SourceForge meeting 2014-01-29

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Ontology Development project about Ubiquitination

Stemming from http://wiki.geneontology.org/index.php/Ontology_meeting_2014-01-23#Ontology_Development_project_about_Ubiquitination

Protozoan classes

https://sourceforge.net/p/geneontology/ontology-requests/10438/

Protozoa is a historical/convenience grouping that includes many unrelated taxonomic groups. We previously discussed whether we should get rid of classes that refer to protozoa altogether - or try to automate by making a taxon union class. We have since been in touch with Thomas Mock, who sent this excellent page summarising problems and detailing potential solutions: http://www.iaszoology.com/protozoa-classification/

I've has a go at mapping the 14(!) phyla of the MODIFIED SLEIGH’S SYSTEM (by A. Pechenik, 2002) to NCBI. Some phyla map directly - others map to multiple groups.

It's looking to me like constructing and maintaining a union class is too hard. So perhaps we should make classes for the major phyla from Sleigh's system for which we have relevant annotations? We could then add 'response to protozoan' as a broad synonym to each.

Protein complexes with other components

Under what circumstances should we allow the addition of terms for protein complexes in combination with some other factor? Presumably stability is the key - especially if the complex is only stable in the presence of the additional factor ?

Examples from recent tickets: - receptor/ligand complexes

- protein + DNA/RNA complexes: https://sourceforge.net/p/geneontology/ontology-requests/10319/ https://sourceforge.net/p/geneontology/ontology-requests/10221/ https://sourceforge.net/p/geneontology/ontology-requests/10156/