<johnbreslin> Hello

Introductions

John Breslin: Natl U Ireland Galway

<chimezie> Susie: my collegue on the phone with me, Sivaram Arabandi would like to introduce himself as well

<chimezie> we are sharing the same line

Kingsley? could you type your name in the irc?

<kidehen> kidehen re. Kingsley Idehen

<kidehen> JohnMadden: my ESW Wiki profile page: http://esw.w3.org/topic/KingsleyIdehen

Tim Clark: Mass General/Harvard working on neurodegenerative diseases + I.T. spec, how scientists talk with each other

SCF and SQAN projects

whoops, SWAN

Ronan Fox: at Derry clinical practice/research works with Holger / Matthias

<johnbreslin> DERI = Digital Enterprise Research Institute (National University of Ireland, Galway - www.deri.ie)

whoops

thanks

<johnbreslin> np ;)

LARKC project at DERI

Mary Kennedy -- College of Am Pathologists

If I missed anybody who wants to add anything -- please do

<johnbreslin> No the LARC project is somewhere else - missed the name

Vipul -COI status report

How do you map across terminologies?

<vipul> http://esw.w3.org/topic/HCLS/ClinicalObservationsInteroperability/DrugMapping.html

If we can answer, we can go to proof of concept

Want to formulate sparql query and map to actual trials/clinical DB

e.g. how to map drug classes from Samson's ontology to clinical vocabs (e.g. RxNorm)

our dataset has NDC codes, so we actually need NDC-to-RxNorm in addition

Ultimately, want Samson-to-NDC-to-RxNorm

Olivier B at NLM is helping -- gave RxNorm API for NLM mapping software

John Kilbourne at CAP is also working on these mappings

Jyoti at Mayo is working on this

how to represent maps? Not the focus just yet

For now, will make SQL tables

EricP suggests that mapping language is not critical, all the possibilities are of similar expressivity and can be automatically cross-represented

Scot: will you use SKOS?

Vipul: that's an option. We have lots of many-to-many mappings

<ericP> +1 to q+

Next item: Scott HCLS KB update

<vipul> Sorry, I have another meeting to go to... Talk to you guys later.

Big todo list currently

1. improve interface , make it gui

2. add more data, esp supporting ongoing tasks in hcls

3. distribution infrastructure (mirrors, etc.)

4. would like to have at least two endpoints for sparql queries

Kei will coordinate BioRDF

starting in fall

Kei: september 8 will be first BioRDF call
... work on 1-4 and also want to revisit objectives in this meeting

Susie: thanks, kei

Next item: Tim Clark & John Breslin

<ericP> John's slides

<ericP> Tim's slides

<Susie> http://www.w3.org/Talks/Tools/Slidy/

<ericP> John's slides

First, John: Semantically-Interlinked Online Communities and SWAN in HCLS

<Donald_Doherty> Am I the only one still not seeing the slides? (Interminable download)

<ericP> Motivation for SIOC

SIOC 2-3 yrs old at DERI Slide 1: Motivation: social engineering for SW

web is very diffuse

can we leverage social web as a medium for knowledge

<ericP> connecting virtual fora

e.g. can trackback blogs, but result isn't "knowledge", too disconnected

<Donald_Doherty> Hmmm. Moved to Safari and it works. (Didn't load in my Firefox 3)

<ericP> SIOC lens

SIOC creates middleware layer between social web and knowledge-focused image of social web

<ericP> The SIOC solution

slide 6: high level structure of SIOC

<ericP> SIOC ontology

<ericP> SIOC Food Chain

<ericP> Producing SIOC data

SIOC API's allow anybody to export their data in SIOC

<ericP> Collecting SIOC data

<ericP> Consuming SIOC data

<ericP> 3. Dissemination

http://sioc-project.org

http://www.w3.org/2008/Talks/0723-SIOC/#(13) lists some adopters

http://www.w3.org/2008/Talks/0723-SIOC/#(15) augment SIOC for various domains

Next: Tim Clark

<ericP> SWAN SIOC slides

<ericP> [slide 2]

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (2) SQN & SIOC complementary

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (3) ecocystem emerging around SWAN and SCF, may integrate with SIOC

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (4) now in beta with 60 Alzheimer's researchers to test if software meets their needs

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (5) what is SWAN?

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (6) SWAN website runs off a triplestore

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (7) what is SCF?

a special distro of Drupal designed to work with SWAN

vision: SCF may be infrastructure base for many biomedical research communities

<Huajun> Zakim +??P25 is Huajun

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (8) stembook is scf-based stemcell website

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf(9) PDOnline is an scf-based parkinson's site

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (10) SWAN architecture

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf 11) SWAN ontology overview

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (12) SWAN has some interesting properties that capture hypothesis-making process

including disagreement/gap issues

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (13) summarizes some of how hypotheses can interrelate in SWAN

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (14) want feedback!

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (15) Bibliography

http://www.w3.org/2008/Talks/0723-SIOC/SWAN-SIOC.pdf (16) team and SWAN/DERI collab

Susie: SIOC/SWAN integration will be an HCLS task. If want to praticipate, sed email to Susie or tim

Next item: Susie--- open drug data

<Susie> http://esw.w3.org/topic/HCLSIG/LODD

<kidehen> johnbreslin: do ping me re SIOC/SWAN, naturally interested in the SIOC mapping

<johnbreslin> sure kidehen

identifying public datasets with drug data

will then see if can formulate juicy questions

and see if can query in federated fashion

Susie will send out email on project with ???

Also, chris bizer is interested in federation principles

Next item: Chime

Task project idea #1: standard med terminologies to OWL/RDF

<kidehen> JohnMadden: I am interested in the LODD deployment efforts in relation to Linked Data principles etc..

This is for medical record terminologies (SNOMED CT, UMLS)

How can develp methods for taking these legacy terminologies and seeing if can extract OWL

without violating license restrictions

for example, can you develop extract/subset of a legacy terminology, create OWL and use without violating license

anybody want to suggest a use case?

Tim: disconnect now -- semweb is focused on FMA from WashU, but brain imagers don't use it

they use NeuroNames

it's informal vocabulary

Mary Kennedy: SNOMED was sold to IHTSDO in Denmark, now freely available in member countries. Also SNOEMD has drug subset

Helen: EU funded project ongoing in SNOMED Infect dis and antibiotics. Will contribute use case

Will SNOMED ever be released as OWL

<ericP> JohnMadden: i don't think SNOMED will ever be released as OWL

<ericP> ... Kent has created a translater from SNOMED triples to OWL

which I can get from Kent

face to face

<ericP> next HCLS face to face 20-21 October (Mon-Tue) near Cannes FR, W3C Technical Plenary is the next day.

Next item: Next F2F

<ericP> Pullman Cannes Mandelieu Royal Casino, Mandelieu, (FR)

<ericP> TPAC Overview page

<ericP> Chimé's announcement

<ericP> Registration page

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