Ontology meeting 2014-03-06

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Attendees:

Minutes:

Follow-up: Next steps in the post-megafile world

Sorting out issues, etc.

For reference: discussion from last week: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-02-27#Follow-up:_Next_steps_in_the_post-megafile_world


SOP for adding relations

From last week

  DOS: If I've added a new relation to the relations ontology, is it sufficient to have this is in gene_ontology_write.obo:
  [Typedef] id: some_obo_only_readable_id xref: RO:nnnnnnn 
 for RO-imports to be automagically updated? (presumably adding more could cause problems with duplication of APs)
This should work. Let's see if that happens. Two day process. Will report back.
 Or should I be using the new term imports file (extensions/imports_requests.obo) but with a typedef filled in?

Doesn't seem to work (only brings across very limited properties of relations in ro_import.owl).

Dealing with multiple terms with same label in Protege

 Related JIRA issue: GO-273

DOS: There is a potentially serious issue for searching, querying and editing in Protege when there are multiple terms with the same label. Not possible to know which term has been chosen when writing axioms; search will randomly go to one of two terms and not show other. The obvious solution to this is to use OBO foundry Unique names to disambiguate - Protege can be set to display these instead of label if they are present , but this will only be practical if we can do this while making sure new term generation defaults to rdfs:label.

DOS: have tested this - and it works fine.

TODO: work out how to include obo foundry unique label (http://purl.obolibrary.org/obo/IAO_0000589) in standard set of annotation properties in GO file.

ETINEs

Can we move forward with these - there are several ETINEs that need removing for cell cycle.


Tolerance

Trudy needs some terms for annotating tolerance in bacteria e.g. tolerance to ethanol. We'd agreed that 'development' or 'acquisition' of tolerance terms would be okay - or could tolerance itself be a process, in the same way that we have homeostasis as a process?

In addition, we already have tolerance terms for plants - e.g. acquisition of desiccation tolerance - would we want to group these with the bacterial terms or are the processes too disparate?

We decided to use 'process resulting in tolerance to x' for these. These will be is_a 'response to x'. The plant and immunology terms are not to be connected to the new terms.

editor's guide

http://wiki.geneontology.org/index.php/Editor_Guide

Agenda for GOC meeting

Let's check it all looks okay - anything to add change?

Pattern for defining membrane regions - will this cause problems ?

[David OS]

I've recently added the term 'membrane region', defined as EquivalentTo membrane that part_of some membrane.

I added in response to a request for 'external side of apical plasma membrane' and 'cytoplasmic side of apical plasma membrane'. The standard pattern for these requires that they be define as part of some membrane, but it turned out that 'apical plasma membrane' was not defined as a type of membrane.

I thought it made sense to group these under 'membrane region' and 'plasma membrane region'. Autoclassification finds some membranes that are already defined as part of membranes. Adding this has not triggered any Jenkins errors, but I just wanted to check that this will not cause problems down the line. Particularly, will this pattern make it impossible to generate a go-basic.obo file?