James Malone

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. doi request reprint Measuring the level of activity in community built bio-ontologies
    James Malone
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
    J Biomed Inform 46:5-14. 2013
  2. pmc Automating generation of textual class definitions from OWL to English
    Robert Stevens
    School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    J Biomed Semantics 2:S5. 2011
  3. pmc Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
  4. pmc Modeling sample variables with an Experimental Factor Ontology
    James Malone
    Microarray Informatics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Bioinformatics 26:1112-8. 2010
  5. pmc Gene expression atlas at the European bioinformatics institute
    Misha Kapushesky
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 38:D690-8. 2010
  6. pmc ArrayExpress update--trends in database growth and links to data analysis tools
    Gabriella Rustici
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 41:D987-90. 2013
  7. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011
  8. pmc Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments
    Misha Kapushesky
    European Bioinformatics Institute, EMBL, Hinxton, UK and Dana Farber Cancer Institute, Boston, MA, USA
    Nucleic Acids Res 40:D1077-81. 2012
  9. pmc MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB
    Tim F Rayner
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, UK
    Bioinformatics 25:279-80. 2009
  10. pmc EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
    Jon Ison
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 29:1325-32. 2013

Collaborators

Detail Information

Publications13

  1. doi request reprint Measuring the level of activity in community built bio-ontologies
    James Malone
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
    J Biomed Inform 46:5-14. 2013
    ..Overall, we show that it is possible to objectively measure the activity in an ontology and to make some prediction about future activity...
  2. pmc Automating generation of textual class definitions from OWL to English
    Robert Stevens
    School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    J Biomed Semantics 2:S5. 2011
    ..The application described here uses NLG to automatically provide text-based definitions from an ontology that has logical descriptions of its entities, so avoiding the bottleneck of authoring these definitions by hand...
  3. pmc Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
    ..AVAILABILITY : OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl...
  4. pmc Modeling sample variables with an Experimental Factor Ontology
    James Malone
    Microarray Informatics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Bioinformatics 26:1112-8. 2010
    ..These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users...
  5. pmc Gene expression atlas at the European bioinformatics institute
    Misha Kapushesky
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 38:D690-8. 2010
    ..Currently, the database contains information about more than 200,000 genes from nine species and almost 4500 biological conditions studied in over 30,000 assays from over 1000 independent studies...
  6. pmc ArrayExpress update--trends in database growth and links to data analysis tools
    Gabriella Rustici
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 41:D987-90. 2013
    ..Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data...
  7. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011
    ..Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy...
  8. pmc Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments
    Misha Kapushesky
    European Bioinformatics Institute, EMBL, Hinxton, UK and Dana Farber Cancer Institute, Boston, MA, USA
    Nucleic Acids Res 40:D1077-81. 2012
    ..08 (August 2011), the database supports 19 species, which contains expression data measured for 19,014 biological conditions in 136,551 assays from 5598 independent studies...
  9. pmc MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB
    Tim F Rayner
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, UK
    Bioinformatics 25:279-80. 2009
    ....
  10. pmc EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
    Jon Ison
    EMBL European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 29:1325-32. 2013
    ..Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required...
  11. doi request reprint Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
    Robert Petryszak
    European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL EBI, Hinxton, CB10 1SD, UK
    Nucleic Acids Res 42:D926-32. 2014
    ....
  12. pmc Anatomy ontologies and potential users: bridging the gap
    Ravensara S Travillian
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    J Biomed Semantics 2:S3. 2011
    ..To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations...
  13. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
    ..In this update, we describe the ArrayExpress developments over the last two years...