Publikation:

KNIME-CDK : Workflow-driven cheminformatics

Lade...
Vorschaubild

Dateien

Beisken_264832.pdf
Beisken_264832.pdfGröße: 478.07 KBDownloads: 792

Datum

2013

Autor:innen

Beisken, Stephan
Figueiredo, Luis F. de
Steinbeck, Christoph

Herausgeber:innen

Kontakt

ISSN der Zeitschrift

Electronic ISSN

ISBN

Bibliografische Daten

Verlag

Schriftenreihe

Auflagebezeichnung

ArXiv-ID

Internationale Patentnummer

Angaben zur Forschungsförderung

Projekt

Open Access-Veröffentlichung
Open Access Gold
Core Facility der Universität Konstanz

Gesperrt bis

Titel in einer weiteren Sprache

Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published

Erschienen in

BMC Bioinformatics. 2013, 14(1), 257. eISSN 1471-2105. Available under: doi: 10.1186/1471-2105-14-257

Zusammenfassung

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.

Zusammenfassung in einer weiteren Sprache

Fachgebiet (DDC)
004 Informatik

Schlagwörter

Konferenz

Rezension
undefined / . - undefined, undefined

Forschungsvorhaben

Organisationseinheiten

Zeitschriftenheft

Zugehörige Datensätze in KOPS

Zitieren

ISO 690BEISKEN, Stephan, Thorsten MEINL, Bernd WISWEDEL, Luis F. de FIGUEIREDO, Michael R. BERTHOLD, Christoph STEINBECK, 2013. KNIME-CDK : Workflow-driven cheminformatics. In: BMC Bioinformatics. 2013, 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>

Interner Vermerk

xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter

Kontakt
URL der Originalveröffentl.

Prüfdatum der URL

Prüfungsdatum der Dissertation

Finanzierungsart

Kommentar zur Publikation

Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Ja
Begutachtet
Diese Publikation teilen