Manager Call 2016-06-1
From GO Wiki
Identifier Space in GO Annotations
- In response to the May 18th call's discussion on gene and gene product identifier space (see minutes), I've put together a spreadsheet that documents our current practice wrt for GAF and GPAD:
- Annotated Entity IDs
- With/From Entity IDs (note only for gene and gene product)
- Annotation Extension Entity IDs (note only for gene and gene product)
- Annotation Isoform Entity IDs
- Then, for the purposes of discussion, I also added two other possible approaches:
- Gene IDs only
- Broad range of gene, transcript, protein, protein complex entity IDs
- At the top of the spreadsheet are three general questions that we need to consider - there may be more; please add if needed
- The plan was to review the different approaches, debate the pros and cons and then either get more feedback or finalize the proposal for presentation on an annotation or all-hands call
Review action items from Geneva meeting, and add items to Trello if necessary
Periodic review of the Trello board
Attendees: Chris, David H, Kimberly, Moni, Paola, Paul T.
Regrets: Moni Munoz-Torres (Teaching 9th & 10th graders about research and the scientific method from 7:00AM - 9:30AM PDT).
Agenda: Paola; Minutes: Kimberly
Identifier Space in GAF and GPAD
- We discussed different options for what to use as gene and gene product identifiers in GAF and GPAD.
- Much of the discussion was centered around cost/benefit for curators and users of using gene or gene-centric protein identifiers vs using more specific or granular identifiers, such as UniProtKB protein isoform IDs or PRO IDs for modified forms of proteins, for annotations.
- There is currently an important distinction between GAF and GPAD in that GPAD specs indicate that Column 2 can use the more granular identifier, e.g. P34187-1, while in GAF Column 2 uses canonical identifiers for gene, protein, ncRNA, or protein complex.