Annotation Conf. Call, February 11, 2014
Agenda
http://wiki.geneontology.org/index.php/PAINT_-_Apoptosis
QA checks (Rachael, Heiko)
Tony sent Heiko (copied here) details of all the checks we do on our annotation sets with a view to including our checks if they were missing from Jenkins. It would be good to know how far along this is and if there are checks that cannot be included in Jenkins but that UniProt-GOA does have checks for.
As far as I can see from the validation report, Jenkins checks for obsolete relations and checks GO terms in annotation extensions, but does it check for appropriate use of relations, e.g. if an entity type is out of range? Does it check for orphan ISS?
If Jenkins can't incorporate these checks, are groups interested in UniProt sending each group an error log for their annotations?
For example, the PomBase Jenkins check is clean; http://build.berkeleybop.org/job/gaf-check-pombase/lastSuccessfulBuild/artifact/gaf-validation-report.txt
but the UniProt-GOA check brings up several errors in 'domain/range'; e.g. [[GO:0005829] [happens_during(GO:0034605)] [Invalid domain for happens_during: GO:0005829]] [[GO:1990188] [not_dependent_on(PomBase:SPCC736.11),occurs_at(SO:0001843)] [Invalid range for occurs_at: SO:0001843]] [[GO:1990188] [not_dependent_on(PomBase:SPCC736.11),occurs_at(SO:0001843)] [Invalid range for occurs_at: SO:0001843]]
Heiko, would you be available to give an update on this?
Coming soon
- Feb 24th: David OS will talk about formalizing the representation of symbiotic relationships and annotations to describe them in the ontology
- March 11th: Sandra Orchard will talk about the IntAct Complex portal