J. Malone

发表

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

Gang Fu, Evan Bolton, Chris Mungall, 2014, Nucleic Acids Res..

Observations in collaborative ontology editing using Collaborative Protégé

Daniel Schober, R. Stevens, J. Malone, 2009 .

Critical Assessment of Microarray Data Analysis Contest Datasets Emerald Dataset : a Microarray Experiment to Study the Relative Magnitudes of Technical and Biological Variation Talks Keynote towards Cracking the Code of Transcription and Chromatin Regulation Analysis of Comparative Genomic Hybridiz

W. Langdon, R. King, E. Segal, 2022 .

10 Simple rules for design, provision, and reuse of persistent identifiers for life science data

María Martín, Michel Dumontier, Carole Goble, 2015 .

Dataset Descriptions: HCLS Community Profile

Gary D. Bader, Michel Dumontier, Alasdair J. G. Gray, 2015 .

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Chris Morris, John Kunze, Michel Dumontier, 2017, bioRxiv.

Identifiers for the 21 st century : How to design , provision , and reuse identifiers to maximize data utility and impact

Alan R. Williams, H. Parkinson, N. Novère, 2016 .

Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments

Aedín C. Culhane, Robert Petryszak, James Malone, 2011, Nucleic Acids Res..

The cellular microscopy phenotype ontology

Simon Jupp, James Malone, Helen E. Parkinson, 2016, Journal of Biomedical Semantics.

Gene Expression Atlas at the European Bioinformatics Institute

Ibrahim Emam, James Malone, Helen E. Parkinson, 2009, Nucleic Acids Res..

Automating class definitions from OWL to English Conference or Workshop Item

R. Power, Sandra Williams, R. Stevens, 2018 .

Translating standards into practice: one semantic web API for gene expression

Helena F. Deus, Michael Miller, P. Rocca-Serra, 2011, SWAT4LS.

The Open University ’ s repository of research publications and other research outputs Automating class definitions from OWL to English Conference Item

R. Power, Sandra Williams, R. Stevens, 2010 .

Report on the scalability of semantic web integration in BioMedBridges

Andrew M. Jenkinson, Chris Morris, Mark Davies, 2015 .

Anatomy ontologies and potential users: bridging the gap

Michael Gruenberger, John M. Hancock, Paul N. Schofield, 2011, J. Biomed. Semant..

The Vertebrate Bridging Ontology (VBO)

John M. Hancock, Paul N. Schofield, James Malone, 2011, ICBO.

Introducing the disease and phenotype OAEI track

Peter Woollard, Martin Romacker, Yasmin Alam-Faruque, 2016, OM@ISWC.

10 Simple rules for design, provision, and reuse of identifiers for web-based life science data

María Martín, Michel Dumontier, Carole Goble, 2015 .

Open Targets: a platform for therapeutic target identification and validation

Gautier Koscielny, Robert Petryszak, Maria Keays, 2016, Nucleic Acids Res..

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Nuno A. Fonseca, Robert Petryszak, Maria Keays, 2013, Nucleic Acids Res..

ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression

Ibrahim Emam, Marco Brandizi, Faisal Ibne Rezwan, 2008, Nucleic Acids Res..

Modeling sample variables with an Experimental Factor Ontology

Anna Zhukova, James Malone, Helen E. Parkinson, 2010, Bioinform..

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Akira R. Kinjo, Yue Wang, Katsuhiko Murakami, 2019, F1000Research.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Chris Morris, John Kunze, Michel Dumontier, 2017, bioRxiv.

The Ontology for Biomedical Investigations

Jessica A. Turner, Chris F. Taylor, Mathias Brochhausen, 2016, PloS one.

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

H. Parkinson, S. Jupp, Danielle Welter, 2016, J. Biomed. Semant..

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

H. Parkinson, I. Dunham, Gary Saunders, 2016, J. Biomed. Semant..

ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments

Ibrahim Emam, Marco Brandizi, James Malone, 2010, Nucleic Acids Res..

MIREOT: The minimum information to reference an external ontology term

Alan Ruttenberg, Daniel Schober, James Malone, 2009, Appl. Ontology.

ArrayExpress update—trends in database growth and links to data analysis tools

Maria Keays, Ibrahim Emam, Marco Brandizi, 2012, Nucleic Acids Res..

Modeling biomedical experimental processes with OBI

Jessica A. Turner, et al., Alan Ruttenberg, 2010, J. Biomed. Semant..

CLO: The cell line ontology

Yue Liu, David J. States, Yu Lin, 2014, Journal of Biomedical Semantics.

