[Ontology-editors] linking GO terms to docs

Harold Drabkin hjd at informatics.jax.org
Wed Mar 25 10:39:23 PDT 2009 

Harold Drabkin wrote:
> 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.
>
sample link: http://www.informatics.jax.org/searches/GO.cgi?id=GO:0016718
>
> 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
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>> 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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