Transcript Harnessing the Semantic Web to Answer Scientific Questions: A Health Care and Life Sciences Interest Group demo.

Harnessing the Semantic Web to
Answer Scientific Questions:
A Health Care and Life Sciences Interest Group demo
Scientific Domain Focus
• Use case focuses on Alzheimer’s Disease
• AD is a devastating illness that impacts 26.6 million
people worldwide
• Prevalence is predicted to quadruple to 106.8 million
by 2050
• An active Web community exists for AD research
• Many different types of evidence need to be
integrated
Which Biological Processes occur in Dendrites?
• Alzheimer’s disease is
characterized by neural
degeneration. Among other
things, there is damage to
dendrites and axons.
• What resources do we
have available to learn
more about biological
processes in dendrites?
Scientific Data Sets
• Integration and analysis of heterogeneous data sets
•
Hypothesis, Genome, Pathways, Molecular Properties, Disease, etc.
PDSPki
Gene
Ontology
NeuronDB
Reactome
BAMS
Antibodies
NC
Annotations
Entrez
Gene
Allen Brain
Atlas
BrainPharm
MESH
Mammalian
Phenotype
SWAN
AlzGene
PubChem
Homologene
Publications
Technological Approach
• Careful modeling that reflect biology to enable
integration of data sources
• All bio-entities were assigned URIs
• Data translated to RDF/OWL and managed in a
triple store
• Using a reasoner to infer triples to increase
expressiveness of queries
• Query data with SPARQL and visualization tools
Acknowledgements
HCLS Demo Contributors
HCLS Demo Contributors
• John Barkley (NIST)
• Susie Stephens (Eli Lilly)
• Olivier Bodenreider (NLM, NIH)
• Mike Travers (
• Bill Bug (Drexel University College of Medicine)
• Gwen Wong (SWAN)
• Huajun Chen (Zhejiang University)
• Elizabeth Wu (SWAN)
• Paolo Ciccarese (SWAN)
• Kei Cheung (SenseLab, Yale)
Data Providers
• Tim Clark (SWAN)
• Judith Blake (MGD.)
• Don Doherty (Brainstage Research Inc.)
• Mikail Bota (BAMS)
• Kerstin Forsberg (AstraZeneca)
• David Hill (MGD)
• Ray Hookaway (HP)
• Oliver Hoffman (CL)
• Vipul Kashyap (Partners Healthcare)
• Minna Lehvaslaiho (CL)
• June Kinoshita (AlzForum)
• Colin Knep (Alzforum)
• Joanne Luciano (Harvard Medical School)
• Maryanne Martone (CCDB)
• Scott Marshall (University of Amsterdam)
• Susan McClatchy (MGD)
• Chris Mungall (NCBO)
• Simon Twigger (RGD)
• Eric Neumann (Teranode)
• Allen Brain Institute
• Eric Prud’hommeaux (W3C)
• Jonathan Rees (Science Commons)
• Alan Ruttenberg (Science Commons)
• Matthias Samwald (Medical University of Vienna)
Vendor Support
• OpenLink - Kingsley Idehen, Ivan Mikhailov, Orri Erling, Mitko Iliev, Patrick van Kleef
• HP - Ray Hookaway, Jeannine Crockford