Ontology meeting 2014-03-27

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Attendees:

Minutes:

Newest release of OBO-Edit

We all need to switch to 2.3.1 before we can include taxon rules in editors file. I've tested it [Paola] and it looks ok. Download from:

http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.3.1/

We're all now switched over to 2.3.1 - Chris will add the taxon constraints to the editors file tomorrow or early next week.

Taxon rules

Once we include taxon rules in the editors file, will the rules propagate over relationships other than is_a and part_of?

E.g. 'gap junction' only_in Metazoa

'gap junction assembly' results_in_assembly_of 'gap junction'

'gap junction assembly' only_in Metazoa?

See https://sourceforge.net/p/geneontology/ontology-requests/10740/

ANSWER: Yes! Note that you can look in Protege or OntoBee under 'property chains' http://purl.obolibrary.org/obo/RO_0002162

COMMENT: Good, but 'results_in_assembly_of' is not included for now. Before including it, we need to answer the question "Are there any multi-species assembly instances?". Jane says "Yes there are e.g. 'pore formation in membrane of other organism ; GO:0035915'". So we may not want to add 'results_in_assembly_of' to that list of property chains. Bit frustrating, but we probably can't check all assembly terms manually...

We discussed this and decided that we would not want to propagate the taxon rules over results_in_assembly_of because of the multi-species interactions where one organism assembles a cc in another. We considered altering the definition  of never_in_taxon, only_in_taxon to give a get-out clause for MOPs, but we decided against this. 
We'll add the individual constraints as we see necessary and perhaps do a periodic check of what the implications would be if we did automatic propagation of cc -> bp

gene expression/transcription 'involved in' terms

Following a discussion with Ruth and Rachael, it seems that using the TG 'involved in' template for gene expression/transcription may have been wrong e.g. 'regulation of gene expression involved in extracellular matrix organization'. Here the regulation of gene expression shouldn't be part of the process extracellular matrix organization, I think instead it should be 'causally_upstream_of'.

Here is the full list of terms:

GO:0060807	regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification
GO:2000976	regulation of transcription from RNA polymerase II promoter involved in detection of glucose
GO:1900094	regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry
GO:0003258	regulation of transcription from RNA polymerase II promoter involved in endocardial precursor cell differentiation
GO:0021882	regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment
GO:1901213	regulation of transcription from RNA polymerase II promoter involved in heart development
GO:0060994	regulation of transcription from RNA polymerase II promoter involved in kidney development
GO:0060500	regulation of transcription from RNA polymerase II promoter involved in lung bud formation
GO:0060597	regulation of transcription from RNA polymerase II promoter involved in mammary gland formation
GO:0061216	regulation of transcription from RNA polymerase II promoter involved in mesonephros development
GO:0072212	regulation of transcription from RNA polymerase II promoter involved in metanephros development
GO:0003256	regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
GO:0021918	regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment
GO:0090236	regulation of transcription from RNA polymerase II promoter involved in somitogenesis
GO:1902064	regulation of transcription from RNA polymerase II promoter involved in spermatogenesis
GO:0021909	regulation of transcription from RNA polymerase II promoter involved in spinal cord anterior-posterior patterning
GO:0021920	regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification
GO:0021912	regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification
GO:0021913	regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification
GO:0090019	regulation of transcription involved in anterior neural plate formation
GO:0044324	regulation of transcription involved in anterior/posterior axis specification
GO:0060850	regulation of transcription involved in cell fate commitment
GO:0060899	regulation of transcription involved in eye field cell fate commitment of camera-type eye
GO:0000083	regulation of transcription involved in G1/S transition of mitotic cell cycle
GO:0000117	regulation of transcription involved in G2/M transition of mitotic cell cycle
GO:0060849	regulation of transcription involved in lymphatic endothelial cell fate commitment
GO:0090020	regulation of transcription involved in posterior neural plate formation
GO:0060796	regulation of transcription involved in primary germ layer cell fate commitment
GO:0060852	regulation of transcription involved in venous endothelial cell fate commitment
GO:1901311    regulation of gene expression involved in extracellular matrix organization

The cell cycle ones may be a special case, I'll need to confer with Val. But what about the development ones? Is the transcription regulation really part of the process or is it really upstream?

