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Meeting record: 28 August

From: Eric Prud'hommeaux <eric@w3.org>
Date: Tue, 28 Aug 2007 16:59:57 -0400
To: public-semweb-lifesci@w3.org
Message-ID: <20070828205957.GP7359@w3.org>


27 Aug 2007

   See also: [2]IRC log


          Alan DanielRuben Don_Doherty Kei_Cheung P14 P19 Scott_Marshall
          Susie ericP matthiassamwald




     * [3]Topics
         1. [4]Demo extensions - Alan
         2. [5]Use cases - All
         3. [6]Documentation of SenseLab conversion - Kei
         4. [7]Demo extensions - Alan
         5. [8]Use cases - All
         6. [9]text mining
     * [10]Summary of Action Items

   <scribe> ACTION: Susie to ask Johnathan what he needs for TAG access
   [recorded in

   ericP: not sure what more direct access there could be

Demo extensions - Alan

Use cases - All

Documentation of SenseLab conversion - Kei

   Kei: we have created a wiki page documenting the senslab conversion

   <matthiassamwald> [12]http://esw.w3.org/topic/HCLS/Senselab_Conversion

   Kei: we converted NeuronDB to RDF and later to OWL
   ... in this, we learned ontology design features
   ... was focused on the NeuronDB database structure
   ... matthiassamwald joined the team and helped convert to a more
   generic OWL structure
   ... that data was used in the Banff demo
   ... contents of Senelab's native DB change from time to time
   ... working out how to reflect in RDF
   ... considering two-step approach:
   ... - syntactic conversion to RDF
   ... ... automated
   ... - semantic conversion to OWL
   ... ... needs human intervention
   ... .
   ... had a meeting with some HCLS folks about conversion process
   ... want to make sure we follow best practices and that we track the
   demo ontology changes

   Susie: what's the goal, W3C note?

   Kei: not sure. this is just an initial version
   ... want feedback from more people
   ... suggestions?

   Susie: given that you are grappling with modeling/data/ontology
   changes, can you call it finished in say, a month?
   ... and then release future [coherent] versions

   Kei: seems reasonable

   ericP: let me know if you'd like to publish it as a SPARQL interface to
   your database

   Kei: may be easier with a complete RDF dump
   ... but some folks may wish to access the DB directly [with queries]

   Susie: senselab is in Oracle?
   ... could publish in MySQL and use mapping stuff we're working on

   Kei: yes, interested in working on mapping

Demo extensions - Alan


     Leeet is a Semantic Web application that allows rapid and intuitive
     creation, editing and querying of Semantic Web content and
       -- [13]http://neuroscientific.net/leeet/
     * [14]http://kaukoluwiki.opendfki.de/wiki/TripleStore

   Don: not on extension yet; still working on installation
   ... ran into glitch on loading DBs
   ... we have Virtuoso installed
   ... running into problem with perl script
   ... AlanR is helping

   Susie: any progress on the poster?

   Don: will be ready to talk about poster in about two weeks
   ... want to dive into matthiassamwald's poster and target to a
   neuroscience audience

   matthiassamwald: will upload my demo to a server and send a pointer to

   Susie: AlanR is working with DERI to install DB

   alanr: DERI has machine back up
   ... not sure if they've installed Virtuoso
   ... considering hiring someone to write install scripts
   ... my schedule should be more calm now
   ... expect progress in next couple weeks

   Susie: hosted at MIT in the interim?

   alanr: yes. dunno if we will always host it

   Susie: EricN is working on UI
   ... we considered working with UI experts, but seems we don't want to
   do that now

   alanr: I have an idea for a UI; am looking for an implementor
   ... idea: wiki page with queries
   ... ... fill in a form to tailor the queries on the wiki
   ... ... and an interface to add specific predicates and structures for
   say, MESH
   ... .

   ScottM: very interested, but don't want to commit to time

   matthiassamwald: I will be starting in DERI in october/november

   alanr: would like an auto-completer like for google search in firefox


   [ discussion of related libraries, including leeet and a
   Sesame-tailored completion engine ]

   Susie: noting everyone is on vacation, any progress on data conversion?

   alanr: nope

   <matthiassamwald> [Leeet] features an autocomplete mechanism based on
   Sparql queries.

   alanr: talked to a fellow from EBI who is interested in expression data
   ... Marco Brandisi (SP?)

   Susie: would be interesting to work on DrugDB. will prod people who
   ... may be some folks at Lilly who will want to contribute

   <alanr> 1) Representing the information about the samples, experiment,
   protocols leading to the hybridization, technical aspects of the
   hybridization, etc.

   <alanr> 2) Representing what the computed intensity of the spots on an
   array, as well as how those were computed (e.g. MAS5, rma, d-chip, etc)

   <alanr> 3) Representing which genes are thought to be relatively highly
   expressed by interpreting the intensity of the spots as amount of
   expression of certain genes.

