Annotation Conf. Call 2016-11-22

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Bluejeans URL:


  1. 2016 Progress Reports
  2. github go-annotation tracker will house and track action items from GO meetings, e.g. USC 2016
  3. Annotation Consistency Exercise - Sabrina, Zfin


  • On call: Barbara, Chris, David H., Doug, George, Giulia, Helen, Jim, Kimberly, Li, Midori, Moni, Paola, Paul T. Petra, Sabrina, Stacia, Suzi, Tanya

Progress Reports

  • Organized by aims in accordance with NIH specs
  • Google folder has templates
  • Groups need to fill out their progress as they have previously, but in the appropriate Specific Aims
  • Tables are still very useful for progress reports, but now they can either be embedded in the Google doc or in a separate spreadsheet
  • MOD = institution
  • Other work that specifically addresses the aims and crosses institutions, e.g. ontology development, annotation, can go directly into the main report

GO-Annotation Tracker on github

  • Action items from USC meeting will be tracked on Gene Ontology's go-annotation repo in github
  • We will review these action items in coming meetings

Annotation Consistency Exercise

  • Zebrafish paper: Fscn1 is required for the trafficking of TGF-β family type I receptors during endoderm formation.
  • Key points:
    • Each gene product represented in the model must be associated with a molecular function, even if it is to the root node
    • Using inferred relations vs making direct connections, for example when a gene product is part_of process #1 that is causally_upstream_of process #2. By inference, the gene product would then also be causally_upstream_of process #2. The inferred relations will eventually be generated.
    • Different approaches to LEGO modeling
      • Data from a single paper
        • Curators would add annotations just from the experiments performed in a single paper
        • If desired, TAS annotations can be used to indicate where information is known but not demonstrated in the paper being annotated
        • We could possibly use scripts to fill in TAS annotations with experimental evidence when available or perhaps this is a curation task that is well suited for student projects
        • Textpresso queries also help with filling in missing experimental evidence
      • Data from multiple papers
        • A more comprehensive model of the biology can be built this way
        • Can be a good QC exercise
      • Curators can choose which approach they would like to use
    • Experiments in cell culture vs experiments in a cell line - are these treated differently?
      • MGI captures cell line in curation notes, but also can be captured in evidence
    • LEGO models may display both molecular-level and organismal-level processes
      • Would be nice to have some visual cue that distinguishes these