| 1. |
- Bradley, Jean-Claude, et al.
(author)
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Beautifying Data in the Real World
- 2009. - 1
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In: Beautiful Data. - Sebastol, USA : O'Reilly. - 9780596157111 ; , s. 259-278
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Book chapter (pop. science, debate, etc.)
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| 2. |
- Kuhn, Thomas, et al.
(author)
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CDK-Taverna : an open workflow environment for cheminformatics
- 2010
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 11, s. 159-
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Journal article (peer-reviewed)abstract
- Background Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open-source and available for everyone. Results Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios. Conclusions The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.
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| 3. |
- Willighagen, Egon, 1974-
(author)
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3D Molecular Representations
- 2010
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In: Handbook of Chemoinformatics Algorithms. - Boca Raton : CRC Press. - 9781420082920
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Book chapter (other academic/artistic)
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| 4. |
- Willighagen, Egon, 1974-, et al.
(author)
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Linking Open Drug Data to Cheminformatics and Proteochemometrics
- 2010
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In: SWAT4LS-2009 - Semantic Web Applications and Tools for Life Sciences. - Aachen, Germany : Sun SITE Central Europe.
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Conference paper (peer-reviewed)abstract
- Semantic Web technologies have made great steps forwardin data exchange in health care and life sciences in the past years. Thework presented here focuses to a some extent on making drug discoveryrelated data available as RDF, and even more so on the integration ofRDF approaches with data analysis of molecular information in drugdiscovery fields like cheminformatics and proteochemometrics. We hereshow how the chem- and bioinformatics workbench Bioclipse and theChemistry Development Kit can be used to this purpose.Abstract. Semantic Web technologies have made great steps forwardin data exchange in health care and life sciences in the past years. Thework presented here focuses to a some extent on making drug discoveryrelated data available as RDF, and even more so on the integration ofRDF approaches with data analysis of molecular information in drugdiscovery fields like cheminformatics and proteochemometrics. We hereshow how the chem- and bioinformatics workbench Bioclipse and theChemistry Development Kit can be used to this purpose.
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| 5. |
- Willighagen, Egon, 1974-, et al.
(author)
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Linking the Resource Description Framework to cheminformatics and proteochemometrics
- 2011
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In: Journal of Biomedical Semantics. - 2041-1480. ; 2:Suppl 1, s. 6-
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Journal article (peer-reviewed)abstract
- BACKGROUND :Semantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet. The semantic web technology Resource Description Framework (RDF) and related methods show to be sufficiently versatile to change that situation.RESULTS :The work presented here focuses on linking RDF approaches to existing molecular chemometrics fields, including cheminformatics, QSAR modeling and proteochemometrics. Applications are presented that link RDF technologies to methods from statistics and cheminformatics, including data aggregation, visualization, chemical identification, and property prediction. They demonstrate how this can be done using various existing RDF standards and cheminformatics libraries. For example, we show how IC50 and Ki values are modeled for a number of biological targets using data from the ChEMBL database.CONCLUSIONS :We have shown that existing RDF standards can suitably be integrated into existing molecular chemometrics methods. Platforms that unite these technologies, like Bioclipse, makes this even simpler and more transparent. Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility. The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.
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