HCLS Telecon -- 01 Jul 2010

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> 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

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 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

HCLS Telecon

01 Jul 2010

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