Signalling Workshop Agenda

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Signaling Workshop Agenda


  • Ruth (UCL) will chair the morning session; Kimberly (WB) will chair the afternoon session

Meeting Schedule

Time Item Minutes
9:00am - 9:15am Opening Remarks - Ruth (UCl) Val (PomBase)
9:20am - 9:45am Summary of Approach to Analysis and Project Organization - David H. (MGI) and Kimberly (WB) Val (PomBase)
9:50am - 10:50am Canonical Wnt Signaling - Helen (FB) and Kimberly (WB) Val (PomBase)
11:00am - 11:30am BREAK na
11:30am - 12:30pm MAPK Signaling - David H. (MGI) and Sabrina (ZFIN) Ruth (UCL)
12:30pm - 1:30pm LUNCH na
1:30pm - 2:30pm GPCR Signaling - Pascale (SIB) and Petra (dictyBase)
2:30pm - 3:00pm JAK/STAT Signaling - Giulia (FB) and Ruth (UCL) Pascale (SIB)
3:00pm - 3:30pm Ca2+ Signaling involved in Mammalian Fertilization - Penelope (UniProt) Sabrina (ZFIN)
3:30pm - 4:00pm BREAK na
4:00pm - 5:00pm Discussion

General Outline for Presentations

  • Since the different signaling topics are at various stages of analysis, not all groups will be expected to report on each aspect listed below.
  • However, we'd like to have an overall similar structure to the presentations, so please follow this outline as much as you can.
  • Also, the proposed changes to annotations and the ontology will likely go hand-in-hand, so feel free to combine these areas as needed to make the most effective presentation.
    • Summary of analysis
    • Proposed changes to annotations
    • Proposed changes to ontology
    • Outstanding issues
    • GO-CAM model (please include model URL)
  • Possible discussion topics for the end of the day
    • Did this approach to topic-focused curation/analysis work?
    • Did it improve the annotations?
    • Did it improve the ontology?
    • Do we have suitable GO-CAM models?
    • How will the ontology design patterns and MF refactoring help with modeling signaling pathways?
    • Overall - things that worked; things that didn’t work
    • Suggestions for improvements to this process and analysis tools that might help make the process more efficient
    • What are the plans going forward?



Proposed topics for discussion (suggested prior to meeting; please see table above for actual topics and schedule)

Proposer (and group) Signaling pathway Reference What this pathway offers link to uploaded figures and noctua model
Judy (MGI) General information [ cell signaling pathways useful overview of lots of different types of pathways
Ruth (UCL) Gastrin signaling PMID:26205660 Multiple intracellular signaling pathways converge to regulate transcription (see Fig 2) Fig2B nicely groups different 'parts' of the pathway. Also brings to discussion annotation of entities responsible for release of the ligand. impossible to get this modelled in GO-CAM before October
Ruth (UCL) Apoptosis Apoptosis working group this has already been worked on in GO and guidelines established, need to consider aligning to these Apoptosis curation manual

Other databases with signalling pathway s

Additional Notes

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