly activates' is a child of 'directly positively regulates'
  • Should these two relations be merged? What is the distinguishing feature of each?

For Next Call - July 17th

  • Curators should continue to identify papers that they'd like to model for transcription factors and regulation of transcription
    • Particularly, look for papers that study single vs multiple TFs
  • We will review the three transcription template models above to make sure everyone understands the approach and the type of experimental evidence used to support the annotations