Ontology meeting 2014-01-23: Difference between revisions

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Seems there has been lots of discussion internally and there are other groups that would like to see improvements in this area.
Seems there has been lots of discussion internally and there are other groups that would like to see improvements in this area.
  Mike Livstone has noted that curators from BIND have found inadequacies in our representation of Ubiquitination.  
  Mike Livstone has noted that curators from BioGRID have found inadequacies in our representation of Ubiquitination.  
  We may need experts (if need be, do we need a content meeting).
  We may need experts (if need be, do we need a content meeting).
   
   

Revision as of 15:14, 29 January 2014

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

Minutes: Harold


Follow-up: Website documentation - ontology related pages

We need to split up review and editing content jobs. Basic formatting is mostly done. Push next week to do as much as possible. Need to be ready by GOC meeting.

Google doc

Note: some pages can be seen in two ways:  
1. documentation for editors on maintaining the ontology or 
2. documentation for biologists on what relationships, etc. mean.
In any event: 
ACTION ITEM FOR ALL:
pick/assign yourself a page to work on by the end of today.
If original document has images, put a tag MISSING IMAGE where this should go in the new page.

Follow-up: Assert inferences job

David OS: Some progress in fixing EXISTS, TAGGED-INFERRED, NOT-ENTAILED (ETINE) links. 
(see mail entitled ETINEs  on the [go-ontology] mailing list for summary of progress).  
Work on fixing these uncovered some serious problems with our current cycle:
(i)  our redundancy flagging system has been deleting axioms necessary for inference, 
after which Kosher inferences get flagged as ETINEs.  We have a proposed fix for this.
(ii) There is a bug, as yet untraced, causing some entailed classifications to be flagged as ETINEs.
Notes on these issues, including examples, can be found here: 
https://docs.google.com/document/d/1g8gM_PKEKMncNgzZ9RZKRNSTyavVKduZMu7xVrnD8Ss/edit

AI: Chris and Heiko will work on fixing the assert inference job.  
Editors should hold off on fixing remaining ETINEs until these fixes are in place. 
This means that we may have a delay of a further week before the assert inferences job is turned back on.

How direct does regulation have to be to justify a regulates relationship?

These inferred links result from regulates relationships that have been in GO for some time.

ADD GO:0007272 'ensheathment of neurons' GO:0051969 'regulation of transmission of nerve impulse' ADD GO:0007272 'ensheathment of neurons' GO:0098900 'regulation of action potential'

Paola notes: The ensheathment has an effect on action potential and therefore impulse transmission, but it's not a type of regulation, it's a separate process... what do you think? DOS: The regulating effect is clearly quite indirect (via changing the electrical environment of the membrane) - but do we have guidance on how direct regulation of a process has to be before we make a relationship? The documentation on regulation does not make this clear.

Paola will remove the link between GO:0007272 and GO:0051969 and GO:0098900. DONE

Should regulation of quality and regulation of biological process be disjoint?

If so, the hierarchy will need much untangling as many terms are under both.

(DPH) No. In almost all cases, once we know enough we will find that regulating a quality will be the result of regulating a process.

(DOS) OK. Thinking about it I can see how this could be true, but I'm not sure it is necessarily true. (To be fair, you did write 'in almost all cases'). Right now we have action potential as a process that regulates membrane potential (a quality). I'm not sure it does so by regulating a process, rather parts of the process (the flow of ions through membrane channels) result in changes to this quality. So perhaps it is still worth adding declarations of disjointness further down the hierarchy.

Megafile update

Notes from yesterday: https://docs.google.com/document/d/1zjE0nLB_Kw8q6XoHG8wSmOMzrEYeNYgscrVKGHZaJo4/edit#

Chris has tested; DPH and Tanya also. Lots of troubleshooting in Berkeley. Ready to go live, we think.  Paola will test with 
her machine on Monday with DavidOS looking on.

Protege Plugin for OBO related data

Chris has started to spec out the requirements for a new Protege Plugin.

The main task is to provide a concise and useful representation of OBO-relevant annotation properties (label, def, synonyms, ...).

The plugin itself will not be OBO-specific, but will provide a default mode for OBO (GO?). Here is the current out-line/discussion: https://docs.google.com/document/d/17tph3jwrDGEaa7DyYPOK8HCi2dCDdJxi3VrTWNQpbqc/edit?pli=1#

Draft formalisation of multi-species annotation (bumped to next week)

https://docs.google.com/document/d/196nLKiQ2Go4toilCq226w7u0p52odvCkq-bU5qgtzu0/edit?usp=sharing

There are two versions. The first is probably best. The second doesn't make individuals for classes and as a result uses some odd nominalisation patterns in the class expressions.

OWL files implementing these examples are here:

http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/experimental/David/multi_species_annotation/

Have a look at the query classes. Can you think of any more useful queries?

One piece of formalisation I feel unsure about right now: I'm wondering whether we need to have the relationship between gene product and organism be 'encoded by' rather than 'expressed in' or 'expressed by'. In the case of viruses - it is arguably the host that does the expressing.

A second issue: I'd like to make this consistent with the formalisation we're working on in PCO - I still think we need some kind of formal bridge between NCBI taxon and organism terms in CARO2/PCO. I guess this could be a simple as making an equivalence mapping between the root of NCBI taxonomy and some term for an individual organism (or organism, virus or viroid).

Also to discuss - how this fits with Lego.

Ontology Development project about Ubiquitination

Seems there has been lots of discussion internally and there are other groups that would like to see improvements in this area.

Mike Livstone has noted that curators from BioGRID have found inadequacies in our representation of Ubiquitination. 
We may need experts (if need be, do we need a content meeting).

ACTION ITEM FOR DAVID H: 
See if expert(s) and Paul T are available to discuss this on our next SF call, i.e. Wed. Jan. 29th (8:30am US West Coast, 11:30am US East Coast, 4:30pm UK). 
Then let Paola know.

Import vs transmembrane transport

Stemming from https://sourceforge.net/p/geneontology/ontology-requests/10621/

Can we think of any import that isn't across a memberane (transmembrane)? Some of us think we  might have seen something about
calcium transport involving vesicles, but can't find it at the moment. In the meantime, most likely 99+% of the time 
import is across a membrane. Suggest renaming terms to make this explicit.
ACTION ITEM FOR ALL: 
Can we find good references? If not, Tanya suggested looking for a recent review on calcium signaling and contacting the authors.
We'll resume discussion next week, either at the SF call (if we can't have ubiquitination discussion then) or at the Editors call.
We need to come up with a strategy, then Paola will implement.