1. BioRDF Task: Building a Knowledgebase for Neuroscience
Eric Prud’hommeaux, W3C

2. BioRDF Introduction BioRDF participants BioRDF activities include:
The task is lead by Kei Cheung (Yale)
Has approximately 20 participants
BioRDF activities include:
Explore the effectiveness of current tools for making data available as RDF/OWL
Build a life sciences demo that spans from bench to bedside using RDF/OWL to help scientist better understand the value of the Semantic Web
Document our finding to help accelerate the adoption of the Semantic Web by others
BioRDF Publications
A Prototype Knowledge Base for the Life Sciences -
Experience with the Conversion of SenseLab Databases to RDF/OWL –
More Information on the group is available at

3. Answering Questions
Goals: Get answers to questions posed to a body of collective knowledge in an effective way
Knowledge used: Publicly available databases, and text mining
Strategy: Integrate knowledge using careful modeling, exploiting Semantic Web standards and technologies

4. Looking for Alzheimer Disease Targets
Signal transduction pathways are considered to be rich in “druggable” targets
CA1 Pyramidal Neurons are known to be particularly damaged in Alzheimer’s disease
Casting a wide net, can we find candidate genes known to be involved in signal transduction and active in Pyramidal Neurons?

5. Answering Questions with Google

6. Answering Questions with PubMed

7. Answering Questions across Data Sets

8. Integrating Heterogeneous Data Sets
NeuronDB
BAMS
Literature
Homologene
SWAN
Entrez Gene
Gene Ontology
Mammalian Phenotype
PDSPki
BrainPharm
AlzGene
Antibodies
PubChem
MESH
Reactome
Allen Brain Atlas

9. Integrating Heterogeneous Data Sets

10. Integrating Heterogeneous Data Sets
PDSPki
Gene Ontology
Reactome
NeuronDB
BAMS
Allen Brain Atlas
Antibodies
BrainPharm
Entrez Gene
MESH
Literature
PubChem
Mammalian Phenotype
SWAN
AlzGene
Homologene

11. SPARQL Query Spanning Data Sources

12. Results: Genes, Processes
DRD1, adenylate cyclase activation
ADRB2, 154 adenylate cyclase activation
ADRB2, 154 arrestin mediated desensitization of G-protein coupled receptor protein signaling pathway
DRD1IP, dopamine receptor signaling pathway
DRD1, dopamine receptor, adenylate cyclase activating pathway
DRD2, dopamine receptor, adenylate cyclase inhibiting pathway
GRM7, G-protein coupled receptor protein signaling pathway
GNG3, G-protein coupled receptor protein signaling pathway
GNG12, G-protein coupled receptor protein signaling pathway
DRD2, G-protein coupled receptor protein signaling pathway
ADRB2, 154 G-protein coupled receptor protein signaling pathway
CALM3, 808 G-protein coupled receptor protein signaling pathway
HTR2A, G-protein coupled receptor protein signaling pathway
DRD1, G-protein signaling, coupled to cyclic nucleotide second messenger
SSTR5, G-protein signaling, coupled to cyclic nucleotide second messenger
MTNR1A, G-protein signaling, coupled to cyclic nucleotide second messenger
CNR2, G-protein signaling, coupled to cyclic nucleotide second messenger
HTR6, G-protein signaling, coupled to cyclic nucleotide second messenger
GRIK2, glutamate signaling pathway
GRIN1, glutamate signaling pathway
GRIN2A, glutamate signaling pathway
GRIN2B, glutamate signaling pathway
ADAM10, 102 integrin-mediated signaling pathway
GRM7, negative regulation of adenylate cyclase activity
LRP1, negative regulation of Wnt receptor signaling pathway
ADAM10, 102 Notch receptor processing
ASCL1, 429 Notch signaling pathway
HTR2A, serotonin receptor signaling pathway
ADRB2, 154 transmembrane receptor protein tyrosine kinase activation (dimerization)
PTPRG, ransmembrane receptor protein tyrosine kinase signaling pathway
EPHA4, transmembrane receptor protein tyrosine kinase signaling pathway
NRTN, transmembrane receptor protein tyrosine kinase signaling pathway
CTNND1, Wnt receptor signaling pathway
Many of the genes are related to AD through gamma secretase (presenilin) activity

13. Another View of the Query

14. Discoverable, Queryable and Accessible on the Web
Allen Brain Institute Servers
Javascript
SPARQL AJAX
Query
URL
Google Maps API
Neurocommons Servers 14

15. Use Exhibit to Visualize Results

16. Technology So far about 350M triples (~20Gb on disk)
Openlink Virtuoso - open source triple store
Commodity Hardware: 2x2core duo/2 disks/8G Ram 16

17. Going Forwards Incorporate additional data sources into the HCLS KB
Make the interface easier for scientists to use
Focus on processes for updating the data sources
Find additional places to host the HCLS KB 17

18. Conclusions
The Semantic Web offers a flexible approach to data integration
BioRDF has integrated over a dozen neuroscience related resources to simplify answering scientific questions
The HCLS KB is accessible on the Web today
Please let us know if you are interested in participating in the BioRDF task