QCQA call 2018-10-02
New error reports
http://snapshot.geneontology.org/reports/gorule-report.html https://github.com/geneontology/go-site/issues/709
- Discuss - feedback and priorities
Discussion: New error reports
Feature requests:
- GO rule info (hover)
- Copy original GAF header to the top of the report
- Rewrite owlchecks rules
- Display SPARQL results
-> Emailed Eric
github tickets
Ontology tracker: x catabolism in other species
Discussion: x catabolism in other species
Keep for now; it's ok to annotate 'x catabolic process' if a cell is degrading x, even if it doesn't produce it.
How to blacklist papers
This would include retracted papers and predatory journals https://github.com/geneontology/go-annotation/issues/2029
Discussion: How to blacklist papers
- For now, we'll do an exclusion list of papers that we dont want to annotate, or papers/Gene/GOID
- Discuss the idea of creating a 'paper skipped' list (Google form ? Other more sophisticated mechanism?)
- AI: Add to Annotation documentation: List of predatory journals
New QC check?
- Check for genes annotated to an MF as well as BP 'regulation of that same MF'?
- Would that ever make sense?
- See https://www.uniprot.org/uniprot/Q7Z7L7 as an example
Discussion: New QC check?
- AI: Add new rule proposal
DONE: https://github.com/geneontology/go-site/issues/838
Reported from the previous meeting
- Should Taxon checks be a hard check:
https://github.com/geneontology/go-site/issues/660 https://github.com/geneontology/go-site/issues/758
- Unmaintained annotation sets:
https://github.com/geneontology/go-annotation/issues/1724#issuecomment-390136730
- AI: check status with Tony - Unmaintained annotation sets
TIGR, JCVI, PAMGO ISS annotations: Michelle: The ISS annotations from at least TIGR (and should be also JCVI and PAMGO) were all manual. They were either matches to HMMs or based on pairwise alignments. We used IEA for any annotations that were automatic from our pipeline and not reviewed. I assume JCVI continued that process after I left - at least until they stopped using their pipeline and shifted completely to using the NCBI PGAP tool (prokaryotic genome annotation pipeline). I think we (and hopefully PAMGO) were pretty good about using the GO_REFs to indicate whether it was HMM or pairwise. The problem with replacing our HMM annotations with InterPro2GO mappings is that we made much more specific annotations based on HMMs than what the InterPro mappings often do. I'd hate to lose those but I understand your desire to keep the annotations current.
SPKW hierarchy - at odds with transitivity as found in GO ontology?
- https://github.com/geneontology/go-annotation/issues/2036
- emailed Chris, Seth about help with querying the GO database for non-redundant SPKW-based annotations (2018-08-16)
Discussion: SPKW
Kimberly: WB looking into the information added by SPKW in WormBase. From that evaluation we can perhaps decide whether we want to keep them.
Annotation redundancy - non-experimental annotations
- Can we come up with a proposal for the Montreal meeting?
- http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda#Handling_redundant_information
Discussion: 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
On the Montreal agenda - we will document then (or before)
To discuss at future meeting
- GO-CAM QC plan
- including SynGO, > 90 % of the production models