Ontology meeting 2016-04-21

Attendees: Paola, Melanie, David H, David OS, Harold, Tanya, Chris, Paul T

Minutes: Paola

Follow-up: vesicular transport

Proposal here: https://github.com/geneontology/go-ontology/issues/12317#issuecomment-199771185 See GH ticket for complete discussion and details of suggested changes.

Discussion:

General agreement that new defs for transport, localization and establishment of localization are good. DH and TB both like them.

AI: DOS to implement ASAP.

Discussion of 'occurs in'. DOS: important to use this where possible in order to maximise inference to other transport processes (e.g. cytosolic transport). Relying on start and end location alone has caused problems.

David OS proposal is to merge the two branches: vesicular transport and vesicle mediated transport. To be able to do that, he suggests to add an optional new relationship called ’has_carrier’.

Qs: Any other tweak we’d suggest? Would we be happy with merging the two branches and using the ‘carrier’ relationship?

David H: Major issue - how do we distinguish cases where transport along a fiber is direct vs in a vesicle. DOS: Agree that this is a problem. Can think of some formal patterns for recording this, but they are ugly and hacky. May need to hold off on implementing until there is a solutiion.

Discussed examples.

MC is concerned about implications of merging. DOS explains why they shouldn’t be troublesome. Discussion on whether this proposal would affect any future representation of extracellular-related processes. Probably not.

Another issue: With this in place, we could add 'vesicle-mediated protein transport' terms. DH suggests bringing this proposal up at an annotation call and ask curators if they’ve been co-annotating or not. DOS: Val has been. The change won't make anything wrong, but If we add 'vesicle-mediated protein transport' then there will be a single term that could be used where now there is co-annotation.

Melanie suggests sending an email beforehand so people can think about special cases.

DH: Alternatively, explain the merge at an annotation call and go over how that would affect annotations.

AI: DOS will make the main changes, will think a bit more about the merge. Will discuss that on an annotation call, aiming at the one after the next.

Behaviour - limit to metazoa?

And if not, when to use development instead?

Motivating example: Petra: "Dictyostelium is a social amoeba, and during development cooperation is essential, but e.g. there are cheaters who preferentially become 'spore' instead of altruistically 'stalk'. Several studies have been published, and I annotated genes involved in cheating (isn't that a behavior?) with GO:0035176 social behavior. " https://github.com/geneontology/go-ontology/issues/12357 Note - these 'cheaters' only cheat in chimeras with cells not carrying the mutation.

So - not very similar to social behavior of say, fruit flies.

See GH ticket for discussion + details. Discussion:

Group leans towards associating ‘behavior’ with the presence of a nervous system.

At the same time we need to account for community usage of the terms - for plants, bacteria etc.

We could restrict behavior-related wordings to synonyms in those cases.

CM: why not call the term ‘neurobehavior’?

PT: animal-type behavior?

DOS: http://www.nytimes.com/2009/07/21/science/21angier.html?_r=1; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760923/

DH: nervous system-mediated behavior?

DH: We need to give curators like Petra viable alternatives to use for annotation.

TB: To clean up: regulation of chemotaxis terms are children of regulation of behavior terms, but chemotaxis is not is_a behavior, may need to remove the relationships for the regulation terms DH DONE

Decision to make: split behavior heirarchy at the top into neural and non-neural? Or treat non-neural 'behaviors' outside of this branch. DH advises against splitting at the top, but is open to suggestions.

AI: Need to discuss non-neuro-based 'behaviors' with curators. Do we have good enough homes for these cases? If not, what new terms should we add?

Action items from GOC meeting in Geneva

At the managers call yesterday, minutes of the GOC meeting in Geneva were examined for action items. (Minutes are here: https://docs.google.com/document/d/12CDf4s8YsylPMNHM3UuPis9NyVQ9WFpBpNYTFYAH7kc/edit#heading=h.e45uvzyvuaj0) Melanie made tickets on various GH repositories for these.

AI: all, please keep an eye on the trackers and on tickets where you're mentioned.

Protein Complex WG (bumped)

Pilot project to remove leaf nodes cancelled. Carry on as normal?

https://github.com/geneontology/protein-complex-refactor/issues/17

Inheriting taxon rules from UBERON (bumped)

See https://github.com/geneontology/go-ontology/issues/12411#issuecomment-212806374