Ontology meeting 2014-06-26

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Attendees: Paola, Jane, David H, Becky, Tanya, Harold, Heiko, Chris, David OS

Minutes: Paola

Links to annotation guidance (carried over)

For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2014-05-08#Links_to_annotation_guidance

Chris added 'curator guidance link' RO_0002484.

To discuss today:

- how should we record the propagation rule (I,P,R) - axiom annotation

This becomes a bit of an issue when we are concerned with the viral terms. For component terms, can we make a rule that identifies them as part_of virion? Jane will get a list of the examples of the problematic terms.

- using axioms rather than regexps

- consistent location of docs: go wiki, drupal, or go nuts?

Chris had commented by email: "Propagation of annotation guidance - open to ideas about how best to encode the propagate-down rules. Worst case we could just add the UniProt codes and regexps as a property but I'd rather than a more logic-based way to do this."

On further analysis, Chris retracts his original suggestions, and proposes to simplify by checking Rachael's files into svn, and using those to add the rules.

AI: Chris and Heiko will create Jenkins job(s) to do that.

We won't see the rules in the editors file, but we'll still use the new annotation property via Jenkins, and we can add any new rule in the checked files.

'negative regulation of response' terms

Stemming from this SF ticket - could you all please take a look and comment:

https://sourceforge.net/p/geneontology/ontology-requests/10927/

Outcome of discussion is recorded in SF ticket.

As a rule of thumb, if we spot TG-generated term names that don't sound well, we can (should) change the names to make them easier for a human to understand, as long as the underlying structure of logical definitions is fine.

(Related) better divide response to X terms into the response class and it parts - the processes that result from a stimulus

https://sourceforge.net/p/geneontology/ontology-requests/10958/

Missing logical definitions

CHEBI reclassifying structures as roles?

Next week's call

Paola will be on leave, so could someone else please do agenda and send invite. Thanks.

AI: Jane will send round agenda.