HCLS Task Force Alignment

W3C Semantic Web in Health Care and Life Sciences.

Eric Prud'hommeaux, Sanitation Engineer. Last modified: $Date: 2009/11/04 00:10:03 $

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6 Task Forces

BioRDF – integrated neuroscience knowledge base
Linking Open Drug Data – aggregation of Web-based drug data
Clinical Observations Interoperability – patient recruitment
Scientific Discourse – building communities through networking
Terminology – SemWeb representation of existing resources
Translational Medicine Ontology – patient-centric upper level

Other Projects: Clinical Decision Support...

Real Query

Linking Open Drug Data

Evaluating LODD sources

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.

Scientific Discourse ...

Scientific Discourse expresses hypotheses

Scientists use this!

SWAN screenshot

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

COI

clinical protocol
health care:
- active ingredient
- pharmaceutical product -- approved
- prognosis -- likely course of a disease
- ‣disposition
- clinical subject
- inclusion criteria
- exclusion criteria
- diagnosis result
- medical history
- sign - physical patient feature
- symptom
- payer
- study
- study arm -- e.g. control vs. variable
- ‣‣disease
- ‣‣toxicity
- dosage

BioRDF

bilogic -- antibody as ingredient
target -- research target
molecular structure record
‣disease
‣toxicity
‣‣metabolite
‣protein
‣SNP
‣gene
‣‣genetype

Scientific Discourse

piece of evidence
hypothesis

other

expert
patent
environmental measure
phenotypic measure
institution
regulatory authority
image
cell line

keys

ChEBI curators

unknown

planned process (OBI 11)
information content entity
information entity about a realizable
copy_number_variation