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Re: Reminder: BioRDF telcon NOW at 11AM EDT (4PM UK, 5PM CET)

From: Maryann Martone <maryann@ncmir.ucsd.edu>
Date: Mon, 7 Feb 2011 15:11:58 -0800
Cc: Anita Bandrowski <bandrow@gmail.com>, HCLS <public-semweb-lifesci@w3.org>, "'Jeffrey S. Grethe'" <jgrethe@ncmir.ucsd.edu>, Amarnath Gupta <gupta@sdsc.edu>
Message-Id: <EF874E4A-398C-422E-A267-37B816342D57@ncmir.ucsd.edu>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>
Thanks Scott.  It was a pleasure to talk with you.  I'm adding  
Amarnath and Jeff to this thread as they are the ones that need to be  
looking at this, I think.

On Feb 7, 2011, at 2:46 PM, M. Scott Marshall wrote:

> On Mon, Feb 7, 2011 at 6:55 PM, anita bandrowski <bandrow@gmail.com>  
> wrote:
>> Thanks for inviting us to talk to you today, Scott et al.
>> I think that several synergies emerged.  So below are a couple of  
>> "to do's"
>> that will hopefully help us proceed:
>
> Thanks to you and Maryann for showing us NIF and discussing it with us
> in the context of microarrays and federation. It is good that we have
> a common interest toward making microarray studies available for
> programmatic access (through RDF). That increases our chances of
> arriving at a consensus about the RDF.
>
>> Please take a look at the NIF and give us a list of datasets that  
>> you would
>> like to have in RDF and we will work to get this to you (not all  
>> data is
>> sitting inside of the same database and we do have data in MySQL,  
>> Postgres,
>> Oracle and others so the index is unified but not all the data are).
>
> Ok, we will work on a list of datasets, probably with an immediate
> preference for datasets that are accessible via a database connector
> for mySQL or Postgres to begin with (because we can probably make more
> rapid progress if we can use SWObjects, which hasn't been tested as
> much with Oracle SQL).
>
>> Here are some hopefully helpful links:
>> main developers page (SPARQL endpoint, ontology services, and  
>> federated data
>> indexes linked to from here): http://neuinfo.org/developers/
>> list of data sources: http://neuinfo.org/nif_components/data_federation.shtm
>> list of our current BRO/Biositemaps compliant resources can be  
>> found here:
>> http://neuinfo.org/nif/nifgwt.html?tab=registry
>
> Thanks for the tips.
>
>> Can you send a link to the tool that you told us about that will  
>> transform
>> MySQL into RDF?  We would like to evaluate it with our group.
>
> http://precedings.nature.com/documents/5538/
>
> Eric, Lena, and I gave a tutorial on SWObjects at SWAT4LS in December.
> Hopefully, this will provide a good starting point. The software is
> not industrial strength but could be strengthened with extra hands.
> It's open source and Eric is open minded.:) Eric is adding some
> improved logging and there have been requests to integrate more
> tightly with Apache.
>
> There has been some difficulty creating generic builds for Macs
> because of dynamic libraries (can only build to static paths) so we
> could use some help testing the Mac binaries. If you run your SPARQL
> endpoint services and database connectors on Linux or Windows, then
> you needn't bother with the Mac binaries.
>
> The basic idea behind SWObjects is to use SPARQL Constructs to create
> maps from one SPARQL query to another, and/or create a SPARQL view of
> SQL (has been tested with mySQL). The essential approach is nicely
> light-weight.
>
>> Please put us on the list of people who could potentially  
>> contribute to the
>> RDF specification of microarray data (and perhaps others?).
>
> Ok. Here is the GoogleDoc where we've just gotten started:
> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?hl=en&authkey=CK-y8Y8C
>
> Best,
> Scott
>
> -- 
> M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
> http://staff.science.uva.nl/~marshall
>
>> On Mon, Feb 7, 2011 at 8:03 AM, M. Scott Marshall <mscottmarshall@gmail.com 
>> >
>> wrote:
>>>
>>> On Fri, Feb 4, 2011 at 7:51 PM, M. Scott Marshall
>>> <mscottmarshall@gmail.com> wrote:
>>>> A reminder of the BioRDF telcon on Monday:
>>>>
>>>> Maryann Martone and Anita Bandrowski from NIF (Neuroscience
>>>> Information Framework) will join us to give us a small tour of NIF
>>>> with a focus on how microarray resources are currently handled in  
>>>> NIF.
>>>>  Maryann and Anita can give us a (NIF) user perspective on
>>>> microarrays.
>>>>
>>>> Please call in to Zakim for the audio and use
>>>> http://connect.neuinfo.org/webinar for the screen sharing.
>>>>
>>>>
>>>> http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2011/02-07_Conference_Call
>>>>
>>>> Cheers,
>>>> Scott
>>>>
>>>> == Conference Details ==
>>>> * Date of Call: Monday, January 31, 2011
>>>> * Time of Call: 11:00 am Eastern Time, 4 pm UK, 5 pm CET
>>>> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
>>>> [Note: limited access to European dial in numbers below]
>>>> * Dial-In #: +33.4.26.46.79.03 (Nice, France)
>>>> * Dial-In #: +44.203.318.0479 (Bristol, UK)
>>>> * Participant Access Code: 4257 ("HCLS")
>>>> * IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page
>>>> for details, or see Web IRC), Quick Start: Use
>>>> http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel= 
>>>> %23hcls for
>>>> IRC access.
>>>> * Duration: ~1 hour
>>>> * Convener: M. Scott Marshall
>>>> * Scribe: TBD
>>>>
>>>> == Participants ==
>>>>
>>>> ==Agenda==
>>>> * Introductions
>>>> * Microarrays and NIF ([http://connect.neuinfo.org/webinar screen
>>>> share access]) - Maryann Martone and Anita Bandrowski
>>>> * Microarray RDF - Getting started on the W3C note
>>>> * AOB
>>>>
>>>> --
>>>> M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/ 
>>>> hcls
>>>> http://staff.science.uva.nl/~marshall
>>>>
>>>
>>>
>>>
>>> --
>>> M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
>>> http://staff.science.uva.nl/~marshall
>>
>>
>>
>> --
>> Anita Bandrowski, Ph.D.
>> NIF Project Curator
>> UCSD 858-822-3629
>> http://neuinfo.org
>> 9500 Gillman Dr.#0446
>> la Jolla, CA 92093-0446
>>
>

Maryann Martone, Ph. D.
Professor-in-Residence
Department of Neuroscience
University of California, San Diego
San Diego, CA 92093-0446

858-822-0745
Received on Monday, 7 February 2011 23:12:36 GMT

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