[Ontology-editors] linking GO terms to docs

Harold Drabkin hjd at informatics.jax.org
Wed Mar 25 10:37:12 PDT 2009 

MGI also shows the comments in the GO browser.  They can also check a 
box to see an obsolete term, and the comments of course usually say why 
the term was obsolete and tips on what to use. I think this informatiion 
IS valuable to a user as well as a curator.


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
>>>>>>>
>>>>>
>>>>>
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>>>>
>>
>>
>> -- 
>>
>>
>> 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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