title: New publicly available chemical query language, CSRML, to support chemotype representations for application to data mining and modeling.
abstract: Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Markup Language (CSRML), and can be encoded not only with connectivity and topology but also with properties of atoms, bonds, electronic systems, or molecules. CSRML has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory, and commercial-use chemical space, as well as to represent chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper has also been developed and made publicly available in order to enable chemotype searching and fingerprinting against a target structure set. The public ChemoTyper houses the ToxPrint chemotype CSRML dictionary, as well as reference implementation so that the query specifications may be adopted by other chemical structure knowledge systems. The full specifications of the XML-based CSRML standard used to express chemotypes are publicly available to facilitate and encourage the exchange of structural knowledge.
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.|‡Altamira LLC, Columbus, Ohio 43235, United States.|∥US Food and Drug Administration Center for Food Safety and Applied Nutrition, Office of Food Additive Safety (FDA CFSAN OFAS), College Park, Maryland 20740, United States.
authors: Chihae
authors: C
authors: Yang
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Aleksey
authors: A
authors: Tarkhov
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Jörg
authors: J
authors: Marusczyk
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Bruno
authors: B
authors: Bienfait
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Johann
authors: J
authors: Gasteiger
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Thomas
authors: T
authors: Kleinoeder
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Tomasz
authors: T
authors: Magdziarz
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Oliver
authors: O
authors: Sacher
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Christof H
authors: CH
authors: Schwab
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Johannes
authors: J
authors: Schwoebel
authors: †Molecular Networks GmbH, 91052 Erlangen, Germany.
authors: Lothar
authors: L
authors: Terfloth
authors: ∥US Food and Drug Administration Center for Food Safety and Applied Nutrition, Office of Food Additive Safety (FDA CFSAN OFAS), College Park, Maryland 20740, United States.
authors: Kirk
authors: K
authors: Arvidson
authors: ⊥National Center for Computational Toxicology, US Environmental Protection Agency (EPA), Research Triangle Park, North Carolina 27711, United States.
authors: Ann
authors: A
authors: Richard
authors: #EC Joint Research Centre (JRC), I-21027 Ispra, Italy.
authors: Andrew
authors: A
authors: Worth
authors: ‡Altamira LLC, Columbus, Ohio 43235, United States.|§Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States.
authors: James
authors: J
authors: Rathman
mesh_terms: D002621:Chemistry; D057225:Data Mining; D016208:Databases, Factual; D015394:Molecular Structure; D010756:Phosphoric Acids / Q000737:chemistry; D011381:Programming Languages; D012984:Software; D013329:Structure-Activity Relationship; D014116:Toxicology / Q000379:methods; D014584:User-Computer Interface
chemical_list: D010756:Phosphoric Acids; C030242:phosphoric acid