GO-CAM Working Group Call 2018-07-17

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Meeting URL





  • Noctua tool
    • Updates:
      • References - preferred reference is a PMID, followed by a doi, and then a MOD paper ID. GO_REFS may also be used.
      • Activities mediated by intervening biological processes - for example, transcription - to be discussed today
  • Annotation relations

Modeling Transcription in GO-CAM

  • 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.'
  • Kimberly - unc-86 regulates transcription of mec-3

Relations between MF and BP

Relations between MF and Input(s)

Relations between BP and input(s)

  • Duplicating has_input for MF and BP results in multiple entries in the AE field of the BP annotation in the GPAD

Relations between BP and MF of transcriptional target


  • On call: David, Karen, Kimberly, Laurent-Phillipe, Paul T., Petra, Rob, Sabrina, Suzi A, Suzi L (please add your name if it is not already listed)

Landing Page

  • Curators should test the landing page and add comments to the tracker for either bugs or enhancements
  • There will be an additional landing page for curators to look at models under development


  • Noctua documentation has been updated to reflect policies regarding use of references

Transcription Models

Relations between MF and BP

  • We discussed models of transcription factors and their relation to transcription BP terms
  • Transcription factor activities are modeled as 'part of' a regulation of transcription process
    • Why? In the ontology, regulation is modeled is a biological process, and so functions need to be part of biological processes that regulate other processes.
    • This can be captured succinctly in models by stating that a transcription factor activity is part_of '(+/-) regulation of transcription'.
    • This will also produce the correct annotations in the GPAD output file.
    • If a transcription factor activity is connected to the process of transcription with a regulates relation, the reasoner cannot then use the logical definitions of the process terms to infer that the transcription factor activity is 'part_of' a regulatory process.

Relations between MF and Inputs

  • We discussed the relation to use when capturing the input of the transcription factor.
  • Even in conventional annotations, groups have differed on how they do this.
    • To illustrate, groups have used: has_input, has_direct_input, has_regulation_target
  • For MFs, is there any real difference in meaning between has_input and has_direct_input?
    • No, an input to an MF is, by necessity, a direct input to the activity.
  • For BP, the use of has_input may mean something different, though.
    • For BP, curators have used has_input to indicate the entity that is affected by a process but for which the precise MF that directly mediates that effect is not known.
    • As an example, Rob described how SGD has annotated IDA vs IMP for protein kinase activity and phosphorylation.
  • The curation task of indicating inputs for MFs vs BPs needs to be clear for GO-CAM models.
  • Rob was asked to create a GO-CAM model for the phosphorylation example.
  • Sabrina's paper from last month also touches on this; in one case, the evidence for direct regulation of transcription was supported by several different pieces of evidence, whereas in the other cases, there wasn't sufficient evidence to assert the direct regulation. We need to re-visit this model to make sure we have a satisfactory way of distinguishing between these two cases. This will likely be a common occurrence during curation of transcription papers.