Annotation Conf. Call, March 13, 2012

From GO Wiki
Revision as of 18:44, 13 March 2012 by Rama (talk | contribs)
Jump to navigation Jump to search

Agenda

Present: SGD: Rama, Karen, Jodi
UK: Ruth, Varsha, Emily, Yasmin, Susan
USC: Paul Thomas
dicty: Petra
MGI: Li
Worm: Kimberly
Reactome: Peter

New documentation for TermGenie Help (TermGenie tool)(Yasmin)

Comments for new ISC 'ISS from IC evidence' evidence code

  • Michelle and Marcus's concerns regarding the need for a new code.

* Naming preferences:

- Inferred from Sequence Similarity, using Curator Judgement (makes it seem as if the curator is judging an alignment)

- Inferred by curator based on sequence similarity (could still be mistaken to mean a curator reviewed a sequence alignment)

A. Inferred from Sequence similarity from Curator inferred annotation

B. Curator inference transferred based on Sequence Similarity

Discussion on the appropriate mechanism for filtering out 'redundant annotations'

- specifically aimed at the authoritative GO Consortium annotation files for a specific species. Background available here

Developing new documentation for IKR, continued from the 24th Jan GOC annotation call

Minutes/Discussion

ISC Discussion

Several of us felt that we are overloading the evidence code to indicate more than just the evidence. Marcus (and Michelle)expressed concerns that the evidence code used in this fashion is trying to capture evidence from previous annotations (chain of evidence)and ECO is not the place to do it. This is an issue with the annotation system and we should document this to make sure we take care of it in the context of Increased expressivity. Decision on this evidence code is hence deferred. Emily will talk to Ruth about how to handle these in the mean time.

Redundant annotations

The goal for defining non-redundant annotation is to enable integration of annotations from all sources for a given taxon. We are talking about redundancy with respect to GAF file and not what the individual groups display at their sites.

  • Can we say that a unique 'GOID+ genePID + evidence + with/from + reference' constitutes non-redundant annotation?
  • Two annotations that are same in the above fields but differs in the Assigned_by column are considered redundant.
  • Two annotations that are same in the above fields but differ in the with column ID (for example 2 InterPro IDs mapping to the same GO term) are considered non-redundant. In the GAF file, the 2 (or more) IDs can be provided in the same row separated by a pipe (|).
  • There was some discussion about defining redundancy in terms of parent-child terms. Some groups keep only the granular annotations because annotations to the parent term contributes to the clutter. But most of us did not think this was a huge issue.
  • Paul asked the InterPro and Ensemble group to talk about what their concerns are. [FILL IN]