Annotation Conf. Call 2019-08-20

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October GOC Meeting - Berkeley

GO-CAMs and Annotation Extensions

  • After USC hackathon in June, we formed a small working group to fully articulate the GO-CAM model specifications
  • This will allow for consistent GO-CAM curation using Noctua workbenches, import projects (e.g. Reactome and MOD imports)
  • Will also allow us to move forward with harmonizing AE relations used in GO-CAM and conventional annotation


  • Google spreadsheet for happens during
  • Current recommendations are that 'happens during' is used to define a biological phase or life stage during which a molecular function occurs
  • However, happens_during is not defined in the relations ontology
  • There is a comment, however:
    • X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
    • This implies that the start and end of the molecular function and phase are known
    • For things like cell cycle phases or development stages this seems fairly straightforward
  • But what about annotations that referred to a function that 'happens during' a biological process, such as 'response to oxidative stress'?
  • What do we mean when we make these statements?
    • WB had seven MF annotations with 'happens during' extensions that needed review.
      • One used a WBls term, so that was okay.
      • The remaining six used 'response to' terms and in reviewing them, I changed the extension relation to 'part of' the 'response to' term. The MFs were all transcription-related functions that mediated the transcriptional response to unfolded protein, or hypoxia, or heat.
    • (Pascale): If we want to allow happens_during for 'response to' terms, then we should treat them as 'biological phases', and disallow direct annotations. Are there cases where using 'part_of' versus 'happens_during' makes sense ?


  • Present: David, Giulia, Harold, Helen, Jim, Judy, Karen, Kimberly, Laurent-Philippe, Li, Midori, Pascale, Petra, Sabrina, Seth, Shur-Jen, Tanya, Val