[Go] GO Web Services

[Pankaj Jaiswal]

Plant Ontology group is also very interested in this aspect, as many of 
our users are also interested in having a PO web services. Incidentally 
there is some work going on at NCGR via their project on Virtual Plant 
Information Network (VPIN) [http://vpin.ncgr.org/index.shtml] on 
ontology platforms [http://vpin.ncgr.org/ontologies.shtml], that is 
funded by NSF. Damian Gessler is the project PI.

Pankaj

Suzanna Lewis wrote:
> 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
>>>>>>>>