[Go] GO Web Services
Pankaj Jaiswal
pj37 at cornell.edu
Mon Apr 21 11:06:34 PDT 2008
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
>>>>>>>>>>
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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
>
>
>
--
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
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