Annotation Conf. Call August 13, 2013

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Consolidating Protein Binding annotations

Proposal: To consolidate all 'direct' interactions captured by other Interaction pipelines into the respective GAF files.

  • We will integrate 'Direct' interactions only
  • Of course all interaction databases capture the interacting protein name. We will capture that data in the With column
  • When possible, the interaction will be mapped to a granular term instead of retaining the annotation as protein binding (histone binding instead of protein binding). This process will need some work (evidence code, assigned_by etc).
  • Should we take results from small scale experiments only? What about HTP experiments?
  • Should we integrate only those interactions that have been reported by more than one paper or one method?
  • Any other issues?

Col-16 curation

We have some documentation on the GOC website- Now that there are more groups annotating col-16, for consistency sake, we will go through specific examples at future annotation calls. We would like each group to send a paper out ahead of time so we can go through the annotations as a group.


Protein binding

  • Regarding mapping down to granular terms- we should absolutely do this, otherwise the annotations are useless. We will write some specs on how we want the mapping done etc.
  • There was consensus to include all types of data (HTP/small scale)
  • Regarding including only those annotations that were reported in more than one method. We don't want to have this restriction because we have captured some interactions manually which might be from one paper/method.
  • Does BioGRID have the same kind of scoring system like IntAct? Rama: So far I don't think so, i will look into it.
  • IntAct hass a scoring system. Everybody is comfortable including these first. We will include Intact interactions in Phase 1 and look into BioGRID for phase 2.
  • IntAct is going to integrate MINT interactions soon. They might consolidate BioGRID annotations also.
  • How do we treat redundant annotations from BioGRID and IntAct? We will deal with this after we look at BioGRID annotations.
  • Petra- annotating in protein2GO. She mentioned that the protein2GO interface will not let her fix a manual protein binding annotation if the same annotation was there from IntAct. Protein2GO's check for duplicate annotations is not looking for assigned_by in protein2GO. Rachael, Petra, Rama, Kimberley will talk about it separately (since this is a protein2GO issue and these 4 groups use protein2GO to curate).


  • We will do these consistency exercise once a month
  • Rama send a simple paper around for discussion for the next annotation call (we will talk about col-16 only, not GO-term etc).
  • She will request groups to select paper(s) for the future calls.