Spatio-temporal neural data mining architecture in learning robots. - James Malone; Mark Elshaw; Ken McGarry; Chris Bowerman; Stefan Wermter (IJCNN, 2005)

Semantic Grid Services for Video Analysis. - Gayathri Nadarajan; Yun-Heh Chen-Burger; James Malone (IAT Workshops, 2006)

Dynamic Access Control Prediction for Ordered Service Sequence in Grid Environment. - Gayathri Nadarajan; Chuanjiang Yi; Yun-Heh Chen-Burger; Hai Jin 001; James Malone; Chengwei Wang (Web Intelligence, 2006)

Automated trend analysis of proteomics data using an intelligent data mining architecture. - James Malone; Kenneth McGarry; Chris Bowerman (Expert Syst. Appl., 2006)

Data mining using rule extraction from Kohonen self-organising maps. - James Malone; Kenneth McGarry; Stefan Wermter; Chris Bowerman (Neural Comput. Appl., 2006)

The OWL of Biomedical Investigations. - Mélanie Courtot; William J. Bug; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan Remy Brinkman; Alan Ruttenberg (OWLED, 2008)

Soft Computing in Bioinformatics: Genomic and Proteomic Applications. - James Malone (Soft Computing Applications in Industry, 2008)

Developing an Ontology from the Application Up. - James Malone; Tomasz Adamusiak; Ele Holloway; Misha Kapushesky; Helen E. Parkinson (OWLED, 2009)

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. - Tim F. Rayner; Faisal Ibne Rezwan; Margus Lukk; Xiangqun Zheng Bradley; Anna Farne; Ele Holloway; James Malone; Eleanor Williams; Helen E. Parkinson (Bioinform., 2009)

ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. - Helen E. Parkinson; Misha Kapushesky; Nikolay Kolesnikov; Gabriella Rustici; Mohammadreza Shojatalab; Niran Abeygunawardena; Hugo Bérubé; Miroslaw Dylag; Ibrahim Emam; Anna Farne; Ele Holloway; Margus Lukk; et al. (Nucleic Acids Res., 2009)

Modeling sample variables with an Experimental Factor Ontology. - James Malone; Ele Holloway; Tomasz Adamusiak; Misha Kapushesky; Jie Zheng 001; Nikolay Kolesnikov; Anna Zhukova; Alvis Brazma; Helen E. Parkinson (Bioinform., 2010)

Modeling biomedical experimental processes with OBI. - Ryan Remy Brinkman; Mélanie Courtot; Dirk Derom; Jennifer Fostel; Yongqun He; Phillip W. Lord; James Malone; Helen E. Parkinson; Björn Peters; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; et al. (J. Biomed. Semant., 2010)

Gene Expression Atlas at the European Bioinformatics Institute. - Misha Kapushesky; Ibrahim Emam; Ele Holloway; Pavel Kurnosov; Andrey Zorin; James Malone; Gabriella Rustici; Eleanor Williams; Helen E. Parkinson; Alvis Brazma (Nucleic Acids Res., 2010)

Rapid Development of an Ontology of Coriell Cell Lines. - Chao Pang; Tomasz Adamusiak; Helen E. Parkinson; James Malone (ICBO, 2011)

Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. - Sirarat Sarntivijai; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Brian D. Athey; Yongqun He (ICBO, 2011)

The Vertebrate Bridging Ontology (VBO). - Ravensara S. Travillian; James Malone; Chao Pang; John M. Hancock; Peter W. H. Holland; Paul N. Schofield; Helen E. Parkinson (ICBO, 2011)

MIREOT: The minimum information to reference an external ontology term. - Mélanie Courtot; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan Remy Brinkman; Alan Ruttenberg (Appl. Ontology, 2011)

Automating generation of textual class definitions from OWL to English. - Robert Stevens 001; James Malone; Sandra Williams; Richard Power; Allan Third (J. Biomed. Semant., 2011)

Anatomy ontologies and potential users: bridging the gap. - Ravensara S. Travillian; Tomasz Adamusiak; Tony Burdett; Michael Gruenberger; John M. Hancock; Ann-Marie Mallon; James Malone; Paul N. Schofield; Helen E. Parkinson (J. Biomed. Semant., 2011)

ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments. - Helen E. Parkinson; Ugis Sarkans; Nikolay Kolesnikov; Niran Abeygunawardena; Tony Burdett; Miroslaw Dylag; Ibrahim Emam; Anna Farne; Emma Hastings; Ele Holloway; Natalja Kurbatova; Margus Lukk; et al. (Nucleic Acids Res., 2011)

The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies. - Maria Copeland; Andy Brown; Helen E. Parkinson; Robert Stevens 001; James Malone (ICBO, 2012)

Taking a view on bio-ontologies. - Simon Jupp; Andrew Gibson; James Malone; Robert Stevens 001 (ICBO, 2012)

Semantic Web Atlas: Putting Gene Expression Data into Biological Context. - Simon Jupp; Helen E. Parkinson; James Malone (SWAT4LS, 2012)

Translating standards into practice - One Semantic Web API for Gene Expression. - Helena F. Deus; Eric Prud'hommeaux; Michael Miller 001; Jun Zhao 003; James Malone; Tomasz Adamusiak; Jamie P. McCusker; Sudeshna Das 001; Philippe Rocca-Serra; Ronan Fox; M. Scott Marshall (J. Biomed. Informatics, 2012)

Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments. - Misha Kapushesky; Tomasz Adamusiak; Tony Burdett; Aedín C. Culhane; Anna Farne; Alexey Filippov; Ele Holloway; Andrey Klebanov; Nataliya Kryvych; Natalja Kurbatova; Pavel Kurnosov; James Malone; et al. (Nucleic Acids Res., 2012)

Putting OWL into Production at the European Bioinformatics Institute. - James Malone; Tony Burdett; Jon C. Ison; Simon Jupp; Drashtti Vasant; Danielle Welter; Helen E. Parkinson (OWLED, 2013)

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. - Jon C. Ison; Matús Kalas; Inge Jonassen; Dan M. Bolser; Mahmut Uludag; Hamish McWilliam; James Malone; Rodrigo Lopez; Steve Pettifer; Peter M. Rice (Bioinform., 2013)

Measuring the level of activity in community built bio-ontologies. - James Malone; Robert Stevens 001 (J. Biomed. Informatics, 2013)

ArrayExpress update - trends in database growth and links to data analysis tools. - Gabriella Rustici; Nikolay Kolesnikov; Marco Brandizi; Tony Burdett; Miroslaw Dylag; Ibrahim Emam; Anna Farne; Emma Hastings; Jon C. Ison; Maria Keays; Natalja Kurbatova; James Malone; et al. (Nucleic Acids Res., 2013)

Capturing Provenance for a Linkset of Convenience. - Simon Jupp; James Malone; Alasdair J. G. Gray (LISC@ISWC, 2014)

The EBI RDF platform: linked open data for the life sciences. - Simon Jupp; James Malone; Jerven T. Bolleman; Marco Brandizi; Mark Davies; Leyla J. García; Anna Gaulton; Sebastien Gehant; Camille Laibe; Nicole Redaschi; Sarala M. Wimalaratne; Maria Jesus Martin; et al. (Bioinform., 2014)

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. - James Malone; Andy Brown; Allyson L. Lister; Jon C. Ison; Duncan Hull; Helen E. Parkinson; Robert Stevens 001 (J. Biomed. Semant., 2014)

CLO: The cell line ontology. - Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma D. Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Yue Liu; Terue Takatsuki; et al. (J. Biomed. Semant., 2014)

Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. - Robert Petryszak; Tony Burdett; Benedetto Fiorelli; Nuno A. Fonseca; Mar Gonzalez-Porta; Emma Hastings; Wolfgang Huber; Simon Jupp; Maria Keays; Nataliya Kryvych; Julie A. McMurry; John C. Marioni; et al. (Nucleic Acids Res., 2014)

Collaborative Ontology Development Using the Webulous Architecture and Google App. - Simon Jupp; Danielle Welter; Tony Burdett; Helen E. Parkinson; James Malone (SWAT4LS, 2015)

2015 SWAT4LS International Conference Editorial. - James Malone; Robert Stevens 001; Kerstin Forsberg; Andrea Splendiani (SWAT4LS, 2015)

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. - Warren A. Kibbe; Cesar Arze; Victor Felix; Elvira Mitraka; Evan Bolton; Gang Fu; Christopher J. Mungall; Janos X. Binder; James Malone; Drashtti Vasant; Helen E. Parkinson; Lynn M. Schriml (Nucleic Acids Res., 2015)

