[Ontology-editors] linking GO terms to docs

[Jennifer Deegan (nee Clark)]

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
>>>
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>>> Ontology-editors at geneontology.org
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>>>
> 
>