GO-CAM November 8th, 2017

From GO Wiki
Jump to: navigation, search

Zoom URL

https://stanford.zoom.us/j/679970729

Agenda

Noctua GitHub Organization

  • Using projects to organize tickets
  • Using milestones for ticket prioritization
  • Creating new tickets - do we need a different SOP?

Requirements/Roadmap

Noctua Requirements/Roadmap

Attribution

Attribution with GO-CAM exports to GOC annotation files

GPAD Outputs

Simple Annoton Editor

dealing with blank MF in the simple annoton editor

Extend form to include standard GO-CAM model fields

Bare MF annotation should generate part-of triples

  • Editor enhancements to come:
    • Ability to add basic set of annotation extensions, e.g. has_input for an MF
    • Ability to just add a CC annotation and get the resulting part_of annotation in the graphical interface

Minutes

  • On call: David H., Dmitry, Harold, Jim, Karen, Kimberly, Pascale, Paul T., Rob, Sabrina, Seth, Stacia

Attribution

Current Annotation

  • We need to have groups properly captured in the Assigned By field of output GPAD files
  • All current and future Noctua curators who are associated with one or more curation groups need to fill out the groups field in their entry in the users.yaml file
  • Full path: https://github.com/geneontology/go-site/blob/master/metadata/users.yaml
  • Groups are entered as URLs, e.g. http://www.wormbase.org, in single quotes
  • If curators belong to multiple annotation groups, the first group will be considered the default
  • To change groups in Noctua, select from the drop-down list next to the curator name in the upper right of the tool
  • ACTION (DONE): Added to agenda for 2017-11-14 annotation call
  • ACTION (DONE): Added github ticket to go-site repo

Legacy Annotation (in the sense of "old GO-CAM models")

  • For legacy models, and here legacy refers to models that were created before the providedBy tag was populated for each evidence, we will need to decide how to populate providedBy in the evidence
  • For all development and production legacy models:
    • How many models just have a single curator?
      • For single curator models, we will need to confirm with each curator what their preferred annotation group should be
    • How many models have multiple curators?
      • For multiple curator models, we need to determine if there is one annotation group or multiple annotation groups
      • If there are multiple annotation groups, curators will need to decide how they want to handle annotation attribution
    • ACTION: Seth will investigate the distribution of curators on legacy models and report back so we can formulate a plan for populating providedBy in legacy models
  • For legacy models that included annotations from the function companion, it may be difficult to trace, and we may not be able to deal with these annotations via a script.
    • This issue needs a bit more investigating, but note that we always want to preserve the provenance of the annotation and give credit to the correct group.

Assigned By in GPAD Output

  • ACTION:Chris, Jim, and Seth will review what code/pipeline revisions need to be made in order to populate providedBy correctly for GO-CAM models

Prioritization

  • ACTION:All github tickets relating to proper providedBy attribution will be assigned the 1.0 milestone
    • Note that 1.0 milestone exists in the noctua repo but not in the minerva repo or the go-site repo and some relevant tickets are housed in both of those latter repos

Related Issues

  • Several other related issues arose on today's call:
    • Is it important to somehow flag annotations imported into Noctua from some other source, e.g. AmiGO or TextpressoCentral?
      • We need to think this through some more, but if yes, it would require changes to the underlying data model add the appropriate (owl) annotations to mark the data.
    • Importing annotations from AmiGO will result in redundant annotations when groups collate all annotations for their organism.
      • Seth: I believe that we already have some filtering system either in place or in planning; we'll need to verify this, creating tickets as necessary for any gaps.
      • MGI has already dealt with this, but we should have an SOP for all groups to follow.
    • What if Noctua curators don't belong to an annotation group?
      • We will need to have an SOP for this, but this is not a showstopper for the 1.0 release.