Annotation Conf. Call 2017-06-27

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  • Overview of how attributions are going to be made in Noctua-generated annotations.
    • How do groups work and in which files is group information found.
  • Sharing Curation documentation.
    • If groups have curation documention, we are collecting this to try to create SOPs for curation.
  • Brainstorming about topics for co-annotation/consistency exercises.
    • Signaling in anticipation of a small focused workshop the Sunday before the GOC meeting.


  • On call: Chris, David H., Edith, Emily, George, Giulia, Harold, Helen, Judy, Kevin, Kimberly, Li, Midori, Moni, Penelope, Rachel, Ruth, Sabrina, Sage, Shur-Jen, Stacia, Stan, Terry, Val

Attribution in Noctua Models

  • Check go-site repository in Gene Ontology github implementation
  • Under metadata, there is a groups.yaml file (go-site/metadata/groups.yaml)
  • If you want to have proper attribution for your group's annotations in Noctua (and for other reasons to track your group's participation), add you group to the users.yaml file and submit a pull request
  • There is also a users.yaml file, in which users (people/curators) are assigned to groups
  • When you login to Noctua, and then work on a model, you can select the specific group for which you are working when you edit a model
  • We will need to have some guidelines (http vs https; not having a / at the end of the URL, etc.) for URL submission
  • If you are not familiar with using github or editing .yaml files, please email Chris, Eric, or Seth for help
  • ACTION ITEM: Please check your group and user entries on go-site/metadata to make sure everything is up-to-date.

Curation Documentation

  • We are asking groups to share their internal curation documentation so that we can create standard, group-wide curation documentation
  • The curation documentation would be hosted on github (geneontology/go-annotation) with links out to the documentation on readthedocs
  • Our curation documentation is spread out over too many sites, and we need to consolidate and make things consistent
  • The ontology editors have moved to this system
  • Just note that for this call's demo, the view of the docs is not what it usually looks like; it usually looks much nicer :-)
  • ACTION ITEM: Please send David and Kimberly links or text documents to your group's curation documentation, if you have it. Thank you!

Co-Annotation/Consistency Exercises for Topics

  • Important to do this, but we want to make sure it's integrated with group's curation priorities to maximize the benefits of spending time on this work
  • Would like to brainstorm about what are good ways to do this
  • Ruth is hosting/organizing a small, focused signaling workshop on the Sunday before the Cambridge GO meeting, so we thought that working on signaling pathways between then and now would make the most of our time at that workshop
  • One of the key issues for signaling, is defining exactly what is the beginning and end of signaling pathways
    • Look at : MAPK, Akt, pathways, for example
  • For this work, we will create GO-CAM models in Noctua so that we can present clear views of what is part of a pathway, what regulates the pathway, and what is causally upstream of the pathway
  • Ruth suggested that since we really don't have that much time between now and October, we focus on specific pathways and spend some time on each of the intervening calls on this work
  • Note that this will also involve some work on the ontology, as well
  • It will be very helpful for people to look at recent signaling reviews, especially in light of the cross-talk between signaling pathways
  • Initial documentation will be on the minutes of these meetings
  • ACTION ITEM: Think about what signaling pathways your group would like to work on. We will likely not be able to work on all of them (a focused effort is liable to be more productive), but will try to use this time to select pathways relevant to as many groups as possible.
  • ACTION ITEM: David and Kimberly will discuss setting up a github project page for this work and let everyone know what information they should include when suggesting a pathway for review/study.