HCLSIG/Meetings/2010-08-05 Conference Call

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Conference Details

  • Date of Call: Thursday August 5, 2010
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)

[NOTE new numbers for European dial-in]

  • Dial-In #: +33.4.26.46.79.03 (France)
  • Dial-In #: +44.203.318.0479 (UK)
  • Participant Access Code: 4257 ("HCLS").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Click on mibbit for instant IRC access.
  • Duration: ~1h
  • Convener: Scott
  • Scribe: Scott/Eric

Agenda

Minutes

Present: Kei, Matthias, Eric, Michel, Susie, Scott
Regrets: John

Contents

Topics
BioRDF update
COI update
Terminology update
Scientific Discourse
TMO Update
LODD Update
FP7 Grant Opportunites
Summary of Action Items
<mscottm> I'm getting "This passcode is not valid."
<kei> same problem
<matthias_samwald> i got a bad case of "this passcode is not valid".
let your doctor take care of it
<mscottm> Thanks Doc! (ericP)
did it stop?
<mscottm> Scott: Some trouble with Zakim today. Hope that nobody gave up. Let's start the task force updates.
BioRDF update
<mscottm> ..Kei, would you start? I know that you are just back from a month away in Hong Kong.
<mscottm> Kei: Yes, it was a nice break. I would like to thank Jun Zhao for chairing BioRDF while I was away.
<mscottm> ..We have continued working with ArrayExpress and GEO data for microarray use case data related to our neurodegenerative use cases. We are continuing work on representing gene lists and provenance of microarray studies. We are settling on an RDF representation and aiming to submit to the provenance workshop at ISWC in Shanghai (deadline Aug 27).
<mscottm> Scott: Have spoken with people from ArrayExpress (Helen Parkinson, Misha Kapushesky, and James Malone who joined us on a call). Encouraged at the idea of RDF from ArrayExpress.
COI update
<mscottm> Eric: Have reworked query mapping through rules and was able to meet use cases. Now have more confidence that is sound and complete.
<mscottm> ..Have met with Indivo and they are excited about having an RDF and TMO representation of the Indivo data (that is in XML).
<mscottm> ..Have invited Helen Chen to discussions with Indivo. Helen mentioned that Univ of Waterloo is beginning work on clinical record system in earnest.
<mscottm> Susie: A little confused by TMO related mention.
<mscottm> Eric: Helen is interested in clinical records because of work at her univ and therefore interested in the TMO work with Indivo.
<mscottm> Scott: In general, a theme that has come up in several task forces is using each other's information artifacts. Several tf's are looking at info about a patient (i.e. clinical record) so if TMO uses Indivo, the other tf's might like to use both TMO and Indivo.
<scribe> scribenick: ericP
Terminology update

mscottm: discussions with Danny Rubin (radiologist) and JohnM (pathologist) have lead us to a particular mamagram use case
... scenario:
... .. radiologist sees microcyrstalization, [recommends biopsy]
... .. pathology report should match radiology report
... we're looking for funding from colledge of american pathologists
... refers to clinical patient records, ergo we want to use SNOMED, RadLex
... also TMO, in order to link with other HCLS work
... also want to look at Indivo
... we're creating a wiki page
... engaging some French pathologists
... we want an RDF expression of report annotations
... we expect to use ATAGs to record them
... (record our manual annotations)
... we'll want to integrate with text-mined annotations
Scientific Discourse

mscottm: TimC sent a summer report
... a bunch of collabs in process
<mscottm> Tim's summary: These include the CiTO/SWAN ontology alignment project; the SWAN/myExperiment/ISA-TAB/OBI alignment project; the Annotation Ontology (AO); and the coarse-grained rhetorical document model
mscottm: there was an "annotation framework bonanza" during ISMB
<mscottm> Annotation Framework Bonanza http://esw.w3.org/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20100712
<scribe> ... new participants from text-mining groups
UNKNOWN_SPEAKER: i hope the annotation ontology will cover provenance
... need a software ontology to describe the provenance of software-generated annotations
TMO Update

Susie: TMO on recess 'till Sept.
... focusing connecting patient data to other data and querying with the TMO
... interest in going back to the science
... decided that interfaces to EHRs was too niche for us to work on, but supportive of other groups doing interfaces
<michel> presentation : http://www.slideshare.net/micheldumontier/the-translational-medicine-ontology-driving-personalized-medicine-by-bridging-the-gap-from-bedside-to-benchside
Susie: michel did a talk at bio-ont SIG at ISMB
LODD Update

