Ontology meeting 2016-07-28
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Attendees: Chris, David H, David OS, Harold, Tanya
Minutes: Tanya
Regrets: Paola, Melanie
Inference pipeline from Annotation Extensions to GAF
Problem: apparent redundancy in annotations and how to filter these out
Will Jim's (Balhoff) work on LEGO inference feed in to inference on annotation extensions, if so how?
How can LEGO and AE inference be effectively fed back to GOA: need to avoid redundancy with GOA "inference" pipeline (between GO branches) and to be consistent in evidence. Ideally should also include some way to trace to original annotation (LEGO mode/annotation).
AI: DOS to find examples of missing inferences (gp annotated to a process BP1 that regulates another process BP2 but the inference pipeline does not create the gp annotation to regulation of BP2 - create JIRA ticket (which tracker?)
Need to reconcile how GOA is inferring annotations with how GOC is inferring annotations and the evidence codes that are used. For interontology links, GOC retains the original evidence code. For annotations inferred from annotation extension information, GOC uses the IC evidence code and uses the original GO id in the evidence_with column, the annot ext information is not (yet?) retained/referred to in the inferred annotation. Best to unify the way annotations are inferred so that we don't end up with one set of annotations visible in QuickGO that are different from the set visible in AmiGO.
AI: DOS to compare methods of inference, set up discussion time with Tony and interested annotators.
Side discussion on ECO and mapping of classic GO evidence codes to ECO in view of transitioning to using ECO in annotations. https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/gaf-eco-mapping.txt What about the reverse? Mapping of more specific ECO codes to the classic GO codes? Want to avoid creating subsets in ECO, harder to maintain, need manual input.
Other pages looked at: http://geneontology.org/page/annotation-quality-control http://geneontology.org/page/annotation-quality-control-checks
Review capitalisation of terms PUSH TO NEXT TIME
https://github.com/cmungall/capital-offence