[Go] GO Web Services

Suzanna Lewis suzi at berkeleybop.org
Fri Apr 18 14:34:05 PDT 2008 

Did we get this on the agenda for next week?

Hmmm, nope

So I just added it to the Tuesday afternoon agenda (this will likely  
be short, but it should be put on the radar)

-S


On Apr 14, 2008, at 11:38 AM, Chris Mungall wrote:

>
> On Apr 14, 2008, at 7:23 AM, Jim Hu wrote:
>
>> Hi Suzi,
>>
>> I realize this is reviving a discussion from a couple of weeks ago,  
>> but now that I'm in a position to want to actually use them:
>>
>> What web services do we offer from the GOC?
>>
>> For example, can I query a GOC tool with a UniProt or NCBI  
>> identifier and get a list of all the gene associations as an XML  
>> output?  I know I can page-scrape the Amigo page, but I don't think  
>> that counts as a web service.
>
> There are options in a1.5 to export in formats other than html, so  
> you wouldn't need to screen scrape, but even so there are good  
> reasons not to use amigo as a web service (the urls you use may be  
> messy and unstable for one thing)
>
>> Is GOOSE a web service as it currently is set up?  Perhaps the  
>> download as tab-delimited makes it one, but I'm not sure.
>
> I don't see why not. We could add an xml option to make it more web- 
> servicey, but this wouldn't really make sense for GOOSE
>
> Even if we consider GOOSE a web service, it couldn't really be  
> considered complete - one would expect something more API-oriented  
> or service-oriented for web services.
>
> We could extend AmiGO to offer something more akin to real web  
> services
>
> One problem here is that web services are ideal ways to launch  
> killer queries against a database. An option we may consider is to  
> have web services run against the sacrificial database server in  
> berkeley.
>
>> The example above is a real one; I want to prepopulate our  
>> community annotation tables with what is already out there.  What  
>> query do I use if I want all the existing annotations from all  
>> sources for one gene?  This strikes me as running into the dreaded  
>> problem of matching the gene identifiers across sources.
>
> Indeed. We still don't have NCBI identifiers loaded, so even if we  
> had a web service for you, it wouldn't deliver your requirements.
>
> You could in theory compose web services - either manually or via a  
> tool like taverna - using one web service for ID resolution and  
> another for annotation retrieval. But this is maybe a slightly  
> overwrought solution.
>
> What is your time frame for this? I'm guessing yesterday..
>
> If you're willing to be a guinea pig, we have been intending to  
> deploy both web services and ID resolution, running of the berkeley  
> mirror to begin with..
>
> Did you manage to subscribe to the software group?
>
>> Jim
>>
>>
>> On Mar 30, 2008, at 12:52 PM, Suzanna Lewis wrote:
>>> Yep, Jim has it right (including the blurry edges).
>>>
>>> And I believe that we do offer quite a few programmable ways to  
>>> access GO data.
>>>
>>> -S
>>>
>>> On Mar 30, 2008, at 10:08 AM, Jim Hu wrote:
>>>
>>>> Hi Rama,
>>>>
>>>> I'm not sure what the others are talking about, but formally, web  
>>>> services are not the same as web-based tools.
>>>> Web services in my usage is stuff where a structured query  
>>>> dynamically returns something like an XML file that is readable  
>>>> by a computer.  For example, EcoliWiki is a web-based tool, and  
>>>> I've been working on implementing a web service that takes a gene  
>>>> identifier and returns a structured XML document with the GO  
>>>> associations for that gene.  The distinction between web services  
>>>> and frequently updated downloads is a bit blurry in my mind.
>>>>
>>>> Other examples include the E-Utils at PubMed, DAS for gbrowse,  
>>>> and the stuff you don't see in the background that updates Amazon  
>>>> pages from different publishers.   See
>>>>
>>>> http://en.wikipedia.org/wiki/Web_service
>>>>
>>>> Jim
>>>>
>>>>
>>>> On Mar 30, 2008, at 11:49 AM, Rama Balakrishnan wrote:
>>>>> Hi,
>>>>>
>>>>> May be I am missing the obvious here.
>>>>>
>>>>> We already have a page for GO tools-http://www.geneontology.org/
>>>>> GO.tools.shtml
>>>>> and this page is organized by what is web-based, downloadable,
>>>>> provided by GO etc.
>>>>>
>>>>> What will the proposed GO web services page include?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Rama
>>>>>
>>>>>
>>>>>
>>>>> On Mar 28, 2008, at 5:01 AM, Suzanna Lewis wrote:
>>>>>
>>>>>> 2 pages perhaps? One for those services that we (already)  
>>>>>> offer, and a
>>>>>> second for those from others.
>>>>>>
>>>>>> -S
>>>>>>
>>>>>> On Mar 28, 2008, at 12:17 PM, Judith Blake wrote:
>>>>>>
>>>>>>> I think this is an excellent idea...
>>>>>>>
>>>>>>> I particularly like these services that would be useful to our  
>>>>>>> users
>>>>>>> but
>>>>>>> that don't require that we set up toolshops.
>>>>>>>
>>>>>>> judy
>>>>>>>
>>>>>>>
>>>>>>> Michael Ashburner wrote:
>>>>>>>> Should we have a page on GO for GO web services ?
>>>>>>>>
>>>>>>>> GoPubMed
>>>>>>>> Andreas Schlicker (MPI-INF) functional similarity is another
>>>>>>>>
>>>>>>>> M
>>>>>>>> _______________________________________________
>>>>>>>> Go mailing list
>>>>>>>> Go at geneontology.org
>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Go mailing list
>>>>>>> Go at geneontology.org
>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Go mailing list
>>>>>> Go at geneontology.org
>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>> =====================================
>>>> Jim Hu
>>>> Associate Professor
>>>> Dept. of Biochemistry and Biophysics
>>>> 2128 TAMU
>>>> Texas A&M Univ.
>>>> College Station, TX 77843-2128
>>>> 979-862-4054
>>>>
>>>>
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>
>>
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
>

More information about the Go mailing list