[Ontology-editors] linking GO terms to docs
Karen Christie
kchris at genome.stanford.edu
Wed Mar 25 11:03:27 PDT 2009
While I see your point that it would probably be good to make comments
available for both curators and users, changing a tool is a little more
involved than "extreme bribing or pestering of the programmer responsible
for your browser".
First of all, a database change would be required, to have a place to load
this field, before it's even possible to display it via any web interface.
While I can put it on a list of suggestions, the decision of whether or
when to make such a change would go to SGD's management group who would
balance it against other priorities for SGD's database administrator and
programmers to make the changes and for curators to test it. If I put it
on the list today, I would suspect it could take a year or two before such
a change made the priority list to be implemented and actually in
production.
While it's great that QuickGO and MGI are ahead of the curve on this
particular issue, we should be aware that comments will probably remain
really inaccessible to a significant fraction of GO annotators for a while
yet.
-Karen
On Wed, 25 Mar 2009, Emily Dimmer wrote:
> 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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