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[BioRDF] Telcon Minutes

From: Cutler, Roger (RogerCutler) <RogerCutler@chevron.com>
Date: Tue, 14 Mar 2006 09:36:24 -0600
Message-ID: <0C237C50B244FD44BE47B8DCE23A3052011C63BA@HOU150NTXC2MC.hou150.chevrontexaco.net>
To: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>

Minutes from the 3/13 BioRDF telcon are at
rence_Call.  For archival purposes, they are reproduced below.

Conference Details
Date of Call: Monday March 13, 2006 

Time of Call: 11:00am Eastern Time/16:00 UTC 

Dial-In #: +1.617.761.6200 (Cambridge, MA) 

Participant Access Code: 246733 ("BIORDF") 

Duration: ~1 hour 

Convener: Susie Stephens 

Scribe: Roger Cutler 

Draft Agenda
Discuss use case focus 

Review progress on task templates and tasks 

Meeting Minutes
Attendees: Karen Skinner, Susie Stephens, Don Doherty, John Barkley, Kei
Cheung, Alan Ruttenberg, Scott Marshall, Joanne Luciano, Roger Cutler 

Susie: John Wilbanks was going to give update on neuroscience, but
unable to attend this week. Discussion of neuroscience resources is
still important. Perhaps should invite several neuroscience experts and
have a discussion. Shoot for next week. Ideally Tim Clark, John
Wilbanks, June Kinoshita and others would participate. 

Karen: Suggests Dan Gardner. 

Susie: Eric Miller has a strong preference for scientists to join WG
rather than having separate advisory board. 

Tasks Progress: 

Alan: Will start with a task based on reagents, etc. Already has code
that scrapes an antigen Web site that displays information from a number
of vendors. The Alzheimer site has information about antibodies, and a
forum where people ask questions about antibodies. These questions could
form a basis for queries. He'll write up the details of the task by next

Alan: Talked to Davide about whether he could apply company software to
NLP cases - e.g. unstructured description of patient in brain atlas.
Davide is nibbling at the hook. Will arrange demo. Use tool to get XML
out of text parse, then transform XML to RDF. 

Karen: Will talk to Alan offline about antibodies. 

Kei: Has started editing the description of the task on the Wiki. The
general objective is to convert relational data in Oracle Database, to
RDF data in the Oracle Database. The goal is to better understand how to
map the relational structure to the RDF structure. Planning to use D2RQ
for the conversion. Most neuroscience databases are in Oracle. 

Susie: Stanford University has built a pathways database in the Oracle
RDF Data Model that includes KEGG, Ecocyc and Reactome. The database is
available on the Web, and can be queried using Oracle's RDF_MATCH, or
canned queries. Stanford used Jena to parse data from RDF/XML to
NTriple, so that it could be batch loaded into Oracle. Susie agreed to
contact Stanford to see if they could participate in a future call, so
that we could learn more. 

Alan: BIOPAX is in OWL. Stanford would have started with data that had
been exported to BIOPAX from its native format. Each data source has a
custom piece of code specific to the underlying database. 

Susie: Trying to provide a hosted instance of Oracle for people to play.
Is currently exploring whether it'd be possible for the Swiss Institute
of Bioinformatics to host such a system. 

Scott: No bites on Huntington's Disease. 

Susie: Huntinton's Disease is an attractive area to focus on. But
appears that people don't seem to have a real strong preference for what
disease to focus on. The disease that wins will probably be the one
where some scientists agree to participate. 

Don: What would we want from a neuroscience expert? Data? 

Susie: Scientists would help direct us towards the best data sets to
enable answering scientifically valid questions. Formulate questions.
Demonstrate value. 

Don: I am a neuroscientist. Small group putting out data on Web and
human brain. Vast group, however, no good way to publish data to Web.
Biggest challenge is that for the most part, data is currently not
available on the Web. 

Karen: It's really hard to get use cases out of neuroscientists. Showing
demos such as BioDASH helps scientists to better understand what can be
accomplished using the Semantic Web. 

Susie: Other examples include the work that I did with Joanne and
Siderean to integrate many bioinformatics data sets; and the high level
use case I did with Cerebra for drug safety determination. 

Don: Scientists have a real aversion to letting data get out.
Institutions like NIH share data, but individual researchers less
willing. Don't have requirement to publish data in neuroscience. There
are some cultural problems to overcome. 

Karen: NIH resource/data sharing policies are helping. But don't have
good repositories. 

Susie: Will try to get some neuroscientists on the call next week. Will
start with John Wilbanks, and then Nancy Wexsler. 
Received on Tuesday, 14 March 2006 15:36:41 UTC

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