The development ones are fine, the erroneous ones are GO:1901311    regulation of gene expression involved in extracellular matrix organization and  GO:2000976	regulation of transcription 
from RNA polymerase II promoter involved in  detection of glucose. When Heiko is back we will add a note to the involved in template to clarify its use. We will ask Ruth to post-compose the 
causally_upstream_of terms in the annotation.

happens_during

There has been some confusion amongst annotators about the use of happens_during in c16. For example:

Human miR-29b: GO:0035195 gene silencing by miRNA IDA C16: has_ regulation_target human COL1A1 [and COL3A1] happens_during GO:0071560 cellular response to transforming growth 
factor beta stimulus.

In this case the gene silencing by miRNA is actually part_of the response to TGF beta, but the temptation that if you're not sure whether one process is part of another to use happens_during but this doesn't imply causality.

Are we happy restricting the use of happens_during to being between bps and phases as we discussed? ATM in protein2go the only restriction for happens_during is biological process.

Val et al are using happens_during between bps legimately, so we wouldn't want to make that constraint.  Jane to speak to Tony about adding a 'did you mean' note to protein2go when annotators are using happens_during 
to make it clear that no dependency is implied.

[For Chris] Do annotations propagate over 'capable_of'?

Carried over from last week: Stemming from a SF request from Birgit. She asked that 'ripoptosome' be made is_a 'catalytic complex'; where 'catalytic complex' is_a 'protein complex' capable_of 'catalytic activity'. I agree that the ripoptosome as a whole can perform a catalytic function, but this complex often contains non-enzymatic proteins that act as adaptors (FADD, CFLAR, TRIF/TICAM1). These adaptor proteins are indeed annotated to 'ripoptosome'. If I added the link 'ripoptosome' is_a 'catalytic complex', would the adaptor proteins become hard-linked to 'catalytic activity'? That would be incorrect.

This is somewhat similar to the previous issue of 'transmembrane' complexes where some of the components do not span the membrane. See discussion in SF ticket here: https://sourceforge.net/p/geneontology/ontology-requests/10711/

 David OS says that No, annotations do not propagate over 'capable_of', or any other relationship other than is_a, part_of and, possibly, regulates, but we need to make sure. 
 (For 'regulates' Chris said he'd provide documentation/details on exceptions but we couldn't find anything - Chris, did we miss it?) 
 We need documentation and we also need to make sure that this is not tool-dependent (does AmiGO2 do the right thing?). 
 Chris, please comment.
 We will be conservative with propagating over relations other than is_a and part_of. The default is not to propagate. We will write docs to clarify what it means to 
 clarify over these relations.

Follow-up: 'colocalizes with' nuclear chromatin

Carried over from last week as we need Chris too. See http://wiki.geneontology.org/index.php?title=Ontology_meeting_2014-03-13

Where are we with the planned action items? David OS made a start on this. Transitive?

 David OS to put together a proposal for this, run it by Tony. We will discuss again in 3 weeks.

logical def for GO:1990344

Please see SF item for background https://sourceforge.net/p/geneontology/ontology-requests/10730/

 There is an underlying problem with the cc terms, Tanya to follow-up

Protege

Carried over from last week: To discuss with Chris:

Are we really ready for Protege?

David OS will add examples and tips for GO editing and browsing in Protege on the wiki. Chris has started asking people about the plug-in. The plan is to have a meeting to figure out what kind of progress we can have on that in a reasonable time-frame. We need a write-up of the sort of things that are currently hard for editors to do/render in Protege; things that you can do in OE but can't currently do (or easily do) in Protege. E.g. new terms, searches... rendering in tree views is virtually impossible now. We could have a period where we do things using both tools, but one worry is that some of us may not be able to work with both tools open on a machine that doesn't have loads of memory.

AI for all: For the time being, we can all try using Protege in our normal work flow and report on the difficulties we encounter. Jane made a wiki page and we can all add to it: http://wiki.geneontology.org/index.php/Protege_Feature_Requirements.

AI: DOS to add link to the specs document.

Specs doc is here: https://docs.google.com/document/d/17tph3jwrDGEaa7DyYPOK8HCi2dCDdJxi3VrTWNQpbqc/edit

Alpha version of OBO annotation plugin is here: https://github.com/simonjupp/protege-obo-plugins

  The wiki page will be the place to collect use cases, the Google doc will be for specific feature specifications.

Follow-ups and action items from GOC and SAB meetings

Might also be a good time to do a critical assessment/review/update of our Jira tickets in view of the above.