UNKNOWN_SPEAKER: LODD on summer recess
... (somewhat conencted to LODD), Allen Brain Atlas making an LOD representation of the atlas
... others migrating the WHO global health data to LOD
... Chris Buton (SP?) has developed an interface for the LODD datasets
... he's considering a free interface to view LODD
... we're providing a best practice guide for making data available
... hard for orgs to know how to e.g. link ontologies
... outreach: ericP will present at ACS meeting in BOS
... all of the pharma chemists go to ACS
... we've been invited to write a paper
matthias_samwald: per collab with allen brain atlas, in first HCLS, we imported brain slides
... can we build on that? or is this novel? (what's the data we plan to integrate?)
Susie: ABA folks have been working with free-univ berlin (anja, chrisB)
... i expect we'll have a new version soon
... ABA folks saw a few dimensions for how they could contribute
... .. 1. coordinate system, though that's controversial
... .. 2. gene expression levels -- ABA is all about overlaying expression levels on the images
... would be cool to overlay that with drug information
... ABA folks were keen to dive into best use cases, and some seemed conspicuous, but we'd like to hear more
matthias_samwald: maybe we could use brain connectivity or senselab data
Susie: could suggest that to Mark Greeves
kei: what's the state of the LD version? still developing graph structure?
Susie: working on integrating with other sources
... expect it done around Sept/Oct
mscottm: CollabRx proposed improved versions of DrugBank in RDF
... would be nice to see some description of the different versions
... today, we can go to openlink and see *their* LD version, but we don't have a web model [presume multiple versions avail at different endpoints]
Susie: different universities are making different data avail in RDF
... means we need to be able to get fixes/updates even though e.g. a student has gradudated
... i imagine different companies stepping up to offer clean [accountable - EGP] versions
... as a pharma version, i'm reluctant to use data where i can't vouch for the quality of the links
... also, these data sets are being made avail be SW groups, but this is now the ABA making the brain atlas available
... over time, the data generators are likely to be the most motivated to maintain the quality
... +1 to capturing the provenance info
... perhaps it could go into the best-practices document
mscottm: that could become a defacto standard
Susie: we're working on a doc talking about best practices for RDB2RDF
... so ericP [wheover he is] should be interested
FP7 Grant Opportunites

matthias_samwald: almost final draft of FP7 calls
... interesting opportunites around IS&T, mostly around HCLS continuing
... also around clinical models and research-oriented datasets
<mscottm> FP7 is a European grant.
matthias_samwald: "a matter of excellence on top of EU health infrastrcuture" could offer a chance to create a demo around clinical data
<mscottm> FP7 proposals can include partners from outside the EU.
matthias_samwald: calls are due around 2011, so not urgent at this point
... some of us are collaborating already
... would be good for those allready collaborating, but lacking dedicating funding
... can create a consortium for such an EU call
Susie: tx for keeping an eye on ICT grants
... relieves tension where many HCLS contributors can't claim it as their day job
<scribe> ACTION: matthias_samwald to post some snippits to public-semweb-lifesci [recorded in http://www.w3.org/2010/08/05-hcls-minutes.html#action01]
<matthias_samwald> quote from the draft of the FP7 call: "A Network of Excellence on semantic interoperability and European Health
<matthias_samwald> Infostructure.
<matthias_samwald> The aim is to engage leaders and organisations, including professional organisations, national
<matthias_samwald> competence centres, industrial associations and standards development organisations to define
<matthias_samwald> and implement a research agenda on the semantic interoperability of health information
<matthias_samwald> systems and particularly electronic health records. European and international organisations in
<matthias_samwald> the domains of medical terminology, record architecture, medical logic and workflow are
<matthias_samwald> expected to participate. The work will also include set up of the governance of a European
<matthias_samwald> virtual organisation for multilingual, multicultural adaptation of international classifications
<matthias_samwald> and terminology and propose means for the sustainability and governance of health
<matthias_samwald> information info-structure."
Summary of Action Items

[NEW] ACTION: matthias_samwald to post some snippits to public-semweb-lifesci [recorded in http://www.w3.org/2010/08/05-hcls-minutes.html#action01]
 
[End of minutes]