Ontology meeting 2015-04-02

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Attendees: Paola, David H, Harold, Heiko, Tanya, Chris, Judy

Minutes: Paola


results_in strategy

Notes copied from last week:

See emails from Chris (threads on go-ontology 'results_in outliers' and 'results_in refactor'). Chris asked for feedback on his proposal. Discuss, then reply to email thread.

results_in refactor: Looks OK, but has many very indirect cases.

(Note that, since generation of Chris' list above, we've approved a couple of terms created with the old reg_by_reg TG template)

 Have added at least three terms with this relation since last discussion but solution has not been finalized and implemented.
 Need to revisit the email thread. Punted to next week, Chris will try to remember.
id: GO:2000531
name: regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter
intersection_of: GO:0006357 ! regulation of transcription from RNA polymerase II promoter
intersection_of: results_in GO:0042304 ! regulation of fatty acid biosynthetic process

==>

id: GO:2000531
name: regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter
intersection_of: GO:0050789 ! regulation of biological process
intersection_of: regulates 'NEW:transcription from RNA polymerase II promoter and regulates some fatty acid biosynthetic process'

We looked at Chris’ strategy, and at a few outliers highlighted by Chris (see email thread ‘Fwd: results_in outliers’ on ontology list).

AIs: Tanya will take care of outlier number 1, Paola will do 2 and 3, and Harold will do 4. And Chris will implement his proposal.

qualifier for regulation of process or process

Rama emailed the editors on March 26:

"At the Barcelona meeting we talked about implementing a qualifier (implicated_in?) to allow curators to indicate that they don't [know] whether the gene product is involved in the process or in the regulation of the process.

Minutes from Barcelona meeting (check under the Autophagy section)- https://docs.google.com/document/d/1NonH97s8xEpDdx6DfonKPKI_RdHbbG-yft85UZtUmF0/edit#

Should we discuss this option further at an annotation call? (We would need examples to illustrate the point though)."

Discuss, decide, reply to Rama.

David H: you only directly regulate a process if you’re regulating a function that’s part of that process. LEGO would help us to find annotations that don’t adhere to this rationale.

Resolution: we are going to go ahead with this plan and create some type of qualifier that has yet to be named. We will present it at a future annotation call, probably on April 28th. We may quote the same autophagy-related examples that were presented in Barcelona.