[Ontology-editors] linking GO terms to docs

[Chris Mungall]

On Mar 25, 2009, at 10:16 AM, Karen Christie wrote:

> Hi,
>
> I tend to agree with Chris that if we're going to put this kind of  
> comment/tag in, that it should be added to each term for which it is  
> relevant, as that seems the only real chance that it may be seen.
>
> Regarding keeping links current, it seems that since they are to our  
> own wiki, the main thing would be not changing the wiki url once the  
> comments/tags are put in, and then removing the comments/tags once  
> that particular area has been finished.

Note that it's possible to make links to a particular version of a  
wiki page. We do this in the modENCODE project all the time (protocols  
are specified on the wiki). I'd trust this mechanism more than I would  
discipline...

>
> While I don't object to them being added, I really wonder how much  
> they will be seen by the desired target audience. Even in OBO-Edit,  
> you have to specifically think to look at comments, and lots of  
> other tools or browsers don't show them at all. For example, in SGD,  
> I am the only curator/annotator (out of 10) who uses a method of  
> browsing for terms where it is even possible to see comments.
>
> -Karen
>
>
> On Wed, 25 Mar 2009, 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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