QCQA call 2019-03-26
GOC meeting Presentation: https://docs.google.com/presentation/d/1Akm-zNZWNXgyNOYZpgmzpzbkr8r9fNUJX8U2Yx5Guo4/edit#slide=id.p
Annotation review status
Pascale - update ? I haven't closed many tickets - I wonder if people did very much since 2018.
Future of external2GO mapping files
Kimberly added to the Cambridge agenda. We need to make a proposal https://github.com/geneontology/go-ontology/issues/16989
Rules reports - carried over from last call
Question for Seth: Can we remove Rule 26 (IBA being filtered out) from the reports ? The other half of that problem is that not all the rules are summarized on top, so it's hard for people to read their report.
- A new rule type was proposed to be able to configure reports more precisely: https://github.com/geneontology/go-site/issues/945
- Seth mentions that a similar solution was proposed elsewhere (ACTION: he needs to dig out the ticket; then Pascale or someone else can go and fix the report types as appropriate)
- Eric will be available to work on rules again in 1-2 weeks.
GO rules status
Not resolved last time (if still open)
- New gorule-0000051 #935
- Updated gorule-0000046 #933
- new gorule-0000045 #909
- new gorule-0000037 #892
Annotation from mutant phenotypes
Kimberly improved guidelines: Guidelines (draft) : http://wiki.geneontology.org/index.php/Annotating_from_phenotypes
Action items from the Montreal meeting
Pascale: TO DO: Create tickets
- Check groupcontacts.csv in go-site/metadata and please update for GO curators in your group [annotation group].
- Assess where we stand wrt the signaling workshop. What needs to be wrapped up? What are the sticking points and why? How do we capture downstream effects of signaling pathways?
- Develop guidelines for annotation metrics in light of the increased contribution of annotation review to curator efforts. Consider how prioritization of annotating previously unannotated genes will be taken into account. Include metrics for comprehensive annotations and develop guidelines and a system for flagging genes/gene products as annotation complete (gpi specs) and make this publically available.
- Suzi - develop a ‘white list’ for specific pathways
- Review guidelines with curators: http://wiki.geneontology.org/index.php/Tips_to_Produce_High_Quality_Annotations
Topics carried over from previous calls:
Annotation redundancy - non-experimental annotations
- We need to define what constitutes a redundant information, WRT to sources, evidences and references
- There is a ticket that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440
- AI: Rules for flagging redundant annotations need to be documented - Chris
Different types of redundancy
- identical experimental annotations from different sources https://github.com/geneontology/go-annotation/issues/1404
- inferred and IEA, ISO, ISM, IBA annotations when EXP exist
- Redundant inferred annotations from GOC F-P links pipeline e.g. https://github.com/geneontology/go-site/issues/576
- TAS /NAS (special case)
There is no use case for users of MODs and AMiGO to see automated annotations when EXP annotations are present. If somebody wants a complete set of annotations from a mapping resource these could be made available separately.