W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > March 2006

Re: [BioRDF] Telcon Minutes

From: Eric Miller <em@w3.org>
Date: Tue, 14 Mar 2006 11:30:31 -0500
Message-Id: <EBB54243-4919-4C93-AD90-5B2E6277913A@w3.org>
Cc: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
To: "Cutler, Roger (RogerCutler)" <RogerCutler@chevron.com>


Thanks for the timely minutes! Looks like there was a lot of useful  
discussion :)

I'd like to suggest that task groups think more about ACTION tracking  
and linking to the appropriate deliverables (I can't tell from the  
minutes for example if folks are working on already identified tasks,  
or proposing new one). The ultimate goal of this approach of course  
is to make it easier to manage the work both within and across  
various tasks and for others to help contribute.

Please remember, folks will be joining this group over time and  
leaving bread-crumbs now is important for helping them and others  
understand where we're going.

Suggested comments, requests for more detail below...

On Mar 14, 2006, at 10:36 AM, Cutler, Roger (RogerCutler) wrote:

> Minutes from the 3/13 BioRDF telcon are at
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/ 
> 2006-03-13_Confe
> rence_Call.  For archival purposes, they are reproduced below.
> 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
> week.

pls include pointer to Task.  If no task is yet formed ...

(suggested) ACTION: Alan to draft task based on reagents with a focus  
of ... @@ foo @@

> 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.

(suggested) ACTION: Alan to work with Davide on a demonstration of  
tool to get XML out of text parse, then transform XML to RDF,  
documenting work on the WIKI.

> 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.

pls include pointer to Task. pls announce Task when online to the  
group. The goal is to better understand how to map the relational  
structure to the RDF structure was a major theme of the first F2F  
meeting. Is this the task?

- http://esw.w3.org/topic/HCLSIGDataWrappers

or something else?

> 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.

(suggested) ACTION: Susie to contact Stanford to see if they could  
participate in a future call; announcement to be sent in advance to  
HCLSIG list.

> 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.

(suggested) ACTION: Susie write up demonstration / application and  
give this to EricN / Tonya for placement on http://www.w3.org/2005/04/ 

> 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.

(suggested) ACTION: Karen to write up and share NIH repository  

> Susie: Will try to get some neuroscientists on the call next week.  
> Will
> start with John Wilbanks, and then Nancy Wexsler.

(suggested) ACTION: Susie to invite John Wilbanks, and Nancy Wexsler  
to future meeting; announcement to be sent in advance to HCLSIG list.
Received on Tuesday, 14 March 2006 16:31:34 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:20:13 UTC