title: Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data.
abstract: BACKGROUND
  Recently there has been an explosion of new data sources about genes, proteins, genetic variations, chemical compounds, diseases and drugs. Integration of these data sources and the identification of patterns that go across them is of critical interest. Initiatives such as Bio2RDF and LODD have tackled the problem of linking biological data and drug data respectively using RDF. Thus far, the inclusion of chemogenomic and systems chemical biology information that crosses the domains of chemistry and biology has been very limited
  
  
  RESULTS
  We have created a single repository called Chem2Bio2RDF by aggregating data from multiple chemogenomics repositories that is cross-linked into Bio2RDF and LODD. We have also created a linked-path generation tool to facilitate SPARQL query generation, and have created extended SPARQL functions to address specific chemical/biological search needs. We demonstrate the utility of Chem2Bio2RDF in investigating polypharmacology, identification of potential multiple pathway inhibitors, and the association of pathways with adverse drug reactions.
  
  
  CONCLUSIONS
  We have created a new semantic systems chemical biology resource, and have demonstrated its potential usefulness in specific examples of polypharmacology, multiple pathway inhibition and adverse drug reaction--pathway mapping. We have also demonstrated the usefulness of extending SPARQL with cheminformatics and bioinformatics functionality.
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Chen
authors.forename: Xiao
authors.initials: X
authors.lastname: Dong
authors.forename: Dazhi
authors.initials: D
authors.lastname: Jiao
authors.forename: Huijun
authors.initials: H
authors.lastname: Wang
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhu
authors.forename: Ying
authors.initials: Y
authors.lastname: Ding
authors.forename: David J
authors.initials: DJ
authors.lastname: Wild
mesh_terms: D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D020407:Internet; D012660:Semantics; D012984:Software; D049490:Systems Biology; D018511:Systems Integration