[Ontology-editors] linking GO terms to docs

[Alexander Diehl]

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
>>>>>>>>>>

-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131