michel, i'll be there as soon as i get off the SPARQL call

i think you can call in to start it

(even before its scheduled start)

<michel> k

matthias_samwald, calling in?

<michel> f2f meeting - potential amia - end of march; ismb mid-july ;

<michel> ... joanne, michel, matthias can make it to amia

<michel> ... cshals feb 22-24

<michel> mscottm2 - biordf - paper got accepted; w3c note in development;

<michel> ... interest in future work - helena & michael miller - new dataset - (add more details here)

<michel> ... how to produce and use expression array data; not quite there yet, have we fulfilled the requirements?

<michel> ericP Joanne and Jim were looking at LS-DAM

<michel> matthias - were talking about linking ls-dam to tmo

-> http://ncientarch.info/sandbox/LSDAM2_2_1/ LSDAM link

<michel> charlie: bridg started as a UML model, and has now moved to a OWL representation

<michel> ... board of directors recognize the importance of OWL

<michel> ... LS-DAM started 4 years ago, learn from bridge experience, started to work with content using OWL semantics, then reverse engineer to other formalisms

<michel> ... reuse content from other ontologies

<michel> ... valuable and viable content in BRIDG, LS-DAM; firm commitment to move to OWL; interop with other ontologies

<michel> ericP: 1. data? 2. should we adopt these models?

<michel> charlie 1. lots of BRIDG data; LS-DAM data.

<michel> ... including microarray data

<mscottm2> charlie - we lost you again!

<mscottm2> just as you were discussing Jim's work with LSDAM

<michel> charlie: Jim wrote software to semantically annotate data with LSDAM;

<michel> ericp: the SKOS stuff (?details)

<mscottm2> [belated details that Michel requested above when I was talking about some of the ideas for projects discussed in BioRDF]

<mscottm2> from e-mail with Michael Miller: "* translating TCGA data into RDF (the kicker being the sample

<mscottm2> characteristics are in a different set of files than the MAGE-TAB)

<michel> charlie: LSDAM is pretty much from internal NCI ; BRIDG external oriented

<michel> scott: LODD article accepted by journal of web semantics; W3C note analog

<michel> ... enthusiasm for creating RDF datasets

<michel> ... SAGE bionetworks has interesting data, and similar values to HCLS. semantic access to data

<michel> ericP: sage folks are mining literature and homogenizing ways to get articles and supporting data; have they modeled the knowledge?

<michel> scott: not sure... perhaps not further than anybody else

<michel> ... but they have valuable datasets from participants/clients including snp and patient data. SAGE APIs available. If we could expose that as RDF / SPARQL, could integrate with other datasets

<michel> terminology; annotation of image data ; from xml to owl; student from daniel rubin. john madden started looking at that data. how to inject pathology terminology to the image annotation. radiologist + pathologist findings together

<scribe> scribenick: ericP

<michel> michel: oral presentation to AMIA summit for translational bioinformatics

<michel> ... future medicine review accepted

michel: pub date for the future medicine review?

mscottm2: 12 Jan

michel: please send me a copy of the final manuscript and i'll write an HCLS blog article

mscottm2: you already have it

michel: working on an ICBO (int conference on Bio ontologies)
... matthias_samwald is in charge of article
... extending with pharma terms

matthias_samwald: extending the OWL TMO ontology to capture pharmacogenomic categorizations
... using OWL reasoning on matching patient classes to provide automated decision support
... the paper will experiment with two or three OWL representation to see which is most practical
... i started drafting the ontology in an ontology editor
... paper due at end of month

<michel> matthias: use owl reasoning to match individual patients to molecularly defined subgroups for clinical decision support

matthias_samwald: also have a prototype of a larger paper including transforming pharmacogenomic data into RDF, using SPARQL, OWL for reasoning, etc.
... expect to be done in ~ 3 months

michel: we should formalize our relationships with BRIDG and LS/DAM

use cases

michel: need to finalize "enhancing drug product labels" use case

<scribe> ACTION: michel to contact promoters of enhancing drug product labels use case [recorded in http://www.w3.org/2012/01/10-HCLS-minutes.html#action01]

michel: matthias_samwald is pushing on the clinical decision support use case

<matthias_samwald> http://www.w3.org/wiki/HCLSIG/CDS

michel: i see five sub-use cases

matthias_samwald: within TMO, we're taking on the 1st use case: extending TMO to cover pharmacogenomics for personalized and stratified medicine
... also working on the 2nd (using OWL)

michel: lots of work to be done on the business case for the OWL sub-use case
... we need some external partners
... you clearly have interest from the medical center
... can we get support from cleveland clinic and other folks working with OWL?

matthias_samwald: Russ Altman interested in OWL representation for pharmacogenomics (from pharmaco DB perspective)

<scribe> ACTION: matthias_samwald to invite Russ Altman (SP?) to participate in TMO [recorded in http://www.w3.org/2012/01/10-HCLS-minutes.html#action02]

michel: i'll be in Stanford in Feb
... we should pre-empt my arrival with a discussion with him

matthias_samwald: should hash out on the mailing list
... with michel's progress on pharmgk kb, we can have useful material soon
... re: other use cases:
... .. medical SPARQL -- using SPARQL to answer medical questions

<matthias_samwald> OpenCDS

matthias_samwald: .. allignment between [TMO] ontologies and HL7's Open CDS
... this would be the natural next step in bringing our CDS work forward and aligning with other orgs

<matthias_samwald> http://opencds.org/

<mscottm2> http://researchremix.wordpress.com/2012/01/07/rwa-data/

mscottm2: any familiar with Research Works Act?

This is scribe.perl Revision: 1.136  of Date: 2011/05/12 12:01:43  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

Found ScribeNick: ericP
Inferring Scribes: ericP

WARNING: No "Present: ... " found!
Possibly Present: MacTed P2 P31 aaaa aabb aacc aadd charlie ericp matthias matthias_samwald michel mscottm2 scott scribenick
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: 10 Jan 2012
Guessing minutes URL: http://www.w3.org/2012/01/10-HCLS-minutes.html
People with action items: matthias_samwald michel