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Face-to-Face Meeting Semantic Web for Healthcare and Life Sciences Interest Group http://www.w3.org/2001/sw/hcls/ W3C HCLS chairs, Eric Neumann - Clinical Semantics Group – PowerPoint PPT presentation

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Title: Face-to-Face Meeting


1
Face-to-Face Meeting Semantic Web for
Healthcare and Life Sciences Interest Group
http//www.w3.org/2001/sw/hcls/ W3C HCLS
chairs, Eric Neumann - Clinical Semantics
Group Tonya Hongsermeier - Partners Healthcare
2
F2F Agenda
  • Thursday November 8, 2007
  • 1.30pm - 2.00pm - F2F Kickoff, Welcome and
    Introductions (EricN Tonya)
  • 2.00pm - 2.30pm - Clinical Observations
    Interoperability How can Semantic Technologies
    Help? (Vipul)
  • 2.30pm - 3.00pm - Clincal Observations
    Interoperability (COI) Use Case (Rachel)
  • 3.00pm - 3.30pm - Tea/Coffee
  • 3.30pm - 4.00pm - Detailed Clinical Models and
    the COI Use Case (Tom)
  • 4.00pm - 4.15pm - Demo Semantic DB System at
    Cleveland Clinic (Chimezie)
  • 4.15pm - 4.30pm - Demo SHER System by IBM and
    Columbia University (Chintan)
  • 4.30pm - 5.30pm - Round Table and Feedback on
    Next Steps for COI (Moderator Vipul)
  • 5.30pm - 6.00pm - Wrap Up (EricN Tonya)
  • 6.30pm - Dinner with COI participants to work on
    functional requirements spreadsheet, etc.

3
F2F Agenda
  • Friday November 9, 2007
  • 830am - 900am - Welcome and Introductions
    (EricN Tonya)
  • 9.00am - 10.30am - Group Reviews BioRDF, ACPP,
    DSE, BIONT/Clinical Trials EMR
  • 10.30am - 11.00am - Break
  • 11.00am - 12.00pm - HCLS questionnaire results
    and charter discussion (EricP et al)
  • 12.00pm - 1.00pm - Lunch
  • 1.00pm - 2.30pm - BioRDF Understanding and
    enhancing the knowledgebase (Alan, et al.)
  • 2.30pm - 3.00pm - Break
  • 3.00pm - 4.00pm - BioRDF URI note discussion
    (Jonathan)
  • 4.00pm - 5.00pm - Next Steps / Wrap up

4
What is HCLS?
  • The Semantic Web Health Care and Life Sciences
    Interest Group is chartered to develop and
    support the use of Semantic Web technologies and
    practices to improve collaboration, research and
    development, and innovation adoption in the
    health care and life science domains. Success in
    these domains will ultimately depend on a
    foundation of semantically rich systems,
    processes and information interoperability.
  • The scope of HCLSIG includes
  • Core vocabularies and ontologies to support
    cross-community data integration and
    collaborative efforts
  • Guidelines and Best Practices for Resource
    Identification to support integrity and version
    control
  • Better integration of Scientific Publication with
    people, data, software, publications, and
    clinical trials

5
HCLS Themes
  • Principle activities have centered around
  • Building a broad and strong community
  • Exploring and documenting Use Cases
  • Converting resources to RDF-OWL
  • Learning to work with semantic web
    query/inference technology such as SPARQL, OWL,
    and rule engines.

6
Organization
  • Chairs Eric Neumann, Tonya Hongsermeier
  • Group divided in to task forces (coordinator)
  • BioRDF. Established initially to convert
    biomedical data to RDF (Susie Stephens)
  • BIONT. Established initially to be resource for
    ontology needs for other groups (Vipul Kashyap)
  • DSE (Drug Safety and Efficacy). Established
    initially to work on SW technology to support
    monitoring drug safety, pharmacovigilance (Eric
    Neumann)
  • ACPP (Adaptable Clinical Protocols and Pathways)
    Established initially to work on method of
    representing and computing applicability of
    protocols to dynamically changing patient status
    (Helen Chen)
  • COI (Clinical Observations Interoperability).
    Established recently with two goals 1) Establish
    new collaboration with health care industry
    players 2) Work on issues at the intersection of
    electronic medical records and health care
    organization needs. (Vipul Kashyap)

7
Membership
  • 64 participants from 38 organizations
  • 3 Invited Experts
  • Many more non-member participants on-line

8
Meetings to-date
  • Formal F2F, January 2006, Cambridge
  • Formal F2F, October 2006, Amsterdam
  • Workshop, ISWC November 2006, Banff
  • Informal F2F (Demo) 3 x March/April, 2007,
    Cambridge
  • Workshop, WWW 2007, May 2007, Banff
  • Informal F2F (URI), July 2007, Cambridge
  • Formal F2F, November 2007, Cambridge

