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[go-ontology] Linking to annotation guidance

Emily Dimmer edimmer at ebi.ac.uk
Thu Dec 1 02:57:47 PST 2011


Thanks Chris. We agree the regexp using GO term conventions is a hack, 
but its been the easiest way to target certain subsets of terms in a GO 
node.

How about putting this up on QuickGO first - advertising it to groups in 
the GO Consortium and then have a discussion to find out what works/what 
could be improved. We could have it visible just before the next GO 
annotation call. We could then export the data from GOA in the most 
appropriate format whereupon it could be then centrally maintained in 
GO, if folk see value in the resource.

Cheers,
Emily

On 01/12/2011 03:19, Chris Mungall wrote:
>
> So all the guidelines are on the wiki anyway? I really think a
> wiki-based solution is best here. Arrggghh, we're not even using simple
> wiki categories for pages like this:
> http://wiki.geneontology.org/index.php/Annotations_to_Catalytic_activity_with_IPI
>
> Anyway, let's not confuse the implementation with the representation. It
> seems from the below that what you need is a table or stanza like format:
>
> * Term
> * Inherited [over what? isa? isa/part_of? regulates?]
> * Title
> * URL
> * RegExp (what's this? Looks a bit hacky)
>
> This should live in GO CVS where it can be versioned alongside the
> ontologies (when we switch to SVN we can have _much_ better versioning
> of everything, which we get automatically).
>
> It can then be displayed by any application that wants to show it.
>
> Much further down the line, this can easily be incorporated into the OWL
> version of the ontology.
>
> On Nov 30, 2011, at 4:57 AM, Jane Lomax wrote:
>
>> On 30/11/2011 01:48, Chris Mungall wrote:
>>>
>>> On Nov 29, 2011, at 5:59 AM, Jane Lomax wrote:
>>>
>>>> Hi - for the apoptosis work there is a need to provide a stable link to particular annotation guidance docs on a per-term basis. The location of the docs will eventually change so we don't want to embed a URL.
>>>>
>>>> In the past we've used GO_REFS added to the definition dbxrefs of terms but this isn't really correct use of the field.
>>> Is it really overloading this? What are some examples of annotation guidelines?
>> For example:
>>
>> http://www.geneontology.org/GO.annotation.conventions.shtml#Binding_guidelines
>> http://www.geneontology.org/GO.doc.cc-membrane-prots.shtml
>> http://www.geneontology.org/GO.annotation.conventions.shtml#interactions
>>
>>>> Two possible suggestions:
>>>>
>>>> 1. Add a new tag to OBO format for 'annotation documentation' or similar. The value would be a GO_REF which would be to a URL or document.
>>> So you would use GO_REFs? How many are you expecting? Might this get hard to manage?
>>>
>>> Adding a new tag to OBO format is not trivial. It's easier to use the generic property_value tag and request a property from IAO. In either case, it would be invisible in OE until OE is extended to support this.
>>>
>>> Another alternative is to use gonuts. That way it's easy for annotators to contribute. Easy to add hyperlinks, etc
>> The GO_REF would usually be a URL or similar.
>>
>> I don't think GO nuts really helps here - the critical thing is really
>> the rules for the way the documents are indexed with the terms e.g.
>> associate this doc with this term and all its descendants. How the
>> information is displayed would be down to the browser.
>>
>> The GOA group are going to trial this in QuickGO to see how it works
>> out. They're going to build the following in to the QuickGO schema:
>>
>>> Parent GO ID 	Inherited by Children? 	Link text 	Curation guidance
>>> URL 	RegExp 	GO Aspect
>>> GO:0003824 	Y 	Annotating to catalytic activities using the IPI
>>> evidence code
>>> http://wiki.geneontology.org/index.php/Annotations_to_Catalytic_activity_with_IPI
>>> 		F
>>> GO:0003677 	Y 	Considerations when annotating from ChiP assay
>>> results
>>> http://wiki.geneontology.org/index.php/Annotation_consistency_:_ChIP_experiments
>>> 		
>>> GO:0016021 	Y 	Discerning the appropriate spatial relationship
>>> between a membrane and a gene product
>>> http://www.geneontology.org/GO.doc.cc-membrane-prots.shtml 	^integral
>>> to.* 	C
>>> GO:0051704 	Y 	Annotating gene products that interact with other
>>> organisms
>>> http://www.geneontology.org/GO.annotation.conventions.shtml#interactions
>>> 		
>>> GO:0005488 	Y 	Binding term considerations
>>> http://www.geneontology.org/GO.annotation.conventions.shtml#Binding_guidelines
>>> 		
>>> GO:0050896 	Y 	Response to guidelines
>>> http://www.geneontology.org/GO.annotation.conventions.shtml#response_to
>>> 	^response to.* 	P
>>> GO:0031224 	Y 	Discerning the appropriate spatial relationship
>>> between a membrane and a gene product
>>> http://www.geneontology.org/GO.doc.cc-membrane-prots.shtml
>>> ^intrinsic to.* 	C
>>> GO:0019898 	Y 	Discerning the appropriate spatial relationship
>>> between a membrane and a gene product
>>> http://www.geneontology.org/GO.doc.cc-membrane-prots.shtml
>>> ^extrinsic to.* 	C
>>> GO:0031225 	Y 	Discerning the appropriate spatial relationship
>>> between a membrane and a gene product
>>> http://www.geneontology.org/GO.doc.cc-membrane-prots.shtml 	^anchored
>>> to.* 	C
>>>
>>>
>>>
>>>
>>
>>>> 2. Extend the scope of the taxon restrictions file and put the links to the documentation in there. Then browsers could choose to scoop that information from the file and display it or not. Ideally there would be a way to say 'link this particular doc to this term and all its descendants'.
>>> That's extending the scope quite a bit...
>>>
>>> But the basic idea is that you could have a separate file somewhere. Wouldn't have to be obo-format, just something ad-hoc. This seems fine. Doesn't preclude translating to something else later on.
>> Yep - exactly. I think this is the lowest threshold option. Let's see
>> how it works out with QuickGO.
>>
>>>> We need something fairly quickly here...
>>>>
>>>> cheers,
>>>>
>>>> Jane
>>>>
>>>>
>>>> _______________________________________________
>>>> go-ontology mailing list
>>>> go-ontology at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/go-ontology
>>
>


-- 


------------------------------------------------------------------
    Emily Dimmer Ph.D.
    UniProt-GOA Coordinator
    EMBL-EBI
    Wellcome Trust Genome Campus
    Hinxton
    Cambridge CB10 1SD, U.K.
    Tel:     +44 1223 494654
    Fax:    +44 1223 494468
    email:  edimmer at ebi.ac.uk
    URL:    http://www.ebi.ac.uk/goa
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