Janna Hastings

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc The ChEMBL database as linked open data
    Egon 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
  2. pmc UniChem: a unified chemical structure cross-referencing and identifier tracking system
    Jon Chambers
    ChEMBL, Hinxton, CB10 1SD, Cambridge, United Kingdom
    J Cheminform 5:3. 2013
  3. pmc Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
    David P Hill
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Genomics 14:513. 2013
  4. pmc Process attributes in bio-ontologies
    André Q Andrade
    Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
    BMC Bioinformatics 13:217. 2012
  5. pmc The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
    Janna Hastings
    Department of Cheminformatics and Metabolism, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Nucleic Acids Res 41:D456-63. 2013
  6. doi request reprint Ontologies for human behavior analysis and their application to clinical data
    Janna Hastings
    Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland
    Int Rev Neurobiol 103:89-107. 2012
  7. ncbi request reprint Accessing and using chemical property databases
    Janna Hastings
    European Bioinformatics Institute, Hinxton, UK
    Methods Mol Biol 929:193-219. 2012
  8. pmc Unintended consequences of existential quantifications in biomedical ontologies
    Martin Boeker
    Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Freiburg, Germany
    BMC Bioinformatics 12:456. 2011
  9. pmc Structure-based classification and ontology in chemistry
    Janna Hastings
    Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK
    J Cheminform 4:8. 2012
  10. pmc The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web
    Janna Hastings
    Chemoinformatics and Metabolism, European Bioinformatics Institute, Hinxton, United Kingdom
    PLoS ONE 6:e25513. 2011

Collaborators

  • Christoph Steinbeck
  • Paula de Matos
  • Susanna Assunta Sansone
  • Ivo Grosse
  • Stephan Beisken
  • Stefan Schulz
  • Robert Stevens
  • Mickael Guedj
  • Michel Dumontier
  • Ilinca Tudose
  • Marcus Ennis
  • Kirill Degtyarenko
  • Reza M Salek
  • Kenneth Haug
  • Pablo Moreno
  • Venkatesh Muthukrishnan
  • Adriano Dekker
  • Steffen Neumann
  • Jon Chambers
  • Philippe Rocca-Serra
  • Pablo Conesa
  • João D Ferreira
  • Tejasvi Mahendraker
  • Mark Williams
  • Gareth Owen
  • David P Hill
  • Egon L Willighagen
  • Eamonn Maguire
  • Steve Turner
  • André Q Andrade
  • Martin Boeker
  • Franziska Taruttis
  • Bhavana Harsha
  • Stefanie Dornfeldt
  • Mark Rijnbeek
  • Christopher J Mungall
  • Namrata S Kale
  • Heiko Dietze
  • Anna Gaulton
  • Harold J Drabkin
  • Robert Petryszak
  • Anne Hersey
  • Nico Adams
  • Tanya Z Berardini
  • Shaun McGlinchey
  • David J Wild
  • Sameer Velankar
  • Antony J Williams
  • Midori A Harris
  • Andra Waagmeester
  • Louisa Bellis
  • Peter Ansell
  • Namrata Kale
  • Ola Spjuth
  • Julian L Griffin
  • John P Overington
  • Jane Lomax
  • Alejandra González-Beltrán
  • Valery Tkachenko
  • Francisco M Couto
  • Mark Davies
  • Rebecca E Foulger
  • Bin Chen
  • Alejandra N González-Beltrán
  • Colin Batchelor
  • Paola Roncaglia
  • Mike Bada
  • Ward Blondé
  • Daniel Schober
  • Michael Ashburner
  • Alan McNaught
  • Martin Zbinden
  • Michael Darsow
  • Rafael Alcántara

Detail Information

Publications19

  1. pmc The ChEMBL database as linked open data
    Egon 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...
  2. pmc UniChem: a unified chemical structure cross-referencing and identifier tracking system
    Jon Chambers
    ChEMBL, Hinxton, CB10 1SD, Cambridge, United Kingdom
    J Cheminform 5:3. 2013
    ....
  3. pmc Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
    David P Hill
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Genomics 14:513. 2013
    ....
  4. pmc Process attributes in bio-ontologies
    André Q Andrade
    Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
    BMC Bioinformatics 13:217. 2012
    ....
  5. pmc The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
    Janna 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...
  6. doi request reprint Ontologies for human behavior analysis and their application to clinical data
    Janna 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...
  7. ncbi request reprint Accessing and using chemical property databases
    Janna Hastings
    European Bioinformatics Institute, Hinxton, UK
    Methods Mol Biol 929:193-219. 2012
    ....
  8. pmc Unintended consequences of existential quantifications in biomedical ontologies
    Martin 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...
  9. pmc Structure-based classification and ontology in chemistry
    Janna Hastings
    Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK
    J Cheminform 4:8. 2012
    ..abstract:..
  10. pmc The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web
    Janna 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)...
  11. pmc Chemical Entities of Biological Interest: an update
    Paula de Matos
    Chemoinformatics and Metabolism Team, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D249-54. 2010
    ....
  12. pmc OntoQuery: easy-to-use web-based OWL querying
    Ilinca 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...
  13. doi request reprint ChEBI: an open bioinformatics and cheminformatics resource
    Kirill 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...
  14. pmc The MetaboLights repository: curation challenges in metabolomics
    Reza 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...
  15. doi request reprint BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology
    Pablo 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...
  16. pmc MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data
    Kenneth 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...
  17. doi request reprint A database for chemical proteomics: ChEBI
    Paula 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...
  18. pmc ChEBI: a database and ontology for chemical entities of biological interest
    Kirill 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/..
  19. doi request reprint Exploiting disjointness axioms to improve semantic similarity measures
    João 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
    ....