KNIME-CDK : Workflow-driven cheminformatics

Beisken, Stephan; Meinl, Thorsten; Wiswedel, Bernd; Figueiredo, Luis F. de; Berthold, Michael R.; Steinbeck, Christoph

KNIME-CDK : Workflow-driven cheminformatics

Files

Beisken_264832.pdf(478.07 KB)

Date

2013

Authors

Beisken, Stephan

Meinl, Thorsten

Wiswedel, Bernd

Figueiredo, Luis F. de

Berthold, Michael R.

Steinbeck, Christoph

Publication type

Journal article

Published in

BMC Bioinformatics ; 14 (2013), 1. - 257. - eISSN 1471-2105

Abstract

Background

Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in. A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process.

Results

KNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures, fingerprints, and molecular properties. It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence. A comparison with the cheminformatics plug-in RDKit shows that KNIME-CDK supports a similar range of chemical classes and adds new functionality to the framework. We describe the design and integration of the plug-in, and demonstrate the usage of the nodes on ChEBI, a library of small molecules of biological interest.

Conclusions

KNIME-CDK is an open-source plug-in for the Konstanz Information Miner, a free workflow platform. KNIME-CDK is build on top of the open-source Chemistry Development Toolkit and allows for efficient cross-vendor structural cheminformatics. Its ease-of-use and modularity enables researchers to automate routine tasks and data analysis, bringing complimentary cheminformatics functionality to the workflow environment.

Subject (DDC)

004 Computer Science

Cite This

ISO 690

BEISKEN, Stephan, Thorsten MEINL, Bernd WISWEDEL, Luis F. de FIGUEIREDO, Michael R. BERTHOLD, Christoph STEINBECK, 2013. KNIME-CDK : Workflow-driven cheminformatics. In: BMC Bioinformatics. 14(1), 257. eISSN 1471-2105. Available under: doi: 10.1186/1471-2105-14-257

BibTex

@article{Beisken2013KNIME-26483,
  year={2013},
  doi={10.1186/1471-2105-14-257},
  title={KNIME-CDK : Workflow-driven cheminformatics},
  number={1},
  volume={14},
  journal={BMC Bioinformatics},
  author={Beisken, Stephan and Meinl, Thorsten and Wiswedel, Bernd and Figueiredo, Luis F. de and Berthold, Michael R. and Steinbeck, Christoph},
  note={Article Number: 257}
}

RDF

<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/26483">
    <dc:creator>Meinl, Thorsten</dc:creator>
    <dc:creator>Beisken, Stephan</dc:creator>
    <dc:contributor>Figueiredo, Luis F. de</dc:contributor>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
    <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/2.0/"/>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/26483/2/Beisken_264832.pdf"/>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/26483/2/Beisken_264832.pdf"/>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2014-02-25T09:35:55Z</dc:date>
    <dc:contributor>Wiswedel, Bernd</dc:contributor>
    <dc:contributor>Berthold, Michael R.</dc:contributor>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2014-02-25T09:35:55Z</dcterms:available>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:creator>Figueiredo, Luis F. de</dc:creator>
    <dc:contributor>Beisken, Stephan</dc:contributor>
    <dc:creator>Berthold, Michael R.</dc:creator>
    <dcterms:abstract xml:lang="eng">Background&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in. A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Results&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;KNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures, fingerprints, and molecular properties. It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence. A comparison with the cheminformatics plug-in RDKit shows that KNIME-CDK supports a similar range of chemical classes and adds new functionality to the framework. We describe the design and integration of the plug-in, and demonstrate the usage of the nodes on ChEBI, a library of small molecules of biological interest.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Conclusions&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;KNIME-CDK is an open-source plug-in for the Konstanz Information Miner, a free workflow platform. KNIME-CDK is build on top of the open-source Chemistry Development Toolkit and allows for efficient cross-vendor structural cheminformatics. Its ease-of-use and modularity enables researchers to automate routine tasks and data analysis, bringing complimentary cheminformatics functionality to the workflow environment.</dcterms:abstract>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
    <dcterms:issued>2013</dcterms:issued>
    <dcterms:title>KNIME-CDK : Workflow-driven cheminformatics</dcterms:title>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:contributor>Meinl, Thorsten</dc:contributor>
    <dc:creator>Steinbeck, Christoph</dc:creator>
    <dc:language>eng</dc:language>
    <dcterms:bibliographicCitation>BMC Bioinformatics ; 14 (2013). - 257</dcterms:bibliographicCitation>
    <dc:contributor>Steinbeck, Christoph</dc:contributor>
    <dc:rights>Attribution 2.0 Generic</dc:rights>
    <dc:creator>Wiswedel, Bernd</dc:creator>
    <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/26483"/>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
  </rdf:Description>
</rdf:RDF>

Bibliography of Konstanz

Yes