[Ontology-editors] linking GO terms to docs

[Emily Dimmer]

Hi Chris,

The idea of more fully linking discussions on the GO wiki to the terms 
was discussed at the last GO Consortium meeting.

Such links provided between terms and GO wiki pages would help curators 
become more aware of the current ontology/annotation development 
efforts. Curators might not consider themselves expert in a topic and so 
not join a specific working group, but they want to have the option of 
looking at the current relevant GOC discussions when they are choosing a 
term for annotation purposes.  I strongly feel that there is no point 
having extensive discussion regarding a set of terms if this 
conversation hidden in the depths of the GO wiki. If the curator has a 
concern with an ontology or annotation discussion that appears in the 
wiki, then text on wiki pages should direct them an appropriate mailing 
list.

The comment section seems the correct place to put such URLs,  as advice 
on the appropriateness of a term's usage is already included in this 
section (e.g. extracellular region and extracellular space terms). 
Therefore GO browsers which support curator annotation activities should 
already display the comments section for a GO term.

I agree that it would be far better to have such comments propagated in 
OBO than have the individual tools try to do this, esp. if there are 
some comments which are appropriate for a whole node of an ontology 
while others might be specific to a certain term.

Emily



Chris Mungall wrote:
>
> Who is this message aimed at? End-users, annotators, both? How are 
> people meant to react to this information?
>
> I seriously doubt that tools implementors will take the time write 
> ad-hoc one-off code to propagate this one particular comment down the 
> hierarchy.
>
> If this is important, then why not take the low-tech approach and (1) 
> email go-friends and (2) propagate the comment down ourselves and 
> manually remove individual comments as we fix things.
>
> (1) is the most effective at reaching people as not all browsers 
> necessarily show comments, and when they do it's only in certain 
> contexts. You could be browsing the tree or looking at term enrichment 
> results and never see this.
>
> If this kind of thing is to become common then we should figure out a 
> curation status tag in obo, have defined semantics in terms of how it 
> propagates up and down, etc
>
> On Mar 25, 2009, at 7:00 AM, Jennifer Deegan (nee Clark) wrote:
>
>> Hi,
>>
>> The discussion to start overhauling the signaling terms is just 
>> starting to get going now and we would like to make sure all 
>> annotators are aware of this. Emily has suggested that we might put a 
>> pointer to the signaling wiki page into the comment field of the 
>> signal transduction terms to alert users to its existence. She says 
>> that this comment could then be cascaded down to the child terms by 
>> the various browser tools.
>>
>> If no one has any objections I will add a comment to signal 
>> transduction on Friday and it will say:
>>
>> "The signaling terms in GO are currently being overhauled. If you 
>> would like to read about the discussions, or contribute your ideas or 
>> thoughts please visit http://wiki.geneontology.org/index.php/Signaling."
>>
>> I will also improve that page on the wiki so it is clear to people 
>> where to go to read about discussions and contribute ideas.
>>
>> Thanks,
>>
>> Jen
>>
>> _______________________________________________
>> Ontology-editors mailing list
>> Ontology-editors at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>


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------------------------------------------------------------------ 

    Emily Dimmer Ph.D.
    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