A Simple Standard for Sharing Ontological Mappings (SSSOM) pdf

Christopher G Chute, Simon Jupp, Tania Tudorache, 2021, Database J. Biol. Databases Curation.

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

Steve Pettifer, Dan M. Bolser, Rodrigo Lopez, 2013, Bioinform..

Translating standards into practice - One Semantic Web API for Gene Expression

M. Scott Marshall, Ronan Fox, James Malone, 2012, J. Biomed. Informatics.

MIRO: guidelines for minimum information for the reporting of an ontology

Robert Stevens, Chris Mungall, James Malone, 2018, J. Biomed. Semant..

The EBI RDF platform: linked open data for the life sciences

Andrew M. Jenkinson, Maria Jesus Martin, Nicolas Le Novère, 2014, Bioinform..

Data mining using rule extraction from Kohonen self-organising maps

Stefan Wermter, Chris Bowerman, James Malone, 2006, Neural Computing & Applications.

Analysis of Rules Discovered by the Data Mining Process

Kenneth McGarry, James Malone, J. Malone, 2004 .

Ten quick tips for biocuration

James Malone, Eleanor Williams, Melissa Haendel, 2019, PLoS Comput. Biol..

The health care and life sciences community profile for dataset descriptions

Michel Dumontier, Paul T. Groth, Gary D Bader, 2016, PeerJ.

Ten Simple Rules for Selecting a Bio-ontology

Robert Stevens, Catherine Brooksbank, Simon Jupp, 2016, PLoS Comput. Biol..

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative

Peter M Woollard, A. Splendiani, Ernesto Jiménez-Ruiz, 2017, J. Biomed. Semant..

Ontologies Guidelines for Best Practice and a Process to Evaluate Existing Ontologies Mapping Tools and Algorithms

Peter Woollard, Martin Romacker, Yasmin Alam-Faruque, 2016, SEMWEB.

Automating generation of textual class definitions from OWL to English

Robert Stevens, Richard Power, James Malone, 2011, J. Biomed. Semant..

The OWL of Biomedical Investigations

Alan Ruttenberg, Daniel Schober, William J. Bug, 2008, OWLED.

Measuring Expert Performance at Manually Classifying Domain Entities under Upper Ontology Classes pdf

Robert Stevens, Phillip Lord, James Malone, 2018, J. Web Semant..

Spatio-temporal neural data mining architecture in learning robots

S. Wermter, M. Elshaw, J. Malone, 2005, Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005..

Automated trend analysis of proteomics data using an intelligent data mining architecture

Chris Bowerman, James Malone, Kenneth McGarry, 2006, Expert Syst. Appl..

Intelligent hybrid Spatio-temporal mining for knowledge discovery on proteomics data

Chris Bowerman, Kenneth McGarry, James Malone, 2005 .

MIRO: guidelines for minimum information for the reporting of an ontology

C. Mungall, R. Stevens, J. Malone, 2018, Journal of Biomedical Semantics.

Optimising biomedical relationship extraction with BioBERT

Michael Hughes, James Malone, Livia Perfetto, 2020, bioRxiv.

Ten Simple Rules for Biomedical Ontology Development

Chris Mungall, James Malone, Mélanie Courtot, 2016, ICBO/BioCreative.

The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies

Robert Stevens, Andy Brown, James Malone, 2012, ICBO.

Soft Computing in Bioinformatics: Genomic and Proteomic Applications

James Malone, J. Malone, 2008, Soft Computing Applications in Industry.

Contributions of the EMERALD project to assessing and improving microarray data quality.

Audrey Kauffmann, Martin Kuiper, James Malone, 2011, BioTechniques.

Measuring the level of activity in community built bio-ontologies

Robert Stevens, James Malone, R. Stevens, 2013, J. Biomed. Informatics.

Semantic Web Atlas: Putting Gene Expression Data into Biological Context

Simon Jupp, James Malone, Helen E. Parkinson, 2012, SWAT4LS.

A Framework of an Automated Data Mining System Using Autonomous Intelligent Agents

V. Saravanan, J. Rajan, J. Malone, 2008, 2008 International Conference on Computer Science and Information Technology.

Ontology representation and ANOVA analysis of vaccine protection investigation

Bjoern Peters, Alan Ruttenberg, James Malone, 2010 .

Putting OWL into Production at the European Bioinformatics Institute

Simon Jupp, James Malone, Jon C. Ison, 2013, OWLED.

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation

Robert Stevens, Andy Brown, James Malone, 2014, Journal of Biomedical Semantics.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Alan R. Williams, Alejandra N. González-Beltrán, Sarala M. Wimalaratne, 2017, bioRxiv.