[Ontology-editors] linking GO terms to docs

Harold Drabkin hjd at informatics.jax.org
Wed Mar 25 11:23:00 PDT 2009 

On the other hand, anyone can download oboedit and load the GO, and set 
it up to display comments without much difficulty. Once set up, it is a 
excellent browser.
I can't get t Amigo to display an obsolete term, so if someone thinks a 
term was in or should be, they won't get any friendly "hints" from Amgio 
that they might be barking up the wrong tree.  8-(

h

Karen Christie wrote:
> 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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