9
Demonstrations and Examples
  • HCLS NeuroScience Demo - WWW2007 Banff
  • http//esw.w3.org/topic/HCLS/Banff2007Demo
  • Clinical Trials Data Management and Viewing
  • http//eneumann.org/exhibit/clinicaldemo/
  • Taverna, AIDA
  • http//taverna.sourceforge.net,
    http//myexperiment.org/
  • Mining Disease Relations from Semantically
    Integrated Genome - Phenome Maps
  • http//www2007.org/workshops/paper_146.pdf

10
Presentations
  • WWW2007 Demo
  • ISMB 2007 Demo
  • ISMB BioOntology SIG Poster 2007
  • Society for Neuroscience Poster Nov 2007
  • Selection of presentation venues of members
    showing HCLS work
  • Bridging Pharma and IT
  • Drug Discovery Technology of Innovative
    Therapeutics
  • 1st European Semantic Web Conference
  • Bio-IT World
  • Norwegian Semantic Web Day
  • InfoTech Pharma
  • Modern Drug Discovery and Development Summit
  • Massachusetts Biotechnology Panel
  • eScience Institute RDF, Ontologies and
    Meta-Data Workshop
  • Virginia Biotechnology Summit
  • Systems Biology
  • Semantic Web Gathering
  • Allen Institute for Brain Sciences
  • Informatics and Interactomes in Huntingtons
    Disease

11
HCLS Ecosystem
HCPChoices
Insurers
Grants
HMO,PPO
Biomed Research
Publications and Public Databases
BioKB
Gov/Funding
Large Studies
Risks Benefits
Disease Areas
Drug RD
EHR
Mol Path Res
Clin Res
Chem Manuf
Drug Programs
Clin POC
Surveillance
BiomarkerTox
HCP
Public
Preclin
Marketing
Gov/Regulatory
VA System RD
CDC
CROs
Clin Safety
JANUS
SafetyCommons
12
Distributed Nature of RD Information
Registry
  • Silos of Data

Tox
Biomarkers
Targets
Libraries
Assays
HCS
Diseases
Genotypes
MolModels
13
Data Integration
  • Forcing data to fit a specific application

App 2
App 1
?
14
Data Integration
15
Data Aggregation
  • Think Smart Mash-up
  • Data aggregated for any application ins
    semantically consistent way.

16
Semantic Web Basics
17
The Current Web
Resources
  • What the computer sees Dumb links
  • No semantics - lta hrefgt treated just like ltboldgt
  • Minimal machine-processable information

Resources
Resources
Resources
Resources
Resources
Resources
Resources
18
The Semantic Web
Clinical Study
  • RDF- Resource Description Framework
  • Machine-processable semantic information
  • Semantic context published making the data more
    informative to both humans and machines

hasSubject
using
Subject
Design
hasFindings
hasAE
treatment
Finding
Adverse Event
Intervention
derived
hasExpression
BiomarkerSample
GeneExpression
19
The Layer Cake
20
Facts as triples
has_associated_disease
PARK1
Parkinson disease
subject
predicate
object
21
From triples to a graph
MAPT
Parkinson disease
MAPT
Pick disease
PARK1
Parkinson disease
TBP
Parkinson disease
TBP
Spinocerebellar ataxia
has_associated_disease
22
Connecting graphs
  • Integrate graphs from multiple resources
  • Query across resources

23
Recombinant Data
  • Graphs can be filtered and pivoted, without
    losing meaning

24
Where does Semantic Web Fit In?
Connecting Legacy Data to SWD2R, MagLev
25
Semantic Web Applied to Disease Mechanism and
Pharmacology
26
Drug Safety and Efficacy
  • Group focuses on
  • Draft an approach for clinical trial data that is
    in line with the Clinical Data Interchange
    Standards(CDISC) Study Data Tabulation Model
    (SDTM)
  • Can SW standards help with EDC?
  • Work on aggregating patient data with
    pharmacogenomic information.
  • Use Case around Pharmacovigilance
  • Emphasis on display/visualization of clinical
    trial data, rather than query
  • They have a demo that uses the Simile projects
    Exhibit tools to display information merging
    three points of view
  • Demographics
  • Treatments
  • Adverse Events
  • SNP

27
Clinical Observations Interoperability
  • Recently formed http//esw.w3.org/topic/HCLS/Ontol
    ogyTaskForce/BIONTDSEDCM
  • Focusing on problem of identifying clinical trial
    candidates based on constraints of participation
    and information in medical records.
  • Clinical trial recruitment is an everybody-wins
    situation
  • Patients want new cures and development of them
    is dependent on trials
  • Pharma want new drugs to bring huge profits
  • Running clinical trials is profitable for CROs
  • Doctors and hospitals get money for identifying,
    treating, and recording information about
    patients.
  • Technical problems (evaluation of constraints)
    are very similar to those identified and somewhat
    addressed in ACPP. Driver of rule and OWL
    technology.
  • Has brought in new industry and academic
    participants.
  • DSE, ACPP, and BioONT participants are joining
    this effort.

