Literature DB >> 16426051

Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions.

Gemma L Holliday1, Peter Murray-Rust, Henry S Rzepa.   

Abstract

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.

Entities:  

Year:  2006        PMID： 16426051     DOI： 10.1021/ci0502698

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN： 1549-9596            Impact factor:   4.956


  13 in total

1.  Updates in Rhea--a manually curated resource of biochemical reactions.

Authors:  Anne Morgat; Kristian B Axelsen; Thierry Lombardot; Rafael Alcántara; Lucila Aimo; Mohamed Zerara; Anne Niknejad; Eugeni Belda; Nevila Hyka-Nouspikel; Elisabeth Coudert; Nicole Redaschi; Lydie Bougueleret; Christoph Steinbeck; Ioannis Xenarios; Alan Bridge
Journal:  Nucleic Acids Res       Date:  2014-10-20       Impact factor: 16.971

2.  XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services.

Authors:  Johannes Wagener; Ola Spjuth; Egon L Willighagen; Jarl E S Wikberg
Journal:  BMC Bioinformatics       Date:  2009-09-04       Impact factor: 3.169

3.  MACiE: a database of enzyme reaction mechanisms.

Authors:  Gemma L Holliday; Gail J Bartlett; Daniel E Almonacid; Noel M O'Boyle; Peter Murray-Rust; Janet M Thornton; John B O Mitchell
Journal:  Bioinformatics       Date:  2005-09-27       Impact factor: 6.937

4.  The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

Authors:  Weerapong Phadungsukanan; Markus Kraft; Joe A Townsend; Peter Murray-Rust
Journal:  J Cheminform       Date:  2012-08-07       Impact factor: 5.514

5.  Open Babel: An open chemical toolbox.

Authors:  Noel M O'Boyle; Michael Banck; Craig A James; Chris Morley; Tim Vandermeersch; Geoffrey R Hutchison
Journal:  J Cheminform       Date:  2011-10-07       Impact factor: 5.514

6.  ChemicalTagger: A tool for semantic text-mining in chemistry.

Authors:  Lezan Hawizy; David M Jessop; Nico Adams; Peter Murray-Rust
Journal:  J Cheminform       Date:  2011-05-16       Impact factor: 5.514

7.  Rhea--a manually curated resource of biochemical reactions.

Authors:  Rafael Alcántara; Kristian B Axelsen; Anne Morgat; Eugeni Belda; Elisabeth Coudert; Alan Bridge; Hong Cao; Paula de Matos; Marcus Ennis; Steve Turner; Gareth Owen; Lydie Bougueleret; Ioannis Xenarios; Christoph Steinbeck
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

8.  Is EC class predictable from reaction mechanism?

Authors:  Neetika Nath; John B O Mitchell
Journal:  BMC Bioinformatics       Date:  2012-04-24       Impact factor: 3.169

9.  MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.

Authors:  Gemma L Holliday; Daniel E Almonacid; Gail J Bartlett; Noel M O'Boyle; James W Torrance; Peter Murray-Rust; John B O Mitchell; Janet M Thornton
Journal:  Nucleic Acids Res       Date:  2006-11-01       Impact factor: 16.971

10.  Updates in Rhea - an expert curated resource of biochemical reactions.

Authors:  Anne Morgat; Thierry Lombardot; Kristian B Axelsen; Lucila Aimo; Anne Niknejad; Nevila Hyka-Nouspikel; Elisabeth Coudert; Monica Pozzato; Marco Pagni; Sébastien Moretti; Steven Rosanoff; Joseph Onwubiko; Lydie Bougueleret; Ioannis Xenarios; Nicole Redaschi; Alan Bridge
Journal:  Nucleic Acids Res       Date:  2016-10-26       Impact factor: 16.971
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