[Ontology-editors] linking GO terms to docs

[Emily Dimmer]

I agree, links to GO wiki pages should only be created when it is 
strongly believed that the URLs are unlikely to change. For this reason, 
perhaps only the main page for a discussion topic should be linked (such 
as: http://wiki.geneontology.org/index.php/Signaling )

Relevant excerpt from GOC meeting minutes:
"And there is a general issue of not being able to find documentation 
and when it's appropriate to use a term. Particularly since some of this 
information is spread between the wiki, GO web page, meeting minutes, 
annotation camp minutes, etc. This often leads to inconsistent usage - 
"binding" and "regulation" terms were brought up as examples.

Although the definition provides the core usage, it often is not enough. 
Many people voiced support for examples of how to use the term, with 
PMIDs, as well as examples of cases when you wouldn't want to use it. 
Seth and Debby suggested links to GONUTS from AmiGO. Having a wiki would 
not limit the amount of space that's available. If there are links to a 
wiki page, they need to be propagated through to all children terms. A 
few were concerned about displaying this publicly but in general, there 
was support for making it public, particularly since E. coli is trying 
to have the community annotate."




Jennifer Deegan (nee Clark) wrote:
> Hi,
>
> If we do this I would be in favour of having a curation status tag in 
> obo and having defined semantics in terms of how it propagates up and 
> down as Chris suggests. This will make the information easier to keep 
> up to date. My major concern is the amount of work required to keep 
> the links current.
>
> Jen
>
> Emily Dimmer wrote:
>> 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