Affiliation: Wellcome Trust Genome Campus
- ChEBI in 2016: Improved services and an expanding collection of metabolitesJanna Hastings
Cheminformatics and Metabolism, European Molecular Biology Laboratory European Bioinformatics Institute EMBL EBI, Hinxton, UK
Nucleic Acids Res 44:D1214-9. 2016..Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery. ..
- The ChEMBL database as linked open dataEgon L Willighagen
Department of Bioinformatics BiGCaT, Maastricht University, P, O, Box 616, UNS50 Box 19, NL 6200 MD, Maastricht, The Netherlands
J Cheminform 5:23. 2013..RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis...
- UniChem: a unified chemical structure cross-referencing and identifier tracking systemJon Chambers
ChEMBL, Hinxton, CB10 1SD, Cambridge, United Kingdom
J Cheminform 5:3. 2013....
- Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontologyDavid P Hill
Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
BMC Genomics 14:513. 2013....
- Process attributes in bio-ontologiesAndré Q Andrade
Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
BMC Bioinformatics 13:217. 2012....
- The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013Janna Hastings
Department of Cheminformatics and Metabolism, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
Nucleic Acids Res 41:D456-63. 2013..Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization...
- Ontologies for human behavior analysis and their application to clinical dataJanna Hastings
Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland
Int Rev Neurobiol 103:89-107. 2012..We focus on the benefits of ontologies for clinical data management and for facilitating translational research for the development of novel therapeutics to treat challenging and debilitating conditions...
- Accessing and using chemical property databasesJanna Hastings
European Bioinformatics Institute, Hinxton, UK
Methods Mol Biol 929:193-219. 2012....
- Unintended consequences of existential quantifications in biomedical ontologiesMartin Boeker
Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Freiburg, Germany
BMC Bioinformatics 12:456. 2011..Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors...
- Structure-based classification and ontology in chemistryJanna Hastings
Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK
J Cheminform 4:8. 2012..abstract:..
- The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic webJanna Hastings
Chemoinformatics and Metabolism, European Bioinformatics Institute, Hinxton, United Kingdom
PLoS ONE 6:e25513. 2011..The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA)...
- Chemical Entities of Biological Interest: an updatePaula de Matos
Chemoinformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 38:D249-54. 2010....
- OntoQuery: easy-to-use web-based OWL queryingIlinca Tudose
Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland
Bioinformatics 29:2955-7. 2013..To address this gap, we introduce the OntoQuery web-based query utility...
- ChEBI: an open bioinformatics and cheminformatics resourceKirill Degtyarenko
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
Curr Protoc Bioinformatics . 2009..This unit provides a detailed guide to browsing, searching, downloading, and programmatic access to the ChEBI database...
- The MetaboLights repository: curation challenges in metabolomicsReza M Salek
Wellcome Trust Genome Campus, European Bioinformatics Institute, Cheminformatics and Metabolism, Hinxton, Cambridgeshire CB10 1SD, UK
Database (Oxford) 2013:bat029. 2013..Here, we describe the MetaboLights curation pipeline, its challenges and its practical application in quality control of complex data depositions. Database URL: http://www.ebi.ac.uk/metabolights...
- BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontologyPablo Moreno
Cheminformatics and Metabolism, European Molecular Biology Laboratory European Bioinformatics Institute, Cambridge, UK
BMC Bioinformatics 16:56. 2015..While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis...
- MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-dataKenneth Haug
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nucleic Acids Res 41:D781-6. 2013..Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry...
- A database for chemical proteomics: ChEBIPaula de Matos
European Bioinformatics Institute, Hinxton, UK
Methods Mol Biol 803:273-96. 2012..The ChEBI database also provides a central reference point in which to access a variety of bioinformatics data points such as pathways and their biochemical reactions; expression data; protein sequence and structures...
- ChEBI: a database and ontology for chemical entities of biological interestKirill Degtyarenko
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nucleic Acids Res 36:D344-50. 2008..ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/..
- Exploiting disjointness axioms to improve semantic similarity measuresJoão D Ferreira
Department of Informatics, Faculdade de Ciencias da Universidade de Lisboa, 1749 016 Lisboa, Portugal, Cheminformatics and Metabolism, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK, Swiss Center for Affective Sciences, University of Geneva, 7, rue des Battoirs, 1205 Geneva, Switzerland and Evolutionary Bioinformatics Group, Swiss Institute of Bioinformatics, Biophore CH 1015 Lausanne, Switzerland
Bioinformatics 29:2781-7. 2013....