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Minutes from BioRDF telecon 10-Dec-2007

From: Booth, David (HP Software - Boston) <dbooth@hp.com>
Date: Thu, 13 Dec 2007 14:29:26 +0000
To: "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
Message-ID: <184112FE564ADF4F8F9C3FA01AE50009DDE88F7007@G1W0486.americas.hpqcorp.net>

. . . are at
and also below in plain text.  Sorry I forgot to sent them out on Monday.  New action items:

[NEW] ACTION: Kei to provide query that makes use of SenseLab graph [recorded in http://www.w3.org/2007/12/10-BioRDF-minutes.html#action01]
[NEW] ACTION: Susie to ping Wright State University (Amit) to see if there database is up and available [recorded in http://www.w3.org/2007/12/10-BioRDF-minutes.html#action02]

David Booth, Ph.D.
HP Software
+1 617 629 8881 office  |  dbooth@hp.com

Opinions expressed herein are those of the author and do not represent the official views of HP unless explicitly stated otherwise.



      [1] http://www.w3.org/

                               - DRAFT -

                            BioRDF Telecon

10 Dec 2007

   See also: [2]IRC log

      [2] http://www.w3.org/2007/12/10-BioRDF-irc


          Don, Olivier, Scott, Matthias, Adrian, Kei, Susie, DBooth,




     * [3]Topics
         1. [4]Adrian's Slides on Rule Responder Demo
         2. [5]SenseLab Conversion Documentation
         3. [6]Note desribing Knowledge Base
         4. [7]Next Call
     * [8]Summary of Action Items

   <AdrianP> Slides:

      [9] http://ibis.in.tum.de/projects/paw/docs/HCLS_ResponderDemo.pdf

   <Susie> Slides:

     [10] http://ibis.in.tum.de/projects/paw/docs/HCLS_ResponderDemo.pdf

Adrian's Slides on Rule Responder Demo

   <matthiassamwald> sorry, nothing new about the SenseLab conversion,
   still waiting vor CVS access to the W3C site.

   (Adrian goes through slides at
   [11]http://ibis.in.tum.de/projects/paw/docs/HCLS_ResponderDemo.pdf )

     [11] http://ibis.in.tum.de/projects/paw/docs/HCLS_ResponderDemo.pdf

   (Adrian goes through slides at
   [12]http://ibis.in.tum.de/projects/paw/docs/HCLS_ResponderDemo.pdf )

     [12] http://ibis.in.tum.de/projects/paw/docs/HCLS_ResponderDemo.pdf

   <ericP> there are a lot of layers here. i wonder which are backed by
   use cases

   EricP: This treats Prova as the unifying layer. Another approach
   would be to put RDF adaptors on all the data sources and use SPARQL
   as the unifying language.

   <mscottm> another uk project 'comparagrid' also uses rules to create
   views of (OWL) data

   Kei: How does your rules language compare to RUleML and OWL.

   Adrian: Different family. SWRL is a subfamily of RuleML.
   ReactionRuleML is intended for reactive rules.
   ... It can implement workflow-like systems like BPEL.
   ... RuleML is more homogeneous integration, whereas ReactionRule is
   more heterogeneous. You can use external schema vocabularies to type
   the variables. You can have a certain OWL ont and give a variable
   the typ of this class.

   Susie: Plans to integrate with HCLS knowledge base?

   Adrian: You can define conditional decision logic, and then encode
   additional decisions. You could also do transformation al rules:
   pull the data, then update to HCLS knowledgebase, though that would
   need SPARQL update which doesn't yet exist.
   ... If there are queries that always repeat in a certain binding --
   author, patents, etc., -- then you can implement it in a declarative
   rule language.

   DBooth: What are you using this for?

   Adrian: We use it for virtual orgs, where the members are defined as
   a set of autonomous agents with their internal decision logic. Other
   apps are IT service mgmt, where you define quality contracts between
   services and you need to monitor conformance, and that is easy to do
   in this rule language.
   ... In HCLS it could be used as a heterogeneous approach for a HCLS
   ... Please let me know of suggestions for applying this in W3C.

SenseLab Conversion Documentation

   <AdrianP> some links:

   Matthias: Still working with Eric to get it on W3C server. Need to
   update my invited expert status.

   EricP: I'm ready to do the next step, now that invited expert status
   is done.
   ... Send me your SSH public key.

Note desribing Knowledge Base

   Susie: Status?

