Ola Spjuth

Publications (34) View all

• Article: The ChEMBL database as linked open data.

  Egon L Willighagen, Andra Waagmeester, Ola Spjuth, Peter Ansell, Antony J Williams, Valery Tkachenko, Janna Hastings, Bin Chen, David J Wild
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  ABSTRACT: Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs).RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easierto scale up inference and data analysis.Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples.Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO;exposes more information from the database; and is now available as dereferencable, linked data.To demonstrate these new features, we present novel use cases showing further integration withother web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standardontologies for querying.Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL databaseto other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDFresource creates a foundation for integrated semantic web cheminformatics applications,such as the presented decision support.
  Journal of Cheminformatics 05/2013; 5(1):23. · 3.42 Impact Factor
• Article: Applications of the InChI in cheminformatics with the CDK and Bioclipse.

  Ola Spjuth, Arvid Berg, Samuel Adams, Egon L Willighagen
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  ABSTRACT: Background The InChI algorithms are written in C++ and not available as Java library.Integration into software written in Java therefore requires a bridge between C and Java libraries,provided by the Java Native Interface (JNI) technology.Results We here describe how the InChI library is used in the Bioclipse workbench and the Chemistry Development Kit (CDK) cheminformatics library. To make this possible, a JNI bridge to the InChI library was developed, JNI-InChI, allowing Java software to access the InChI algorithms. By using this bridge, the CDK project packages the InChI binaries in a module and offers easy access from Java using the CDK API. The Bioclipse project packages and offers InChI as a dynamic OSGi bundle that can easily be used by any OSGi-compliant software, in addition to the regular Java Archive and Maven bundles. Bioclipse itself uses the InChI as a key component and calculates it on the fly when visualizing and editing chemical structures. We demonstrate the utility of InChI with various applications in CDK and Bioclipse, such as decision support for chemical liability assessment, tautomer generation, and for knowledge aggregation using a linked data approach.Conclusions These results show that the InChI library can be used in a variety of Java library dependency solutions, making the functionality easily accessible by Java software, such as in the CDK. The applications show various ways the InChI has been used in Bioclipse, to enrich its functionality.
  Journal of Cheminformatics 03/2013; 5(1):14. · 3.42 Impact Factor
• Article: Bioclipse-R: Integrating management and visualization of life science data with statistical analysis.

  Ola Spjuth, Valentin Georgiev, Lars Carlsson, Jonathan Alvarsson, Arvid Berg, Egon Willighagen, Jarl E S Wikberg, Martin Eklund
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  ABSTRACT: Bioclipse, a graphical workbench for the life sciences, provides functionality for managing and visualizing life science data. We introduce Bioclipse-R, which integrates Bioclipse and the statistical programming language R. The synergy between Bioclipse and R is demonstrated by the construction of a decision support system for anticancer drug screening and mutagenicity prediction, which shows how Bioclipse-R can be used to perform complex tasks from within a single software system.Availability and Implementation: Bioclipse-R is implemented as a set of Java-plugins for Bioclipse based on the R-package rj. Source code and binary packages are available from https://github.com/bioclipse and http://www.bioclipse.net/bioclipse-r, respectively. CONTACT: martin.eklund@farmbio.uu.se.
  Bioinformatics 11/2012; · 5.47 Impact Factor
• Article: Open source drug discovery with Bioclipse.

  Ola Spjuth, Lars Carlsson, Jonathan Alvarsson, Valentin Georgiev, Egon Willighagen, Martin Eklund
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  ABSTRACT: We present the open source components for drug discovery that has been developed and integrated into the graphical workbench Bioclipse. Building on a solid open source cheminformatics core, Bioclipse has advanced functionality for managing and visualizing chemical structures and related information. The features presented here include QSAR/QSPR modeling, various predictive solutions such as decision support for chemical liability assessment, site-of-metabolism prediction, virtual screening, and knowledge discovery and integration. We demonstrate the utility of the described tools with examples from computational pharmacology, toxicology, and ADME. Bioclipse is used in both academia and industry, and is a good example of open source leading to new solutions for drug discovery.
  Current topics in medicinal chemistry 10/2012; · 4.47 Impact Factor
• Article: On Mechanisms of Reactive Metabolite Formation from Drugs.

  Alf Claesson, Ola Spjuth
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  ABSTRACT: Idiosyncratic adverse drug reactions (IADRs) cause a broad range of clinically severe conditions of which drug induced liver injury (DILI) in particular is one of the most frequent causes of safety-related drug withdrawals. The underlying cause is almost invariably formation of reactive metabolites (RM) which by attacking macromolecules induce organ injuries. Attempts are being made in the pharmaceutical industry to lower the risk of selecting unfit compounds as clinical candidates. Approaches vary but do not seem to be overly successful at the initial design/synthesis stage. We review here the most frequent categories of mechanisms for RM formation and propose that many cases of RMs encountered within early ADME screening can be foreseen by applying chemical and metabolic knowledge. We also mention a web tool, SpotRM, which can be used for efficient look-up and learning about drugs that have recognized IADRs likely caused by RM formation.
  Mini Reviews in Medicinal Chemistry 10/2012; · 2.53 Impact Factor