1. Face-to-Face Meeting
Semantic Web for Healthcare and Life Sciences Interest Group
W3C HCLS chairs,
Eric Neumann - Clinical Semantics Group
Tonya Hongsermeier - Partners Healthcare

2. F2F Agenda Thursday November 8, 2007
1.30pm pm - F2F Kickoff, Welcome and Introductions (EricN & Tonya)
2.00pm pm - Clinical Observations Interoperability: How can Semantic Technologies Help? (Vipul)
2.30pm pm - Clincal Observations Interoperability (COI) Use Case (Rachel)
3.00pm pm - Tea/Coffee
3.30pm pm - Detailed Clinical Models and the COI Use Case (Tom)
4.00pm pm - Demo: Semantic DB System at Cleveland Clinic (Chimezie)
4.15pm pm - Demo: SHER System by IBM and Columbia University (Chintan)
4.30pm pm - Round Table and Feedback on Next Steps for COI (Moderator: Vipul)
5.30pm pm - Wrap Up (EricN & Tonya)
6.30pm - Dinner with COI participants to work on functional requirements spreadsheet, etc.

3. F2F Agenda Friday November 9, 2007
8:30am - 9:00am - Welcome and Introductions (EricN & Tonya)
9.00am am - Group Reviews: BioRDF, ACPP, DSE, & BIONT/Clinical Trials + EMR
10.30am am - Break
11.00am pm - HCLS questionnaire results and charter discussion (EricP et al)
12.00pm pm - Lunch
1.00pm pm - BioRDF: Understanding and enhancing the knowledgebase (Alan, et al.)
2.30pm pm - Break
3.00pm pm - BioRDF: URI note discussion (Jonathan)
4.00pm pm - 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
Clinical Trials Data Management and Viewing
Taverna, AIDA
Mining Disease Relations from Semantically Integrated Genome - Phenome Maps

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 Huntington’s Disease
Ontology for Biomedical Informatics Workshop
Clinical Trial Ontology Workshop
Jackson Laboratories
Pubmed Plus
NIH Blueprint NIF Workshop

11. Publications and Public Databases
HCLS Ecosystem
HCP Choices
Insurers
Grants
HMO,PPO
Biomed Research
Publications and Public Databases
BioKB
Gov/Funding
Large Studies
Risks & Benefits
Disease Areas
Drug R&D
Mol Path Res
EHR
Clin Res
Chem Manuf
Drug Programs
Clin POC
Surveillance
BiomarkerTox
HCP
Public
Preclin
CDC
VA System R&D
Gov/Regulatory
Marketing
Clin Safety
CROs
JANUS
Safety Commons

12. Distributed Nature of R&D Information
Registry
Silos of Data…
Tox
Biomarkers
Targets
Libraries
Assays
HCS
Diseases
Genotypes
Mol Models

13. Data Integration Forcing data to fit a specific application App 1?

14. Data Aggregation Think: Smart Mash-up
Data aggregated for any application ins semantically consistent way. ?
App ?
App ?

15. The Current Web What the computer sees: “Dumb” links
Resources
What the computer sees: “Dumb” links
No semantics - <a href> treated just like <bold>
Minimal machine-processable information
Resources
Resources
Resources
Resources
Resources
Resources
Resources

16. The Semantic Web RDF- Resource Description Framework
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
Intervention
Adverse Event
hasExpression
derived
Gene Expression
Biomarker Sample

17. The Layer Cake

18. Facts as triples has_associated_disease PARK1 Parkinson disease
subject
predicate
object

19. has_associated_disease
From triples to a graph
MAPT
Parkinson disease
PARK1
Parkinson disease
MAPT
Pick disease
TBP
Spinocerebellar ataxia
MAPT
Pick disease
PARK1
Parkinson disease
TBP
Parkinson disease
TBP
Spinocerebellar ataxia
has_associated_disease
PARK1
Parkinson disease
MAPT
Pick disease
TBP
Spinocerebellar ataxia

20. Neurodegenerative diseases
Connecting graphs
Integrate graphs from multiple resources
Query across resources
Alzheimer disease
Parkinson disease
Neurodegenerative diseases
isa
APP
Alzheimer disease
PARK1
Parkinson disease
has_associated_disease

21. Graphs can be filtered and pivoted, without losing meaning
Recombinant Data
Graphs can be filtered and pivoted, without losing meaning

22. Where does Semantic Web Fit In?
Connecting Legacy Data to SW: D2R, MagLev

23. Semantic Web Applied to Disease Mechanism and Pharmacology

24. 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 project’s Exhibit tools to display information merging three points of view
Demographics
Treatments
Adverse Events
SNP

25. Clinical Observations Interoperability
Recently formed
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.

26. 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 I’ve seen semantic web technology do anything useful”
WWW2007: “Thank you from the semantic web”
Some problems solved, many remain, ongoing work.

27. 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.

28. 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

29. 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
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.

30. 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 technology’s 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.

31. Upcoming Event: C-SHALS
Conference on Semantics in Health and Life Sciences
March , Cambridge, MA
Industry Presentations on the State of the Art for intelligent semantic applications in Drug R&D
Sponsors: Pfizer, Merck, …