Ontology meeting 2014-01-30

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Attendees:

Minutes:


Follow-up: Website documentation - ontology related pages

Where are we with these? Remember, new website must be fully ready before the GOC and SAB meetings.

*Some confusion over file format pages, Chris to take these on
*Who will do signaling pages with no Becky? David OS to flesh out a bit
*Reports to stay on wiki

Draft formalisation of multi-species annotation

https://docs.google.com/document/d/196nLKiQ2Go4toilCq226w7u0p52odvCkq-bU5qgtzu0/edit?usp=sharing

There are two versions. The first is probably best. The second doesn't make individuals for classes and as a result uses some odd nominalisation patterns in the class expressions.

OWL files implementing these examples are here:

http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/experimental/David/multi_species_annotation/

Have a look at the query classes. Can you think of any more useful queries?

One piece of formalisation I feel unsure about right now: I'm wondering whether we need to have the relationship between gene product and organism be 'encoded by' rather than 'expressed in' or 'expressed by'. In the case of viruses - it is arguably the host that does the expressing.

A second issue: I'd like to make this consistent with the formalisation we're working on in PCO - I still think we need some kind of formal bridge between NCBI taxon and organism terms in CARO2/PCO. I guess this could be a simple as making an equivalence mapping between the root of NCBI taxonomy and some term for an individual organism (or organism, virus or viroid).

Also to discuss - how this fits with Lego.

Generating Molecular Models from GO

If there is time, Chris will give a demo of the model generation wizard:

Purpose: highlight importance of breaking a process down into its parts (via has_part, starts_with, etc) for model annotation

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 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/