- From: Eric Prud'hommeaux <eric@w3.org>
- Date: Fri, 2 Jul 2010 16:14:05 -0400
- To: public-semweb-lifesci@w3.org
http://www.w3.org/2010/07/01-hcls-minutes
HCLS Telecon
01 Jul 2010
See also: [2]IRC log
Attendees
Present
Regrets
Chair
Scott Marshall
Scribe
ericP
Contents
* [3]Topics
1. [4]BioRDF task for update
2. [5]SciDisc task update
3. [6]Terminology task update
4. [7]COI largely on hold
5. [8]LODD topic update
6. [9]SemTech debrief
* [10]Summary of Action Items
__________________________________________________________________
BioRDF task for update
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
SciDisc task update
timclark: f2f meeting on annotation of articles
... (at MGH in timclark's conference room)
... brought in larry hunter's group
<mscottm>
[11]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> [12]http://www.ebi.ac.uk/Rebholz-srv/CALBC/workshop.html
<mscottm> [13]http://www.calbc.eu/
<scribe> ACTION: mscottm to email timclark an introduction to Dietrich
Rebholz [recorded in
[14]http://www.w3.org/2010/07/01-hcls-minutes.html#action01]
mscottm, will not be at ISMB
Terminology task update
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
COI task update
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 [15]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
LODD topic update
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
SemTech debrief
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
Summary of Action Items
[NEW] ACTION: mscottm to email timclark an introduction to Dietrich
Rebholz [recorded in
[16]http://www.w3.org/2010/07/01-hcls-minutes.html#action01]
[End of minutes]
__________________________________________________________________
Minutes formatted by David Booth's [17]scribe.perl version 1.135
([18]CVS log)
$Date: 2010/07/02 20:12:28 $
__________________________________________________________________
Scribe.perl diagnostic output
[Delete this section before finalizing the minutes.]
This is scribe.perl Revision: 1.135 of Date: 2009/03/02 03:52:20
Check for newer version at [19]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 ma
tthias_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: [20]http://www.w3.org/2010/07/01-hcls-minutes.html
People with action items: mscottm
[End of [21]scribe.perl diagnostic output]
References
1. http://www.w3.org/
2. http://www.w3.org/2010/07/01-hcls-irc
3. http://www.w3.org/2010/07/01-hcls-minutes#agenda
4. http://www.w3.org/2010/07/01-hcls-minutes#item01
5. http://www.w3.org/2010/07/01-hcls-minutes#item02
6. http://www.w3.org/2010/07/01-hcls-minutes#item03
7. http://www.w3.org/2010/07/01-hcls-minutes#item04
8. http://www.w3.org/2010/07/01-hcls-minutes#item05
9. http://www.w3.org/2010/07/01-hcls-minutes#item06
10. http://www.w3.org/2010/07/01-hcls-minutes#ActionSummary
11. http://code.google.com/p/annotation-ontology/wiki/Homepage
12. http://www.ebi.ac.uk/Rebholz-srv/CALBC/workshop.html
13. http://www.calbc.eu/
14. http://www.w3.org/2010/07/01-hcls-minutes.html#action01
15. http://tm.semanticscience.org/sparql
16. http://www.w3.org/2010/07/01-hcls-minutes.html#action01
17. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
18. http://dev.w3.org/cvsweb/2002/scribe/
19. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
20. http://www.w3.org/2010/07/01-hcls-minutes.html
21. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
--
-ericP
Received on Friday, 2 July 2010 20:14:42 UTC