QCQA call 2018-11-13
GOC meeting Presentation: https://docs.google.com/presentation/d/1Akm-zNZWNXgyNOYZpgmzpzbkr8r9fNUJX8U2Yx5Guo4/edit#slide=id.p
Define duplicate annotations
To decide how to implement the proposed rule: Verify that we are not creating a duplicate annotation
Questions about QC rules
- Do we want reciprocal annotations for IGI ? (P2GO has a rule that checks for reciprocal annotations for IPI, except for self-binding): https://github.com/geneontology/go-site/pull/911
-> We probably cannot always have an annotation to the same term.
- Do we want to implement: New rule: Identify annotations to the function term "mRNA binding involved in post transcriptional gene silencing" (GO:1903231) that lack a corresponding annotation to the process term "gene silencing by miRNA" (GO:0035195) or one of its descendants https://github.com/geneontology/go-site/issues/921
-> Decided not to implement this one.
- New gorule Verify that we are not creating a duplicate annotation: is this already in the Noctua tracker ?
-> We probably do not want to implement this - we may need the same annotation/annoton in different models (or in the same model)
- Implement gorule-0000007? IPI should not be used with catalytic activity molecular function terms - are we OK with this ?
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].
- Add more explanation text to the matrix rule check data html page so curators know what they’re actually looking at on this page.
- Val suggests a report/list of violations for review for groups per species: Seth: may require rewriting the tool
- Annotation review tickets will be classified better wrt priority (we also need to articulate how we will assess priority).
- 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.
New error reports - status
Annotation from mutant phenotypes
Guidelines (draft) : http://wiki.geneontology.org/index.php/Annotating_from_phenotypes