[Go] GO Web Services

[Jim Hu]

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.  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.

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.

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
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>>>>>>
>>>>>
>>>>>
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>>>>
>>>>
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>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
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>
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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