Manager Call 2017-04-19

Bluejeans

https://bluejeans.com/588333403

Agenda

GOC meeting

• • Current state of the Agenda: [1]
  • Is there time for more ontology editors training in Corvallis or should we try to schedule another workshop over the summer?

Protege

Follow up on idea of doing an advanced Protegé workshop this summer

• Who will participat ?
• Where will it be?
• When will it be?
• Equivalence axioms - editors would like more guidelines on how to construct these

Ontology

• Term Genie-type/Noctua Requests: We are getting tickets for adding terms that previously would have come in through TermGenie or that should be Noctua models, in particular from CACAO. Should we keep creating those terms?
  • Examples:
    • positive regulation of cilium beat frequency involved in ciliary motility https://github.com/geneontology/go-ontology/issues/13375

Documentation

Pascale

• It is not realistic to expect the documentation to be up to date.

I propose that manageable units of the documentation be reviewed and the last update date be stated for the documentation. I think we all wonder what is stale and what is current.

A few 'basic' point about the scope of GO annotation I would like to review with managers (and then at an annotation call):

• We only annotate the normal function/process and localization of a protein. Hence:
• Localization
  • secreted proteins are not annotated to the secretory pathway (Golgi, vesicle, etc)
  • Should internalized receptors be annotated to endocytic vesicle, and other downstream localizations?
  • Should extracellular hormones be annotated to plasma membrane/extrinsic to the external side of plasma membrane when they are bound to their receptor ?

• Multi-organism processes
  • Should host proteins that are hacked by viruses be annotated? For example in transcription, translation, internalization ? A possibility suggested by the Swiss-Prot viral group is to limit these annotations to terms that contain 'host'

Minutes

Participants: Chris, Pascale, Huaiyu, Suzi, Paul, Judy

GOC Meeting

• The agenda is in good shape. People should use the GO wiki to add topics they want to discuss. It is preferred if they can also include the amount of time needed and the desired date.
• Chris would like to block an hour to talk about software development. This can be under the pipeline.
• Judy noticed that the conference dinner column was added to the attendee table after people started to sign up, so that column is empty. Need to remind people to add the information.
• Pascale asked whether there should be an ontology editor training at the meeting. The consensus is that it should not be part of the main meeting. It can be held in the afternoon of the last day of the meeting, or on the Reactome day.
• It is not clear what the Reactome day entails. Peter is not listed on the attendee list. The PI will follow up with Pankaj about it, and then decide when to hold the ontology editor/Protege training.

Protege

• Postpone until kimberley and david is back.
• Put on the agenda of next week's ontology call.

Ontology Term Genie request

• These terms can be represented in Noctua. Paul will contact Jim to gather more information. For now, those terms are not going to be added.

Documentation

• It is about annotation documentation.
• Issue about secreted protein annotation, they should not be annotated as in Golgi, but there is no documentation.
• Chris thought this should be defined in the ontology, suggested that docs should be updated when ontology is updated.
• Suzi also suggested rules for QC check.
• Put on the agenda of the next ontology call
• About annotating functions hijacked by virus, it is important to specify the host function vs. hijacked function.
  • Action item, Add it to the ontology call. Get an expert involved.