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  • 101.
    Willighagen, Egon
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Jeliazkova, Nina
    Ideaconsult Ltd.
    Hardy, Barry
    Douglas Connect.
    Grafström, Roland
    Karolinska Institutet.
    Spjuth, Ola
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Computational toxicology using the OpenTox application programming interface and Bioclipse2011Inngår i: BMC Research Notes, ISSN 1756-0500, E-ISSN 1756-0500, Vol. 4, nr 1, s. 487-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications.

    Findings: This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources.

    Conclusions: A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers.

  • 102.
    Willighagen, Egon L.
    et al.
    Maastricht Univ, Dept Bioinformat, NUTRIM, BiGCaT, NL-6200 MD Maastricht, Netherlands..
    Mayfield, John W.
    NextMove Software Ltd, Cambridge CB4 0EY, England..
    Alvarsson, Jonathan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Berg, Arvid
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Carlsson, Lars
    AstraZeneca, Innovat Med & Early Dev, Quantitat Biol, Molndal, Sweden..
    Jeliazkova, Nina
    Ideaconsult Ltd, A Kanchev 4, Sofia 1000, Bulgaria..
    Kuhn, Stefan
    Univ Leicester, Dept Informat, Leicester, Leics, England..
    Pluskal, Tomas
    Whitehead Inst Biomed Res, 455 Main St, Cambridge, MA 02142 USA..
    Rojas-Cherto, Miquel
    Quim Clin Aplicada, Amposta 43870, Spain..
    Spjuth, Ola
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap. 4 Hanway Pl, London W1T 1HD, England..
    Torrance, Gilleain
    4 Hanway Pl, London W1T 1HD, England..
    Evelo, Chris T.
    Maastricht Univ, Dept Bioinformat, NUTRIM, BiGCaT, NL-6200 MD Maastricht, Netherlands..
    Guha, Rajarshi
    Natl Ctr Adv Translat Sci, 9800 Med Ctr Dr, Rockville, MD 20850 USA..
    Steinbeck, Christoph
    Friedrich Schiller Univ, Inst Inorgan & Analyt Chem, Lessingstr 8, D-07743 Jena, Germany..
    The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching2017Inngår i: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 9, artikkel-id 33Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms.

    Results: We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism.

    Conclusions: This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.

    Fulltekst (pdf)
    fulltext
  • 103. Willighagen, Egon L
    et al.
    Waagmeester, Andra
    Spjuth, Ola
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Ansell, Peter
    Williams, Antony J
    Tkachenko, Valery
    Hastings, Janna
    Chen, Bin
    Wild, David J
    The ChEMBL database as linked open data2013Inngår i: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 5, nr 1, s. 23-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    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 thedata machine-readable and uses extensible vocabularies for additional information, making it easier to 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 with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying. 

    Conclusions: We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, theChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support.

    Fulltekst (pdf)
    fulltext
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