Ontology meeting 2014-02-06

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Attendees:

Minutes: David H

Response to acid as a stress

Stemming from https://sourceforge.net/p/geneontology/ontology-requests/10492/

We discussed this on a previous Editors call. We thought a good strategy would be for MGI to look at their manual, direct annotations to 'response to acid' and see if they can be moved elsewhere. Based on the outcome, contact other databases if necessary so they also look at their annotations. Then decide what changes we may want to make in the ontology. Where are we with this please?

CL TermGenie

Is now available for basic cell types defined by parthood. We can add the GO eds to the permissions table - who else from GO?

Documentation for megafile

Proposed import dependencies and dataflow post-megafile:

Follow-up: Import vs transmembrane transport

Please add your comments to Paola's proposal(s) here: https://sourceforge.net/p/geneontology/ontology-requests/10621/?page=1

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 had 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.

Comments from Chris: I favor ditching this basket grouping, or at least discouraging future annotations to it. Picked an annotation at random, Slc11a1, http://www.ncbi.nlm.nih.gov/pubmed/8033407, it should be to the more specific T. gondii.

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/


X metabolism/catabolism to Y

Several requests for these types of terms have come through the termgenie free-form recently. Could we generate a new TG template for these with has_input and has_output ChEBI chemicals?

The templates are ready for testing:

  • biosynthesis_from
  • biosynthesis_via
  • catabolism_to
  • catabolism_via