Kei Cheung, Ph.D.

1
BioRDF Task Overview and Update

• Kei Cheung, Ph.D.
• Yale Center for Medical Informatics
• Matthias Samwald, Ph.D.
• Digital Enterprise Research Institute, Galway,
  Ireland
• Semantic Web Company, Vienna, Austria

2
BioRDF participants

• The task led by Kei Cheung (Yale)?
• Participants have diverse backgrounds
• Bioinformatics
• Neuroscience
• Pharmacology
• ...

3
BioRDF activities

• Explore effectiveness of current tools/approaches
  for making data available as RDF/OWL
• Build life sciences demo that spans from bench to
  bedside using RDF/OWL
• Help scientist better understand the value of the
  Semantic Web

4
BioRDF activities

• Document our findings to help accelerate the
  adoption of the Semantic Web by others
• Invite experts in different areas to give
  presentation
• Maryann Martone
• Eric Antenzana
• Olivier Bodenreider...

5
More information

• W3C notes
• A Prototype Knowledge Base for the Life
  Scienceshttp//www.w3.org/TR/hcls-kb/
• Experience with the Conversion of SenseLab
  Databases to RDF/OWLhttp//www.w3.org/TR/hcls-sen
  selab/
• BioRDF Wiki pagehttp//esw.w3.org/topic/HCLSIG_Bi
  oRDF_Subgroup

6
Looking back
7
Answering relevant questions

• Goals Get answers to questions posed to a body
  of collective knowledge in an effective way
• Knowledge used Publicly available databases and
  biomedical literature
• Strategy Integrate knowledge using careful
  modeling, exploiting Semantic Web standards and
  technologies

8
Banff Demo Looking for Alzheimer Disease Targets
Can we find candidate genes known to be
involved in signal transduction and active in
Pyramidal Neurons?
9
Answering questions with Google
10
Answering questions with PubMed
11
Integrating heterogeneous data
12
Integrating heterogeneous data
13
Integrating heterogeneous data
PDSPki
NeuronDB
Reactome
Gene Ontology
BAMS
Allen Brain Atlas
BrainPharm
Antibodies
Entrez Gene
MESH
Literature
PubChem
Mammalian Phenotype
SWAN
AlzGene
Homologene
14
(No Transcript)
15
SPARQL query spanning four data sources
Thanks to Alan Ruttenberg
16
Results Genes, Processes

• DRD1, 1812 adenylate cyclase activation
• ADRB2, 154 adenylate cyclase activation
• ADRB2, 154 arrestin mediated desensitization of
  G-protein coupled receptor protein signaling
  pathway
• DRD1IP, 50632 dopamine receptor signaling
  pathway
• DRD1, 1812 dopamine receptor, adenylate cyclase
  activating pathway
• DRD2, 1813 dopamine receptor, adenylate cyclase
  inhibiting pathway
• GRM7, 2917 G-protein coupled receptor protein
  signaling pathway
• GNG3, 2785 G-protein coupled receptor protein
  signaling pathway
• GNG12, 55970 G-protein coupled receptor protein
  signaling pathway
• DRD2, 1813 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, 3356 G-protein coupled receptor protein
  signaling pathway
• DRD1, 1812 G-protein signaling, coupled to
  cyclic nucleotide second messenger
• SSTR5, 6755 G-protein signaling, coupled to
  cyclic nucleotide second messenger
• MTNR1A, 4543 G-protein signaling, coupled to
  cyclic nucleotide second messenger
• CNR2, 1269 G-protein signaling, coupled to
  cyclic nucleotide second messenger
• HTR6, 3362 G-protein signaling, coupled to
  cyclic nucleotide second messenger
• GRIK2, 2898 glutamate signaling pathway

Many of the genes are related to AD through gamma
secretase (presenilin) activity
Thanks to Alan Ruttenberg
17
Use Exhibit to Visualize Results
18
Looking sideways
19
Looking sideways

• Uniprot RDF
• Bio2RDF
• BioGateway
• Linked Life Data (Astra Zeneca)
• But also DBpedia, the 'Linked Open Data' cloud

20
(No Transcript)
21
(No Transcript)
22
Looking forward!
23
Looking forward!

• Incorporate additional data sources into the HCLS
  KB

24

• Neuroscience Database Gateway
• Molecular Biology Database Collection

25
Looking forward!

• Incorporate additional data sources into the HCLS
  KB
• Make the interface easier for scientists to use

26
Entrez Neuron
27
Looking forward!

• 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 triplestores for hosting
• DERI Galway
• Free University of Berlin (Adrian Paschke)?

28
Different Levels of BioRDF Activities
29
Proof-of-concept vs. practical application?
Long-term sustainability?
First party vs. second party RDFization?
Aggregation vs. distributed queries?
Social Web?
Relevance ranking?
Light-weight vs. very expressive?
RDF heterogeneity?
Natural language processing?
Relation to other HCLS IG task forces?
30
Conclusions

• Integrating you data with other data adding
  value to your data!
• Semantic Web technologies offers a flexible
  approach to data integration
• Please let us know if you are interested in
  participating!