title: CART-a chemical annotation retrieval toolkit.
abstract: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases.
  
  
  
  To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data.
  
  
  
  CART is available as a Galaxy web service (cart.embl.de). Source code and an easy-to-install command line tool can also be obtained from the web site.
  
  
  
  bork@embl.de
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Samy
authors.initials: S
authors.lastname: Deghou
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Murat
authors.initials: M
authors.lastname: Iskar
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Marja
authors.initials: M
authors.lastname: Driessen
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Mercedes
authors.initials: M
authors.lastname: Castillo
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
authors.forename: Vera
authors.initials: V
authors.lastname: van Noort
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D019295:Computational Biology; D003196:Computer Graphics; D066289:Data Curation; D016208:Databases, Factual; D001330:Electronic Data Processing; D016247:Information Storage and Retrieval / Q000379:methods; D011381:Programming Languages; D012984:Software