GO-CAM Working Group Call 2018-06-26: Difference between revisions

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*Landing page - please test using link above
*Landing page - please test using link above
*Provide feedback to Laurent-Philippe, if needed
*Provide feedback to Laurent-Philippe, if needed
== Annotation Discussion ==
=== Transcription ===
*Sabrina presented a paper and model on the clock1a transcription factor and its regulation of smad gene expression
*We discussed what the correct representation of this transcriptional regulation would be
*Models that Paul T. and Astrid have worked on wrt modeling transcription regulation by single vs multiple transcription factors:
**[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000179 Template for single transcription factor activity]





Revision as of 12:23, 26 June 2018

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

Annotation Discussion

Transcription

  • Sabrina presented a paper and model on the clock1a transcription factor and its regulation of smad gene expression
  • We discussed what the correct representation of this transcriptional regulation would be
  • Models that Paul T. and Astrid have worked on wrt modeling transcription regulation by single vs multiple transcription factors: