[Ontology-editors] linking GO terms to docs
Emily Dimmer
edimmer at ebi.ac.uk
Wed Mar 25 10:41:26 PDT 2009
Thanks :-)
I'd advise extreme bribing or pestering of the programmer responsible
for your browser - if the comments section is populated more often, then
it becomes important that your tool is able to properly display this
part of an entry.
Emily
Karen Christie wrote:
> It's great that QuickGO already shows comments, but I think you may be
> in the minority there. SGD curators do pay attention to definitions,
> but as we don't even load comments into the database, there is no way
> to see comments in any SGD user or curator interface showing GO.
>
> My point was that I suspect that's not a particularly rare situation.
>
> -Karen
>
>
> On Wed, 25 Mar 2009, Emily Dimmer wrote:
>
>>
>> With regards to the tools - once the information is made available,
>> then it becomes the curators responsibility to properly view the
>> information attached to a term (e.g. some curators may be in the
>> habit of not opening up a GO term to read its definition, but this
>> practice is strongly discouraged by the group). Tool developers
>> should also be encouraged to make the comments section visible for
>> those tools used for curation purposes.
>>
>> And just to be inflammatory ;-) a curator looking at a term's
>> details in QuickGO already does see the comments section, e.g.
>> http://www.ebi.ac.uk/ego/GTerm?id=GO:0005615
>>
>> Emily
>>
>>
>> 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.
>>>
>>> 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
>>>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Ontology-editors mailing list
>>>> Ontology-editors at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>
>>
>>
>> --
>>
>>
>> Do you need any additional GO annotation resources?
>> Which proteins would you like annotated with GO?
>>
>> Let us know in the GOA User Survey, available at:
>> http://www.ebi.ac.uk/GOA/contactus.html
>>
>> ------------------------------------------------------------------
>> 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
>>
--
Do you need any additional GO annotation resources?
Which proteins would you like annotated with GO?
Let us know in the GOA User Survey, available at: http://www.ebi.ac.uk/GOA/contactus.html
------------------------------------------------------------------
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
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