Kei Cheung, Ph.D.

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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

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BioRDF participants

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

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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

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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...

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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

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Looking back
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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

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Banff Demo Looking for Alzheimer Disease Targets
Can we find candidate genes known to be
involved in signal transduction and active in
Pyramidal Neurons?
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Answering questions with Google
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Answering questions with PubMed
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Integrating heterogeneous data
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Integrating heterogeneous data
PDSPki
NeuronDB
Reactome
Gene Ontology
BAMS
Allen Brain Atlas
BrainPharm
Antibodies
Entrez Gene
MESH
Literature
PubChem
Mammalian Phenotype
SWAN
AlzGene
Homologene
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SPARQL query spanning four data sources
Thanks to Alan Ruttenberg
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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
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Use Exhibit to Visualize Results
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Looking sideways
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Looking sideways

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

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Looking forward!
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Looking forward!

• Incorporate additional data sources into the HCLS
  KB

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• Neuroscience Database Gateway
• Molecular Biology Database Collection

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Looking forward!

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

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Entrez Neuron
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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)?

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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?
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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!