AMBIT open-source cheminformatics data management

  • consists of a MySQL database and functional modules supporting
    • queries
    • data mining
    • building and application of predictive models
  • the database stores
    • chemical substances, structures, and nanomaterials
    • their identifiers such as CAS, Einecs, and Inchi numbers
    • attributes such as molecular descriptors
    • experimental data together with test descriptions
    • literature references
    • QSAR models
  • can generate a suite of 2D and 3D molecular descriptors
  • besides the libraries, several applications are available
    • LRI AMBIT Read across tool
      loaded with REACH data subject to the legal notice; supports substance composition and IUCLID import; provides a comprehensive search functionality allowing structure search, substructure search, and similarity search even in databases not designed for, such as IUCLID, in order to find substances appropriate for read-across and category approaches; enables the inclusion of impurities (important in real industrial conditions) in substance search requests; includes a user interface for creating read across assessment and generating reports in online and downloadable versions
       
    • AMBIT REST Webservices
      provide an OpenTox API compliant REST web service interface to most of AMBIT's functionalities, and also add the ability to describe data, algorithms, and model resources via corresponding ontologies, and to build and apply QSAR models
       
    • AMBIT Discovery
      estimates applicability domain of QSAR models by various methods
  • GPL- (applications) and LGPL- (libraries) licenced

For more information and downloads, please refer to the AMBIT site at Sourceforge.

TOXTREE open-source toxic hazard estimation by decision tree approach

  • can be applied to datasets from various compatible file types
  • supports user-defined molecular structures
  • structures can be entered by SMILES or by using the built-in 2D structure diagram editor
  • GPL-licenced

For more information and downloads, please refer to the Toxtree site at Sourceforge.

TOXMATCH open-source chemical similarity indices encoding

  • facilitates the grouping of chemicals into categories and read-across
  • can compare datasets based on various structural and descriptor-based similarity indices
  • can calculate pair wise similarity between compounds or aggregated similarity of a compound to a set
  • GPL-licenced

For more information and downloads, please refer to the Toxmatch site at European Commision's JRC.