28
BioRDF Demo Neurocommons Triple Store
  • Challenge Go beyond toy size examples of
    Semantic Web
  • Strategy 1) Work on translating a dozen existing
    databases using OBO methodology and OWL, focused
    on neuroscience research questions
  • Pubmed/Mesh mappings
  • OBO ontologies, including Gene functions,
    molecular processes, cellular components
  • Neuroscience ontologies Senselab, BAMS, Allen
    Brain Atlas
  • Strategy 2) Develop capability to run
    interesting SPARQL queries at scale
  • 300 Million triples
  • Open source, reproducible
  • Queries that could only be done previously with a
    lot of effort
  • Demonstrate Practice a useful prelude to
    developing Best Practice
  • Enthusiastic response from community. We often
    hear
  • This is the first time Ive seen semantic web
    technology do anything useful
  • WWW2007 Thank you from the semantic web
  • Some problems solved, many remain, ongoing work.

29
Adaptable Clinical Protocols and Pathways
  • This group was active mostly in the first year
  • Worked on Guideline Reference Ontology
  • Prototyped three instances of guidelines based on
    the ontology
  • Worked on reasoning with inclusion/exclusion
    criteria
  • Developed clear use cases that need temporal
    concepts reasoning
  • Two rule engines used. Helen Chen Euler,
    Chimezie Ogbuji Fuxi (his own work!)
  • This work is great arena for exploring the
    difference between using OWL versus rules
  • Although research is finished, need more manpower
    to write up results
  • AGFA benefited significantly from the work and it
    has influenced their internal models.
  • SW is a strong focus in AGFA health care for
    evidence based patient care, and they expect to
    invest in it for years to come.
  • Helen, Chimezie are now bringing their
    experiences to the new Clinical Observations
    Interoperability group.

30
URI recommendations project
  • Jonathan Rees leading work in BioRDF on upcoming
    note
  • Problem is stable identifiers for knowledge
    resources of import, and for entities in the
    world
  • Proteins, Organs, Symptoms etc.
  • Motivated by complaints about inadequate
    instruction
  • From providers not knowing good practices for
    minting URIs
  • From users not knowing how to name or make
    statements about resources that can be
    effectively integrated
  • Community finds current AWWW and TAG
    documentation and recommendations inadequate
  • Problem is not easily separable from issues of
    providing good practices for making use of the
    URIs, such as having mechanisms for figuring out
    what they mean

31
New charter process
  • Goal is to design one or two charters for working
    group and/or interest group.
  • Initial step was drafting of questionnaire
    circulated to wide swath of life sciences and
    health care community. We listed possible
    activities and asked which would be of interest
    for participation. Currently almost 50 responses
  • http//www.w3.org/2007/06/HCLSForm
  • Next step analyze and draft a charter that is
    responsive to the feedback gained from the
    questionnaire. Target is for new charter to
    circulate early November.

32
Looking Forward
  • Work with TAG over architectural needs for
    Semantic Web for science. Important to get time
    with them at Tech Plenary meeting in November.
  • Find and recruit more members like AGFA, who feel
    they got value from group participation. Current
    membership has no shortage of other organizations
    with some tie to health care/life sciences,
    either as vendors (e.g. IBM) or primary, such as
    pharma (Merck, Pfizer)
  • Targeting pharma, health care, vendors, not
    currently SW-ready standards groups (e.g. CDISC),
    FDA, NIH sponsored projects, and academic
    research leaders.
  • Further recruitment should be based on listening
    to needs, addressing them with focused projects
    within the next HCLS. Focus on increasing
    credibility.
  • Acceptance of SW technologys role in pharma/
    health care is growing, hopefully to soon match
    enthusiasm from life sciences community. They are
    looking for guidance, and we need to provide it.

33
Upcoming Event C-SHALS
  • Conference on Semantics in Health and Life
    Sciences
  • March 5-7 2008, Cambridge, MA
  • Industry Presentations on the State of the Art
    for intelligent semantic applications in Drug RD
  • Sponsors Pfizer, Merck,

34
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