[Go] GO Web Services

Mon Apr 21 10:23:04 PDT 2008

Thanks Pankaj,

The "Semantic Google" front-end to the VPIN is at http://sswap.info.

A portal to using PO and other OBO ontologies in semantic web services 
discovered above is at http://sswapmeet.sswap.info.

Damian.

Pankaj Jaiswal wrote:
> 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
>>>>>>>>>