Ontology meeting 2015-06-25: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
Line 121: Line 121:
Aim for guidance on use of during in Ontology and by annotators. TO be discussed in annotation call.
Aim for guidance on use of during in Ontology and by annotators. TO be discussed in annotation call.


=== Follow-up: Remove redundant relations for release files ===
As discussed last week, we updated the release process to remove redundant super classes for go.{obo|owl} and go-simple.{obo|owl} (go-basic and other legacy files are derived from go-simple, so they should be fine too).
The only remaining one is the go-plus file release, which needs more work. (It is currently also a different Jenkins job)
The


[[Category:Ontology]]
[[Category:Ontology]]
[[Category:Meetings]]
[[Category:Meetings]]

Revision as of 16:21, 24 June 2015

Attendees:

Minutes: Paola


Protein family complex terms

For protein complexes consisting of multiple subunits from the same family (e.g. smads, integrins, some channels), should we just a general family term and then rely on InTact for specific classes.

(We provisionally agreed to this before). For many such cases, our coverage is very spotty and not likely to get better soon.

BUT NOTE: This approach involves obsoleting the more specific classes we currently have. Ideally we'd have a way to reference the INTACT ID in an annotation extension. This rather stretches the semantics of AEs.

GO term request with composed uberon terms

[Chris and David OS] Stems from https://github.com/geneontology/termgenie/issues/71

Follow-up: New TG templates

Where are we with action items on these? Copying over from last discussion:

If the export templates are ready, we'll test them, then advertise them along with the ones below:

cellular component binding

cellular component organization

import_across_membrane

import_across_plasma_membrane

import_into_cell

We resolved to change the template for 'cellular component organization' to make 'cellular process' the genus 
(let’s try that, rather than further up the graph, and see what happens). 
Jira ticket: https://www.ebi.ac.uk/panda/jira/browse/GO-327
UPDATE - THIS IS NOW DONE.
Once that's done and tested, we can advertise the 5 templates above.
As for the export templates, David OS is still working on them. He'll check that he has all the relevant info in one ticket.
 https://www.ebi.ac.uk/panda/jira/browse/GO-348  This has export pattern, ready to be implemented.
 https://www.ebi.ac.uk/panda/jira/browse/GO-331  David looking in to whether patterns for export from cell are safe.
 Paola suggests waiting until all templates are ready to announce.
   
   'import across plasma membrane' terms are currently inferred subclasses of import into cell. 
   Perhaps questionable for cells with cell wall.  But definitely wrong to have reverse inference on export. 
   Hard to see how to formally define export across plasma membrane given this.

Follow-up: No more merges

Where are we with action items on this? Copying over from last discussion:

Ultimate aim: Use obsolete & replaced_by, where replaced_by has a
cardinality of 1.  We will only announce obsoletion where there is
either no suggested replacement, or multiple suggested replacements
(via consider).

Reason: Current strategy causes loss of URIs and their associated
data.  This makes life hard for tracking by groups who rely on the
OWL, and assume URIs will remain stable and resolvable.  It also loses
useful information associated with terms.

Short term: 
 - Change to OBO to OWL conversion to ensure URIs are not lost in the
   OWL side (this has already been done and will be in OWL-API).  
 - Note - with this change to the OWL, need to check AMIGO load (from
   OWL) works OK.
 - Editors merge as usual, but also  Add xref to losing synonym:
   alt_id:GO:nnnnnnn.

Medium term: 
 - AI: Change all 1:many replaced_by to 1:1 :Chris?:
 - AI: Make list of things that would break in GO when we make full change.  :Chris:Heiko:

Long term: 
- AI:Chris takes charge of making anouncement to world of full
  change, giving 1 year lead time. 

 AI: Update doc (for now stays on wiki)

Follow-up: GO-SO issues

Where are we? Copying from last discussion:

There are various problems with our use of SO, some of which requires co-ordination with SO dev:

  1. We need a bridge from SO transcript terms -> ChEBI:RNA. In the absence of this, lots of inference is missing. Will the long planned SO molecular save us, or do we need our own bridge axoims?
  2. We need a differentium for recording which RNA metabolic processes are processing (involve maturation). We may be able to do this using terms from SO (see next item), or we could use a similar strategy to the one we use for developmental progression via a 'results in maturation of' relation. (We may, in fact, need a combination of these).
  3. We use the SO terms nRNA, ncRNA and its children as if they refer to both mature and immature states of transcripts. In fact, according to SO they refer to the mature state. To align with SO properly we would need to review usage and use alternative SO terms where available. SO has an additional set of terms for primary transcripts, but no terms for immature. Primary transcript refers only to before splicing so no terms for intermediate state after splcing and before other modifications involved in maturation such as capping and polyadenylation for mRNA. Need to discuss possibilities of adding these with SO.

DOS organising meeting with Karen Elibeck. Who wants to be involved?

AI: organise a meeting with Mike Bada and Karen Eilbeck. David OS and Chris will be involved. 
AI: David OS will make a doodle poll.  DONE
We need a formal way to refer to transcript maturation; it’s all manual right now. 
It would be nice if we could do it by referring to the participating transcript, but maybe that’s a bit too complicated. 
Otherwise use results_in_maturation_of - currently it’s used strictly in development; could it be expanded? 
No, that may lead to too many unwanted inferences. 
We probably need a whole new relation to refer to transcript maturation. 
AI: come up with a new relation. Do that in discussion with SO.

https://code.google.com/p/sequence-ontology/source/browse/#svn%2Ftrunk%2Fsrc%2Fontology%2Fdev

 AI: DOS to add ticket for new relation to RO repo - with aim of adding to ontology ASAP.
    https://code.google.com/p/obo-relations/issues/detail?id=63&thanks=63&ts=1434641139

Follow-up: X dependent process & involved in

We have many X-dependent process terms. My initial reading of the names and definitions of these terms was that the X must be upstream, but typically X (implicitly) is treated as part of the process that depends on it, as shown by the large number of cases of term of the form X involved in X dependent process Y. This may be a good thing, but perhaps could be made clearer with some design patterns.

Prompted by: https://sourceforge.net/p/geneontology/ontology-requests/11713/#a397

 Ruth & Rachael are already reviewing ~ 2000 annotation extensions using dependent_on.
 They plan to post the results to the annotation extensions GitHub site https://github.com/geneontology/annotation_extensions
 Following this, DOS to review list of terms in ontology using during to see where the same patterns might apply.

Aim for guidance on use of during in Ontology and by annotators. TO be discussed in annotation call.

Follow-up: Remove redundant relations for release files

As discussed last week, we updated the release process to remove redundant super classes for go.{obo|owl} and go-simple.{obo|owl} (go-basic and other legacy files are derived from go-simple, so they should be fine too).

The only remaining one is the go-plus file release, which needs more work. (It is currently also a different Jenkins job) The