W3C

- DRAFT -

W3C HCLS – General Meeting

06 Mar 2012

Attendees

Present
Regrets
Chair
michel
Scribe
ericP

Contents


<michel> /invite zakim #HCLS

<mscottm2> having trouble dialing in with skype again - looking into 'sip' clients..

-> http://www.w3.org/2006/tools/wiki/Zakim-SIP Zakim-SIP

open discussion

<michel> michel: nigam @ stanford, working with clinical notes; using NCBO annotator, odds testing between drugs and adverse events

<michel> ericp: can we link that output with semantic web?

<michel> matthias: aTags to markup sentences, adds knowledge

<michel> ericp: blobs of text such as clinical encounters, nlp -> tag clouds; drug production pipeline? safety/efficacy test

michel: visiting professor is investigating how ontologies can be used to aid navigation
... i.e. get from A to B in fewer clicks
... we could ask how a tag cloud could help

<michel> ericp: having a tag soup is not all that useful ; but having structure might be

<michel> ... can it be used for CDS ?

<michel> mscottm2: ncbo annotator is an entity recognizer; breast cancer use case where labelling is useful

<Bosse> Predicate mappings in LinkedLifeData, http://linkedlifedata.com/sources

<michel> ericp: imagine we had super structured information about these patients - we came up with question we could ask. imagine we had structured events, but only as tag clouds - would the use cases operate in that space

<michel> mscottm2: bag of text could be used to generate a semantic neighbourhood... could also project against ontologies to see what is being talked about

<michel> bosse: causal relation extraction together with hypotheses to try to explain those questions

<michel> ... the tag cloud could be used to help explain a phenomena

<michel> ericP: something to help keep track of assertions

<michel> bosse: if you had a knowledge base where you could annotate and share, it could be very useful

<michel> ... if we could find a community with an interesting enough problem, then the kb could serve as a real resource

<michel> ericP: recording institutional knowledge has to immediately benefit, or has to have a big stick

michel: some pharmas and other organizations track contributions towards a patent
... your motivates is more info that can be used for a product or servce
... is your contribution information that fills a gap and leads to inference?
... that would be a way to measure contributions
... you could pose a question a priori to enhance this metric
... could ask SemWeb folks at elsevier (Alan Yagoda, Sigram, Iker)
... Alan raised the issue of data quality accuracy
... SIDER was based on matching product labels, leading to inaccuracies
... issue: freshness of data

<michel> ericp: are there examples of pharma, do record extra information to help other groups - is it a cultural norm?

<michel> bosse: we could be helped a lot more in content authoring

<michel> ericp: need grant to develop an open source project

michel: Bosse said we have to find the community and the problem
... it would be hard to find funding unless it came from a VC
... for any other funding org, we'd have to present the problem and show how a SemWeb tool is the solution

LODD

mscottm2: LODD Note is waiting for a couple edits, then moving to HTML (1 week)
... we've identified a couple things which need fixing in the expression study note
... we need alpha testers to read the doc and adapt tools to reflect the note
... also need to adapt Jim Mckuster's R script or find equivalent

Terminology

mscottm2: we discussed John's work saturation and stepping down as chair
... decided that we should reach out to IHE (International Health E) contacts
... IHE is for clinical IT. includes imaging

<mscottm2> Here's a link for IHE (about the upcoming Connectathon in Bern in May): http://ihe-europe.net/connectathon/133/cat-2012

michel: John wanted to move away from terminology to applications

Clinical Decision Support

matthias: will have first meeting on Thursday
... am expanding our current data to meet pharmacogenomics use cases

<mscottm2> Another relevant IHE link: http://www.dcm4che.org/confluence/display/ee2/IHE+Integration+Statement

matthias: next step is to see how we can use SPARQL, SPIN and OWL to make context-senstitive decision support algorithms for e.g. reminders, warnings, recommendations

<scribe> scribenick: ericP

systems biology for drug discovery

mscottm2: exploratory discussion with lots of enthusiastic folks
... would need to consult minutes to give accurate summary

Pharmacogenomics

michel: we've been looking at clinical annotations in pharmgkb
... can be released for research (not publication) with contract
... added links to DBSNP
... challenge is to extract and get access to portions of DBSNP

data sources

mscottm2: we've discussed I2B2 or SAGE Bionetworks datasets
... would be good to create an inventory

michel: look for main wiki page link to "potential data sources"

Summary of Action Items

[End of minutes]

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