See also: IRC log
<scribe> ACTION: Susie to ask Johnathan what he needs for TAG access [recorded in http://www.w3.org/2007/08/27-BioRDF-minutes.html#action01]
ericP: not sure what more direct access there could be
Kei: we have created a wiki page documenting the senslab conversion
<matthiassamwald> 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
Leeet is a Semantic Web application that allows rapid and intuitive creation, editing and querying of Semantic Web content and annotations.
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.
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...)
<mscottm> 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> http://whatizit.neurocommons.org
<alanr> 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
This is scribe.perl Revision: 1.128 of Date: 2007/02/23 21:38:13 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ 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 P19 ScottM Scott_Marshall Susie alanr dlrubin ericP inserted matthiassamwald mscottm 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: http://www.w3.org/2007/08/27-BioRDF-minutes.html People with action items: susie[End of scribe.perl diagnostic output]