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

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Mon, 7 Feb 2011 23:46:48 +0100
Message-ID: <AANLkTi=xKnyUTvLGVmNRNqjvHVGz_6oQXia+_Qhq-Ymh@mail.gmail.com>
To: anita bandrowski <bandrow@gmail.com>
Cc: HCLS <public-semweb-lifesci@w3.org>, Maryann Martone <maryann@ncmir.ucsd.edu>
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
>
Received on Monday, 7 February 2011 22:47:21 GMT

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