[Ontology-editors] linking GO terms to docs

[Harold Drabkin]

Yes, I agree; the comments for ALL of them are very useful. So both 
annotator and user needs to be looking at them as well as the def (in a 
perfect world 8-|
h

Alexander Diehl wrote:
> The point should be made that comments are not just for obsolete 
> terms, but often help to clarify the meaning of particular terms or 
> help annotators or users to find related terms which may be more 
> appropriate. All annotators should pay attention to them, particularly 
> when using terms that are new to them.
>
> See "extracellular space" and "extracellular region":
>
> http://www.informatics.jax.org/searches/GO.cgi?id=GO:0005615
> http://www.informatics.jax.org/searches/GO.cgi?id=GO:0005576
>
> -- Alex
>
>
> Harold Drabkin wrote:
>> 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
>>>>>>>>>>>
>