What is the Semantic Web?

• Simple data model.
• Suitable for arbitrary data expression.
• Global identifiers and relations.
• Built-in linking (e.g. HTML's href).
• Ontology languages (RDFS, OWL, SKOS).

Nodes and arcs about people,

medicine,

life sciences, ...

in one universe

Who is HCLS?

W3C Semantic Web Health Care and Life Sciences Interest Group.

90+ members from industry and academia.

1 KB (350m+ triples)

papers

• IG notes
  • Knowledgebase writeup
  • KB extension
  • SWAN
  • SIOC
• BMC Bioinformatics, AMIA, ...

Workshops

Ontology mapping code.

Current Work

• BioRDF – integrated neuroscience knowledge base
  Task lead - Kei Cheung
• Linking Open Drug Data – aggregation of Web-based drug data
  Task lead - Chris Bizer
• Clinical Observations Interoperability – patient recruitment
  Task lead - Vipul Kashyap
• Scientific Discourse – building communities through networking
  Task leads - Tim Clark, John Breslin
• Terminology – SemWeb representation of existing resources
  Task lead - John Madden
• Translational Medicine Ontology – patient-centric upper level.
  Task lead - Susie Stephens

Other Projects: Clinical Decision Support...

HCLS KB

A Knowledgebase for Neuroscience

Built by Neurocommons and the HCLS BioRDF task force.

Precise answers to complex questions:

What proteins are associated with pyramidal neurons
AND are involved in signal transduction.

Real Query

Linking Open Drug Data

Clinical Observations Interoperability

• Bridge relational databases to HL7/RIM.
• Bridge HL7/RIM to SDTM.
• Encode some clinical protocol (inclusion/exclusion criteria) in SDTM.
• Use drug ontology to map drug classes to brands.
• Protocol selection in SDTM translated to RIM, relational query.
• Compare this SemWeb-y approach to other approaches.

Real Hospital Database

• Observation O
• on Patient P
• by Doctor D.

Real Hospital Database as RDF

• Observation O
• on Patient P
• by Doctor D.

... Sharable RDF

   PREFIX :mydb <http://cityhospital.example/dbs>
CONSTRUCT { ?o a               study:SubjectObservation .
            ?o study:subject   ?p .
            ?o study:clinician ?d .
            ?d :foaf:name ?dName }

    WHERE { ?o mydb:patient ?p .
            ?o mydb:doctor  ?d .
            ?d mydb:name    ?dName }

Query Transformation

PREFIX db: <…>
SELECT ?o ?d
 WHERE {
   ?o db:onPatient <Bob> .
   ?o db:byDoctor ?d .
 }

PREFIX db: <…>
SELECT observations... doctors...
  FROM observations, 
   patients ON id=observations.patient ...
   WHERE patients.name = "Bob"
 }

Scientific Discourse ...

Scientific Discourse expresses hypotheses

Scientists use this!

Terminology

Importing terms into Semantic Web.

• Start with pharmacological classifications in SNOMED-CT and UMLS
• Create URL identifiers for terms.
• Express term relationships (e.g. pre-coordinated terms) in OWL.
• Document process and and expressivity of schema languages.

Translational Medicine Ontology

Requires data from bench to bedside.

• vested parties (mostly from pharma)
• specific use cases
• identify data sources
• code as queries
• voila, practical ontology

Spans health care and life sciences

Models drug development lifecycle

Collaboration

We want your help

• excited group of people
• real-world impact
• fun scaling problems
• lots of papers
• good post-grad contacts

Come to G525 or
join per <http://www.w3.org/2001/sw/hcls/#ie>.