Ten Simple Rules for Biomedical Ontology Development. - Mélanie Courtot; James Malone; Chris Mungall (ICBO/BioCreative, 2016)

Introducing the disease and phenotype OAEI track. - Ian Harrow; Ernesto Jiménez-Ruiz; Andrea Splendiani; Martin Romacker; Stefan Negru; Peter Woollard; Scott Markel; Yasmin Alam-Faruque; Martin Koch 001; Erfan Younesi; James Malone (OM@ISWC, 2016)

Ontologies Guidelines for Best Practice and a Process to Evaluate Existing Ontologies Mapping Tools and Algorithms. - Ian Harrow; Martin Romacker; Andrea Splendiani; Stefan Negru; Peter Woollard; Scott Markel; Yasmin Alam-Faruque; Martin Koch 001; Erfan Younesi; James Malone; Ernesto Jiménez-Ruiz (ISWC (Posters & Demos), 2016)

Ontologies Guidelines and Evaluation of Ontologies Mapping Tools and Algorithms. - Ian Harrow; Martin Romacker; Andrea Splendiani; Stefan Negru; Peter Woollard; Scott Markel; Yasmin Alam-Faruque; Martin Koch 001; Erfan Younesi; James Malone; Ernesto Jiménez-Ruiz (SWAT4LS, 2016)

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates. - Simon Jupp; Tony Burdett; Danielle Welter; Sirarat Sarntivijai; Helen E. Parkinson; James Malone (J. Biomed. Semant., 2016)

The cellular microscopy phenotype ontology. - Simon Jupp; James Malone; Tony Burdett; Jean-Karim Hériché; Eleanor Williams; Jan Ellenberg; Helen E. Parkinson; Gabriella Rustici (J. Biomed. Semant., 2016)

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. - Sirarat Sarntivijai; Drashtti Vasant; Simon Jupp; Gary Saunders; A. Patrícia Bento; Daniel Gonzalez; Joanna Betts; Samiul Hasan; Gautier Koscielny; Ian Dunham; Helen E. Parkinson; James Malone (J. Biomed. Semant., 2016)

Ten Simple Rules for Selecting a Bio-ontology. - James Malone; Robert Stevens 001; Simon Jupp; Tom Hancocks; Helen E. Parkinson; Catherine Brooksbank (PLoS Comput. Biol., 2016)

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. - Ian Harrow; Ernesto Jiménez-Ruiz; Andrea Splendiani; Martin Romacker; Peter Woollard; Scott Markel; Yasmin Alam-Faruque; Martin Koch 001; James Malone; Arild Waaler (J. Biomed. Semant., 2017)

Open Targets: a platform for therapeutic target identification and validation. - Gautier Koscielny; Peter An; Denise Carvalho-Silva; Jennifer A. Cham; Luca Fumis; Rippa Gasparyan; Samiul Hasan; Nikiforos Karamanis; Michael Maguire; Eliseo Papa; Andrea Pierleoni; Miguel Pignatelli; et al. (Nucleic Acids Res., 2017)

MIRO: guidelines for minimum information for the reporting of an ontology. - Nicolas Matentzoglu; James Malone; Chris Mungall; Robert Stevens 001 (J. Biomed. Semant., 2018)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

Ten quick tips for biocuration. - Y. Amy Tang; Klemens Pichler; Anja Füllgrabe; Jane Lomax; James Malone; Monica C. Munoz-Torres; Drashtti Vasant; Eleanor Williams; Melissa A. Haendel (PLoS Comput. Biol., 2019)

Measuring expert performance at manually classifying domain entities under upper ontology classes. - Robert Stevens 001; Phillip Lord; James Malone; Nicolas Matentzoglu (J. Web Semant., 2019)

A Simple Standard for Sharing Ontological Mappings (SSSOM). - Nicolas Matentzoglu; James P. Balhoff; Susan M. Bello; Chris Bizon; Matthew H. Brush; Tiffany J. Callahan; Christopher G. Chute; William D. Duncan; Chris T. A. Evelo; Davera Gabriel; John B. Graybeal; Alasdair J. G. Gray; et al. (Database J. Biol. Databases Curation, 2022)