- 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>
http://www.w3.org/2007/08/27-BioRDF-minutes
HCLS
27 Aug 2007
See also: [2]IRC log
Attendees
Present
Alan DanielRuben Don_Doherty Kei_Cheung P14 P19 Scott_Marshall
Susie ericP matthiassamwald
Regrets
Chair
Susie
Scribe
ericP
Contents
* [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
[11]http://www.w3.org/2007/08/27-BioRDF-minutes.html#action01]
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
[SPASQL]
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
annotations.
-- [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
public-semweb-lifesci
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
<matthiassamwald>
[ 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
volunteered
... 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
reasoning
... (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
[18]http://www.w3.org/2007/08/27-BioRDF-minutes.html#action01]
[End of minutes]
__________________________________________________________________
Minutes formatted by David Booth's [19]scribe.perl version 1.128
([20]CVS log)
$Date: 2007/08/28 20:55:55 $
__________________________________________________________________
Scribe.perl diagnostic output
[Delete this section before finalizing the minutes.]
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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
tm
You can indicate people for the Present list like this:
<dbooth> Present: dbooth jonathan mary
<dbooth> Present+ amy
WARNING: No meeting title found!
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<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]
References
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
--
-eric
office: +1.617.258.5741 NE43-344, MIT, Cambridge, MA 02144 USA
mobile: +1.617.599.3509
(eric@w3.org)
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Received on Tuesday, 28 August 2007 21:00:08 UTC