Chem2bio2rdf portal


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Chem2Bio2RDF: a semantic RDF-based framework for studying systems chem

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Chem2bio2rdf portal

  1. 1. CHEM2BIO2RDF:A LINKED OPEN DATA PORTAL FORSYSTEMS CHEMICAL BIOLOGYBin Chen, Ying Ding, Huijun Wang, David Wild, Xiao Dong,Yuyin Sun, Qian Zhu, Madhuvanthi Sankaranarayanan Indiana University at Bloomington
  2. 2. Chemogenomics PPI DiseaseCompound Protein Metabolic Pathway Side effectDrug Gene Gene Regulatory Toxicity Chemical Biology Systems Phenotype interacting mapping What’s Systems Chemical Biology
  3. 3. All the public data are scattered around the web… MATADOR
  4. 4. LODD Bio2RDF (Drug/Chemical Data)(biological data) Chem2Bio2RDF (chemogenomics---how chemical interact with biological data)
  5. 5. Linked Open Data (LOD) Bio2RDF LODD Linked Life Data Chem2Bio2RDF
  6. 6. Workflow for RDF conversion XML Ontology D2R CSV Download Scripts Mapping Dumping Virtuoso Relational D2R Local Triple DB server copy Store TXT Publishing DB …External Sources
  7. 7. We are focusing on how chemicalinteracts with biological data 12 databases 204, 981 compounds 17, 930 genes 646, 608 associations Caveat: Not all binding data! MATADOR
  8. 8. Literature based Systems ChemicalBiology Covering 1865-2009 18,502,916 PubMed/Medline literature records!
  9. 9. Workflow for conversion PubMed/Medlinedata
  10. 10. Chem2Bio2RDF data Other data venders compound protein/gene chemogenomics literature others Node represents each database colored by its RDF vender; Directed edge shows Over 110 million triples! the linkage from one dataset to another dataset, colored by the linkage type. E.g,., the type compound includes CID, CAS, ChEBI, DBID and so on. The size ofChem2Bio2RDF Datasets nodes and the width of edges are dependent on the # of triples and # of linkages respectively.
  11. 11. Dereferenable URI PlotViz: Visualization Bio2RDF Browsing Cytoscape Plugin Virtuoso Triple storeChem2Bio2RDF Linked Path Generation and Ranking LODD uniprot Others SPARQL ENDPOINTS Third party tools
  12. 12. (Dereferenable URI) Link to Bio2RDF disease Link to Chem2Bio2RDF Gene Link to PubMed website Link to Chem2Bio2RDF pathway Link to Chem2Bio2RDF side effect
  13. 13. Facet browsers using Exhibit
  14. 14. Search Chem2Bio2RDF Search engine resultsSPARQL results Cytoscape plugin
  15. 15. Answer scientific questions Give me all information about this compound Give me all information about this target Find chemical associated genes Find gene associated chemicals Find disease associated chemicals Find side effect associated chemicals Find all the drug-like compounds in PubChem BioAssay that share at least two targets with a drug in DrugBank Link KEGG / Reactome Pathways and PubChem to identify potential multiple pathway inhibitors for MAPK More in
  16. 16. CASE study: Adverse drug reaction
  17. 17. 1. Scientific Question Drugs that cause similar adverse side effects often have totally different chemical structures Cholestasis, Bile salt transporters in liver
  18. 18. 2. hypothesis drug targets might function in the same pathway
  19. 19. 3. Methods find KEGG pathways containing at least two of the targets associated with a given sidePath finding and visualization effect (i.e. hepatomegaly) PREFIX chem2bio: <http://localhost:2020/vocab/resource/> SELECT ?pathway_id (count(?pathway_id) as ?count) WHERE { SPARQL ?compound chem2bio:sider_side_effect ?side_effect . ?compound chem2bio:sider_cid ?dbid . ?targetid chem2bio: DrugBankTarget_dbid ?dbid . ?targetid chem2bio: DrugBankTarget_swissport_id ?UniProt_id . ?pathwayid chem2bio:KEGG_pathway _gene_keggid ?UniProt_id . ?pathwayid chem2bio:KEGG_pathway _pathway_id ?pathway_id . FILTER regex(?side_effect,"hepatomegaly","i") . } GROUP BY ?pathway_id ORDER BY ?count DESC;
  20. 20. 4. results Olanzapin Doxazosin Isoflurane Ziprasidone Risperidone ClozapineDrug e GABRA GLRA ADRA1Target PTGS2 PTGS1 GRIA1 HRH1 HTR1A HTR2A ADRA1B ADRB1 DRD2 DRD1 1 1 APathwa Arachidonic VEGF Neuroactive Calcium acid signaling ligand-receptor Small cell Pathways in signaling Gap y metabolism pathway interaction lung cancer cancer pathway Junction Side Hepatic HepatomegalEffect Hepatitis Necrosis y hepatomegaly & Gap Junction?
  21. 21. 5. validationPREFIX medline: <>PREFIX kegg: <>PREFIX sider: <>select *from <>from <>from <>where{ ?kegg_id kegg:Pathway_name ?pathway_name . FILTERregex(?pathway_name,"gap junction","i") . ?pmid medline:pathway ?kegg_id . ?pmid medline:side_effect ?sider . ?sider sider:side_effect ?side_effect . FILTERregex(?side_effect,"Hepatomegaly","i") .} Literature based validation Retrieve literatures talking about hepatomegaly & Gap Junction
  22. 22. Summary Chem2Bio2RDF portal attempts to collect and link all public data related to Systems Chemical Biology Chem2Bio2RDF offer various tools to browse, search and explore the data source Case studies demonstrate that it could serve as an useful portal in drug discovery
  23. 23. THANKS!