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RE: [BioRDF] Telcon Minutes

From: John Madden <john.madden@duke.edu>
Date: Tue, 14 Mar 2006 13:13:50 -0500
Message-Id: <200603141813.k2EIDokd002178@dewinter.duhs.duke.edu>
To: "'Eric Miller'" <em@w3.org>, "'public-semweb-lifesci'" <public-semweb-lifesci@w3.org>

Hi Eric,

Ontology WG just discovered RRSagent and action tracking. We'd like to use
it to keep our minutes.

(1) Could you clarify about setting access rights to minutes in RRSAgent? At
the end of our session I used the "rrsagent, set logs public" command, then
I thought better of it and changed it to "rrsagent, set logs members-only".
What access level is usual for WG's? And if I set it during my IRC session,
does the same setting carry over to the next meeting? (I wouldn't want to
inadvertantly change levels for subsequent users without their consent.)

(2) Peripherally related, our WG has been working on expanding and improving
our Wiki pages. (We're now homepaged at

Some of our users are still a little put off by wiki editing. To help with
functionality and friendliness I'd like to incorporate some Macros from the
moinmoin MacroMarket into our pages.

But according to the instructions (at
34e5139e50d2), the macro files need to go into in one of the designated
directories for macros on the wiki server. I don't seem to have access to
those directories by http or ftp. Can I ask the administrator to include
some macros in there, and if so whom do I contact?



> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Eric Miller
> Sent: Tuesday, March 14, 2006 11:31 AM
> To: Cutler, Roger (RogerCutler)
> Cc: public-semweb-lifesci
> Subject: Re: [BioRDF] Telcon Minutes
> Roger,
> 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
> > 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/ swls/
> > 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 requirements.
> > 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 18:14:04 UTC

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