See also: IRC log
mscottm: spoke with helen
parkinson and misha [ck], james malone (working in owl)
... discussed micro-array RDF work
... spoke with folks from the isa tools
... (reads NCBO ontologies, annotates e.g. microarray
studies)
s/misha \[ck\]/Misha Kapushesky/
mscottm: gene atlas pipeline is a
manually created subset of arrayexpress
... you can say "show me the upregulated genes in human
liver"
... this has been and issue with e.g. mged 'cause otherwise you
have to do text mining
... james malone's group is already generating RDF
... helen agreed to look at the BioRDF microarray and season
their (EBI's) representation
... on hold until 12 july (kei is in iceland, helena in
iceland)
... 12 july conflicts with ismb, but we'll be pushing forward
on provenance
timclark: f2f meeting on
annotation of articles
... (at MGH in timclark's conference room)
... brought in larry hunter's group
<mscottm> http://code.google.com/p/annotation-ontology/wiki/Homepage
timclark: working with folks on
Paolo's Annotation Ontology. vetting with folks in DE, NL,
US
... working with david shotten. paper coming soon
<mscottm> FRBR - Functional Requirements for Bibliographic Records
timclark: instead of "basing on"
the Funtional Requirements for Bibliograph Records (members
like bibliotech nationale), we're using FRBR core
... discussed course-grained rhetorical structure to assist
automated annotation tools (standardised model of document
sections)
... anita brought in an elsevier expert on PRISM (like an
enhanced version of Dublic Core)
... a rhetorical structure model is in the oven
mscottm: EU project coordinated
by Dietrich Rebholz ran entitiy recognition on a silver
standard corpus
... the corpus is manually curated
... folks doing annotation on that material can get feedback
from the analysis on this corpus
... folks developing ontologies can survey deployment and use
of their terms
... the corpus is available in XML. i [mscottm] went there to
suggest RDF or GRDDL
<mscottm> http://www.ebi.ac.uk/Rebholz-srv/CALBC/workshop.html
<mscottm> http://www.calbc.eu/
<scribe> ACTION: mscottm to email timclark an introduction to Dietrich Rebholz [recorded in http://www.w3.org/2010/07/01-hcls-minutes.html#action01]
mscottm, will not be at ISMB
mscottm: discussions with Daniel
Reuben and John Madden led to project connecting to other task
forces
... Reuben provided radiology reports. Madden provided
pathology reports
ericP: where's the coding come from? (on what do we run diff)?
mscottm: using matthias_samwald's ATAGs, TMO
<mscottm> Rebecca Crowley, ODIE - Ontology Development and Information Extraction
mscottm: ODIE is already used on
pathology reports
... idea is to use NCBO ontologies
... will the automated annotations be accurate and detailed
enough to find conflicts with radiology?
... integration with other task forces leads to a story:
... .. patient has a breast cancer
... .. gets a mamagram
... .. gets an excision with is coded in RDF
... .. takes some medication...
... can add biomarker info
... ncbo is responding to our needs (e.g. URIS for terms)
matthias_samwald: tx for pushing the changes to ncbo
ericP: are there any automated annotation systems for radiology?
mscottm: dunno
ericP: fixing filters on SWObjects
ericP: INDIVO
ontology (Harvard) is interested in working in RDF, reaching
turning point
..doing this via XML Schemas and want to interpret it as RDF
mscottm: Use GRDDL?
ericP: Yes,
probably.
..Take patient
data, turn into Indivo XML docs, GRDDL it back to RDF and
check.
mscottm: chris domeru is keen to have an SPARQL endpoint
ericP: I thought http://tm.semanticscience.org/sparql was the endpoint for the TMO synthetic patients:
PREFIX tmo: <tag:eric@w3.org:2009/tmo/translator#> PREFIX foaf: <http://xmlns.com/foaf/0.1/> SELECT ?date ?value ?units WHERE { ?encounter tmo:patient [ foaf:name "Monica Mary Mall" ] ; tmo:dateOfEncounter ?date ; tmo:test [ tmo:testSet [ tmo:testCode [ tmo:description "Platelet Count" ; tmo:value ?value ; tmo:units ?units ] ] ] } ORDER BY DESC(?date)
mscottm: marshfield has a team of
programmers employed to answer clinical research
questions
... chris wants to show the benifit of RDF here
... chris wants to show them how to create a SPARQL endpoint
for *their* data
... indicates need for a process guide
bosse: agreed to dig into
experimental data
... reviewing a paper by susie's group at J&J
mscottm: chimezie ogbuji talked
about patient records at Cleveland Clinic
... i [mscottm] asked him to feed his CPR Cardiac Patient
Records ontology back to HCLS
... CC has a lot to offer
UNKNOWN_SPEAKER: conference has
gotten much larger
... presented HCLS with ongology building talk with christine
goldbrech
... also split with musen and a co-pi on NeuroInformatics
Framework
This is scribe.perl Revision: 1.135 of Date: 2009/03/02 03:52:20 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) FAILED: s/misha \[ck\]/Misha Kapushesky/ Succeeded: s/dietrich F/Dietrich Rebholz/ Found ScribeNick: ericP Inferring Scribes: ericP WARNING: No "Present: ... " found! Possibly Present: Eric IPcaller Julia Scott aaaa aabb aacc bbalsa bosse ericP matthias_samwald mscottm scribenick scribnick timclark tmo 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 WARNING: No meeting chair found! You should specify the meeting chair like this: <dbooth> Chair: dbooth Got date from IRC log name: 01 Jul 2010 Guessing minutes URL: http://www.w3.org/2010/07/01-hcls-minutes.html People with action items: mscottm[End of scribe.perl diagnostic output]