Ontology meeting 2015-06-18
Attendees: Judy, Heiko, Harold, Chris, Paola, DavidOS, Melanie
Minutes: Tanya
Removal of redundant links
Email came in through Judy who will forward to GOhelp. Anomalies found. We will address.
Heiko: Fixing up ROBOT/OWLtools rewrite specifically to handle redundant links. This should be in place by next week and the redundant links will then be dealt with before making the GO public release. Should take care of the subclass redundancy.
https://github.com/ontodev/robot/issues/7
Updates
- obsolete prefixes added
- OBA import and OBA logical definitions added - prompted by SF ticket last week (lumen acidification-related)
- redundancy removal (see above)
- transcription factor name changes - Quick decision ? https://www.ebi.ac.uk/panda/jira/browse/GO-350
DavidOS will email DavidH about this ticket.
Jira tickets
Time for our periodic review of Jira tickets, especially unassigned ones.
Went through all unassigned tickets and added comments, assigned to someone, and/or closed them.
In the future, go through JIRA issues in advance of meeting. Also devote some fixed length of time to JIRA tickets in future meetings (20'?)
Complex X Fn - should the genus be broadened, e.g. to include RNA-containing complexes
Compex X fn terms currently use 'protein complex' as the genus. But there is a case for sometimes including complexes containing RNA as well, e.g.:
https://sourceforge.net/p/geneontology/ontology-requests/11737/
Protein complex: "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor..."
ribonucleoprotein complex: "A macromolecular complex containing both protein and RNA molecules."
These are not declared as disjoint, but based on their defs they should be.
But pushing up the genus to 'macromolecular complex' looks too broad?
Perhaps OK if we're stricter about what goes under 'macromolecular complex' ?
Related, rather old ticket on types of macromolecular complex; https://sourceforge.net/p/geneontology/ontology-requests/10550/
Tighten up what's under 'macromolecular complex.' Examine the children. Do we need a higher level of organization? Perhaps 'supramacromolecular complex' for higher level structures?