   <mscottm> [13]http://www.w3.org/2001/sw/hcls/notes/kb/

     [13] http://www.w3.org/2001/sw/hcls/notes/kb/

   Scott: I have some new items that were requested to be added, and
   I'll try to fill them in. Starting with the motivation, I look at it
   as conveying the steps and thoughts behind the design of this
   knowledgebase, so that people can understand and reproduce it if
   desired -- ambitious. Added a lenghty intro, not sure it should be
   quite so long. We've also got more info about the incorporated
   databases. Would like to add discussion of how it needs to be main
   ... maintained, next steps for improvement, detailed section on 1-2
   conversions to RDF from legacy datastore.
   ... I've mailed to Alan to get input on which conversion to cover.
   ... Added to the wish list: List of current implementation, where to
   find them. Also listing of schema classes and properties used. And
   an additional resources section in the appendix.
   ... i'd like to ask Matthias for comments on next steps.
   ... Also would like input on current doc structure, or if anyone
   wants to provide material. One tricky piece: explanation of how
   evidence is done, but I may have a doc from Alan that talks about

   EricP: Sometimes evidence is handled by providence in the sparql
   query, and sometimes it's in the data itself.

   Scott: Yes, in some cases it's encoded in the properties.
   ... There are a number of approaches that can be used to model
   evidence, and we're using more than one, but we think evidence is
   important, so we should at least describe the approaches taken.
   ... Has everyone looked at it?

   EricP: I have. I had envisioned the SenseLab conversion as being the
   detailed description of importing more than one knowledge base, so
   we wouldn't have to do that in this document -- we'd just reference

   Susie: That makes sense to me.

   Scott: I suppose we'll link out to a separate doc.

   EricP: It woudl be nifty to have the motivated query incorporate
   some of the Senselab data.

   Scott: Good plan. Do we have such a query?

   Matthis: Nothing we can show.

   <scribe> ACTION: Kei to provide query that makes use of SenseLab
   graph [recorded in

   <matthiassamwald> I will just write an e-mail. Arghl.

   <matthiassamwald> We cannot query our ontologies with SPARQL.

   <matthiassamwald> At least not in a very intuitive manner.

   EricP: I arbitratily picked Banff query #2 for clarifying the
   motivations when somenoe is reading the doc. Any other query would
   be fine also if it touches on SenseLab.

   Scott: People involved with incorporating the data should review to
   see if I have left out anything. Could also use help on getting good
   use cases.

   <matthiassamwald> YES IT IS.

   Scott: Was DERI knowlege base send out to public?

   <matthiassamwald> I'm in charge of that. If you have questions,
   please contact me at samwald@gmx.at. The web address is

     [15] http://hcls.deri.ie/

   Don: It's unlikely ours will be ready in time.

   <AdrianP> we might also setup a mirror for the KB if there is a need

   <matthiassamwald> The problem is to keep the installations in sync.

   Scott: The main point is to provide links in this section to
   encourage people to try it out. We could list installations, and
   those taht are publicly accessible could have URLs.

   <matthiassamwald> It is already hard enough to keep the DERI and
   Neurocommons KB in sync. With multiple mirrors, we need to set up
   some automated process.

   <scribe> ACTION: Susie to ping Wright State University (Amit) to see
   if there database is up and available [recorded in

   Susie: in Sec 5, have you been able to incorporate all of the
   databases in Jonathan's ReadMe?

   Scott: No. SOme are listed multiple times (e.g., MESH). We should
   just list it once, and maybe refer out to Jonathan's more complete
   table. Difficult call because keepign these installations in sync is
   impossible, but if people want the details they should see
   Jonathan's table. \
   ... There are still some things missing and I'll be adding them. Do
   we list every little thing that's been put in? That makes th list

   Susie: My inclination: Add a small amount of info about all of the
   datasets, to avoid letting anyone feel unloved.

   Scott: I don't mean leaving anyone out. It's really a technical
   detail. E.g., the mammalian part of OBO is in another section. I'll
   check with Jonathan about how to handle that.

   Susie: You could send out email to ask for feedback.
   ... Finish by 20th?

   Scott: I could use some help. If there are diagrams tha someone
   likes, let me know. Last week I applied jambalaya to your ont, but
   maybe you meant something else.

   Susie: I was hoping for a screen shot of the OB ont.
   ... Screen shot of science commons ont would be interesting for
   people to see.

   EricP: We have until the 21st.

Next Call

   <kei> kei: sorry, got to go because of class

   Monday 17-Dec-2007


   <matthiassamwald> So... I need to generate a SSH key?

   <scribe> Scribe: DBooth

   <ericP> ssh-kegen

   <matthiassamwald> Perfectly.

   <matthiassamwald> Yes.

Summary of Action Items

   [NEW] ACTION: Kei to provide query that makes use of SenseLab graph
   [recorded in
   [NEW] ACTION: Susie to ping Wright State University (Amit) to see if
   there database is up and available [recorded in

   [End of minutes]

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Present: Don Olivier Scott Matthias Adrian Kei Susie DBooth EricP
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Received on Thursday, 13 December 2007 14:33:08 UTC

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