[Go] GO Web Services

Tue Apr 22 08:41:29 PDT 2008

Sounds like a good idea, but I won't be able to schedule this until  
after I give my final exam!

Jim

p.s. Damian - I think you are assuming a higher level of technical  
background than I actually have!

On Apr 21, 2008, at 12:06 PM, Pankaj Jaiswal wrote:

> Jim,
>
> Here is a message from Damian. May be we should invite him for a  
> conf call. or a webex meeting to give us an insight. I know Shuly is  
> working for the PO project and is very excited on starting the web  
> services. I will meet her next week at CSHL.
>
> Pankaj
>
>
>
> -------- Original Message --------
> Subject: Re: [Go] GO Web Services
> Date: Mon, 21 Apr 2008 11:23:04 -0600
> From: Damian Gessler <ddg at ncgr.org>
> To: Pankaj Jaiswal <pj37 at cornell.edu>
> CC: Suzanna Lewis <suzi at berkeleybop.org>, Chris Mungall <cjm at fruitfly.org 
> >,        Suzanna Lewis <suzi at fruitfly.org>, go list <go at genome.stanford.edu 
> >,        software-group Group <software- 
> group at genome.stanford.edu>,        Shuly Avraham <shuly at cshl.edu>
> References: <FA534201-8C1C-4702-B81B-076710A10E4D at gen.cam.ac.uk> <47ECD3BB.6080008 at informatics.jax.org 
> > <6842C21D-992D-486C-ADAF-370C738142A1 at fruitfly.org> <3682B998-64DF-45E6-9433-562AA2B50404 at genome.stanford.edu 
> > <42136EBE-A634-4243-B158-57E899D4E301 at tamu.edu> <7DC51A93-4C36-42D0-A0A4-05CDCB9AE2B9 at fruitfly.org 
> > <6211BE8C-E11F-409B-94DC-A76214C850DD at tamu.edu> <95B247A0-8D7F-46D9-AF91-D44F98FDD441 at fruitfly.org 
> > <C0798F09-26E8-4FC8-A3BD-5C108EEFC147 at berkeleybop.org> <480CCBB8.5090705 at cornell.edu 
> >
>
> 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.
>
> Jim Hu wrote:
>> Hi Pankaj,
>> I heard Shuly talk about this last year at a Stein lab group  
>> meeting.... it sounded really exciting.  I need to learn more about  
>> how the services would be applied.
>> Jim
>> On Apr 21, 2008, at 11:15 AM, 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
>>>>>>>>>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org <mailto: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
>
> -- 
> Pankaj Jaiswal
> G-15, Bradfield Hall
> Dept. of Plant Breeding and Genetics
> Cornell University
> Ithaca, NY-14853, USA
>
> Ph. +1-607-255-3103 / 4199
> fax: +1-607-255-6683

=====================================
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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