Use cases - All

   DanielR: was interested in a use case involving images
   ... want to work with extending images with semantic annotations

   susie: we are working on Use Cases in SWEO

   DanielR: there was a discussion of a mammagraph use case

   ScottM: I have been working on a mammography study in the netherlands

   DanielR: expect NCI-backed standard for annotation medical images on
   the web
   ... controlled terminologies where possiblem for SNOMED, ... ,
   something for regions

   [scribe distracted -- missed stuff]

   alanr: some work on annotations on Alan Brain Atlas
   ... there are existing region taxonomies
   ... another connection: Bijan Parsia said he'd be working on spatial
   ... (above, near...)

text mining

   <mscottm> [15]http://www.biosemantics.org/index.php?page=anni-2-0

   ScottM: looked at Annie
   ... nice handling of synonyms for say, protiens
   ... once you pick a URI system, you will have Biologists who use their
   own names for, say, protein or gene
   ... you need a tool to manage the mapping

   <scribe> ... done internally in text mining systems

   UNKNOWN_SPEAKER: perhaps we can re-use unique concept identifier
   techniques from text mining systems
   ... my group provides web services for text mining packages; does not
   try text mining packages itself
   ... albert shuman has a nice overview of different systems
   ... UIMA framework came up
   ... migrated from IBM to apache
   ... makes text mining sysems more inter-operable
   ... noticed a corpus for huntingtons

   alanr: working on extraction of named entities (diseases, phenotypes,
   ... whatever) and interactions
   ... some results from geneways (SP?)
   ... still pretty noisy
   ... all in PDF -- coding to convert to HTML

   ScottM: Lucine uses PDF format

   alanr: Lucine treats the document as a bag of words -- scrambling the
   order won't change the results
   ... believe HTML is the easiest to work with

   <matthiassamwald> Dietrich Rebholz-Schuhmann

   Susie: can you share Rebholz's tutorial?

   ScottM: sure -- it's on-line

   alanr: matthiassamwald wrote some related code

   matthiassamwald: you can give it a pubmed identifier or query and you
   get back a list of annotated abstracts

   <matthiassamwald> [16]http://whatizit.neurocommons.org

   <alanr> [17]http://svn.neurocommons.org/svn/trunk/nlp/soc_textmining/

   ScottM: advantage of using web services is that you can point at a
   service as the provenance of a piece of extracted data

Summary of Action Items

   [NEW] ACTION: Susie to ask Johnathan what he needs for TAG access
   [recorded in

   [End of minutes]

    Minutes formatted by David Booth's [19]scribe.perl version 1.128
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    $Date: 2007/08/28 20:55:55 $

Scribe.perl diagnostic output

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Guessing input format: RRSAgent_Text_Format (score 1.00)

Succeeded: s/can/will want to /
Succeeded: s/hemo/mamma/
Succeeded: s/spacial/spatial/
Found Scribe: ericP
Inferring ScribeNick: ericP

WARNING: No "Present: ... " found!
Possibly Present: Alan DanielR DanielRuben Don Don_Doherty Kei Kei_Cheung P14 P1
9 ScottM Scott_Marshall Susie alanr dlrubin ericP inserted matthiassamwald mscot
You can indicate people for the Present list like this:
        <dbooth> Present: dbooth jonathan mary
        <dbooth> Present+ amy

WARNING: No meeting title found!
You should specify the meeting title like this:
<dbooth> Meeting: Weekly Baking Club Meeting

Got date from IRC log name: 27 Aug 2007
Guessing minutes URL: [22]http://www.w3.org/2007/08/27-BioRDF-minutes.html
People with action items: susie

   [End of [23]scribe.perl diagnostic output]


   1. http://www.w3.org/
   2. http://www.w3.org/2007/08/27-BioRDF-irc
   3. http://www.w3.org/2007/08/27-BioRDF-minutes#agenda
   4. http://www.w3.org/2007/08/27-BioRDF-minutes#item01
   5. http://www.w3.org/2007/08/27-BioRDF-minutes#item02
   6. http://www.w3.org/2007/08/27-BioRDF-minutes#item03
   7. http://www.w3.org/2007/08/27-BioRDF-minutes#item04
   8. http://www.w3.org/2007/08/27-BioRDF-minutes#item05
   9. http://www.w3.org/2007/08/27-BioRDF-minutes#item06
  10. http://www.w3.org/2007/08/27-BioRDF-minutes#ActionSummary
  11. http://www.w3.org/2007/08/27-BioRDF-minutes.html#action01
  12. http://esw.w3.org/topic/HCLS/Senselab_Conversion
  13. http://neuroscientific.net/leeet/
  14. http://kaukoluwiki.opendfki.de/wiki/TripleStore
  15. http://www.biosemantics.org/index.php?page=anni-2-0
  16. http://whatizit.neurocommons.org/
  17. http://svn.neurocommons.org/svn/trunk/nlp/soc_textmining/
  18. http://www.w3.org/2007/08/27-BioRDF-minutes.html#action01
  19. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  20. http://dev.w3.org/cvsweb/2002/scribe/
  21. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
  22. http://www.w3.org/2007/08/27-BioRDF-minutes.html
  23. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm

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Received on Tuesday, 28 August 2007 21:00:08 UTC

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