James Malone

According to our database, James Malone authored at least 51 papers between 2006 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2022

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 Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall

Database J. Biol. Databases Curation, 2022

2019

Measuring expert performance at manually classifying domain entities under upper ontology classes.

Robert Stevens, Phillip Lord, James Malone, Nicolas Matentzoglu

J. Web Semant., 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

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, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi

F1000Research, 2019

2018

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

Nicolas Matentzoglu, James Malone, Chris Mungall, Robert Stevens

J. Biomed. Semant., 2018

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, Theo Platt, Francis Rowland, Priyanka Wankar, A. Patrícia Bento, Tony Burdett, Antonio Fabregat, Simon A. Forbes, Anna Gaulton, Cristina Yenyxe González, Henning Hermjakob, Anne Hersey, Steven Jupe, Senay Kafkas, Maria Keays, Catherine Leroy, Francisco-Javier Lopez, María P. Magariños, James Malone, Johanna R. McEntyre, Alfonso Muñoz-Pomer Fuentes, Claire O'Donovan, Irene Papatheodorou, Helen E. Parkinson, Barbara Palka, Justin E. Paschall, Robert Petryszak, Naruemon Pratanwanich, Sirarat Sarntivijai, Gary Saunders, Konstantinos Sidiropoulos, Thomas Smith, Zbyslaw Sondka, Oliver Stegle, Y. Amy Tang, Edward Turner, Brendan W. Vaughan, Olga Vrousgou, Xavier Watkins, Maria Jesus Martin, Philippe Sanseau, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham

Nucleic Acids Res., 2017

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, James Malone, Arild Waaler

J. Biomed. Semant., 2017

2016

Ten Simple Rules for Selecting a Bio-ontology.

James Malone, Robert Stevens, Simon Jupp, Tom Hancocks, Helen E. Parkinson, Catherine Brooksbank

PLoS Comput. Biol., 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

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

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

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, Erfan Younesi, James Malone, Ernesto Jiménez-Ruiz

Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 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, Erfan Younesi, James Malone, Ernesto Jiménez-Ruiz

Proceedings of the ISWC 2016 Posters & Demonstrations Track co-located with 15th International Semantic Web Conference (ISWC 2016), 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, Erfan Younesi, James Malone

Proceedings of the 11th International Workshop on Ontology Matching co-located with the 15th International Semantic Web Conference (ISWC 2016), 2016

Ten Simple Rules for Biomedical Ontology Development.

Mélanie Courtot, James Malone, Chris Mungall

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

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

2015 SWAT4LS International Conference Editorial.

James Malone, Robert Stevens, Kerstin Forsberg, Andrea Splendiani

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

Collaborative Ontology Development Using the Webulous Architecture and Google App.

Simon Jupp, Danielle Welter, Tony Burdett, Helen E. Parkinson, James Malone

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

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, James Malone, Karine Megy, Gabriella Rustici, Y. Amy Tang, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E. Parkinson, Alvis Brazma

Nucleic Acids Res., 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, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He

J. Biomed. Semant., 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

J. Biomed. Semant., 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, Nicolas Le Novère, Helen E. Parkinson, Ewan Birney, Andrew M. Jenkinson

Bioinform., 2014

Capturing Provenance for a Linkset of Convenience.

Simon Jupp, James Malone, Alasdair J. G. Gray

Proceedings of the 4th Workshop on Linked Science 2014, 2014

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, Roby Mani, Annalisa Mupo, Rui Pedro Pereira, Ekaterina Pilicheva, Johan Rung, Anjan Sharma, Y. Amy Tang, Tobias Ternent, Andrew Tikhonov, Danielle Welter, Eleanor Williams, Alvis Brazma, Helen E. Parkinson, Ugis Sarkans

Nucleic Acids Res., 2013

Measuring the level of activity in community built bio-ontologies.

James Malone, Robert Stevens

J. Biomed. Informatics, 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

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

Proceedings of the 10th International Workshop on OWL: Experiences and Directions (OWLED 2013) co-located with 10th Extended Semantic Web Conference (ESWC 2013), 2013

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, Olga Melnichuk, Robert Petryszak, Nikolay Pultsin, Gabriella Rustici, Andrew Tikhonov, Ravensara S. Travillian, Eleanor Williams, Andrey Zorin, Helen E. Parkinson, Alvis Brazma

Nucleic Acids Res., 2012

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

Helena F. Deus, Eric Prud'hommeaux, Michael Miller, Jun Zhao, James Malone, Tomasz Adamusiak, Jamie P. McCusker, Sudeshna Das, Philippe Rocca-Serra, Ronan Fox, M. Scott Marshall

J. Biomed. Informatics, 2012

Semantic Web Atlas: Putting Gene Expression Data into Biological Context.

Simon Jupp, Helen E. Parkinson, James Malone

Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Taking a view on bio-ontologies.

Simon Jupp, Andrew Gibson, James Malone, Robert Stevens

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

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, James Malone

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

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, James Malone, Roby Mani, Ekaterina Pilicheva, Gabriella Rustici, Anjan Sharma, Eleanor Williams, Tomasz Adamusiak, Marco Brandizi, Nataliya Sklyar, Alvis Brazma

Nucleic Acids Res., 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

Automating generation of textual class definitions from OWL to English.

Robert Stevens, James Malone, Sandra Williams, Richard Power, Allan Third

J. Biomed. Semant., 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

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

Proceedings of the 2nd International Conference on Biomedical Ontology, 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

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Rapid Development of an Ontology of Coriell Cell Lines.

Chao Pang, Tomasz Adamusiak, Helen E. Parkinson, James Malone

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

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

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, Larisa N. Soldatova, Christian J. Stoeckert Jr., Jessica A. Turner, Jie Zheng, et al.

J. Biomed. Semant., 2010

Modeling sample variables with an Experimental Factor Ontology.

James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, Helen E. Parkinson

Bioinform., 2010

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, James Malone, Roby Mani, Ekaterina Pilicheva, Tim F. Rayner, Faisal Ibne Rezwan, Anjan Sharma, Eleanor Williams, Xiangqun Zheng Bradley, Tomasz Adamusiak, Marco Brandizi, Tony Burdett, Richard Coulson, Maria Krestyaninova, Pavel Kurnosov, Eamonn Maguire, Sudeshna Guha Neogi, Philippe Rocca-Serra, Susanna-Assunta Sansone, Nataliya Sklyar, Mengyao Zhao, Ugis Sarkans, Alvis Brazma

Nucleic Acids Res., 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

Developing an Ontology from the Application Up.

James Malone, Tomasz Adamusiak, Ele Holloway, Misha Kapushesky, Helen E. Parkinson

Proceedings of the 5th International Workshop on OWL: Experiences and Directions (OWLED 2009), 2009

2008

Soft Computing in Bioinformatics: Genomic and Proteomic Applications.

James Malone

Proceedings of the Soft Computing Applications in Industry, 2008

The OWL of Biomedical Investigations.

Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, 2008

2006

Data mining using rule extraction from Kohonen self-organising maps.

James Malone, Kenneth McGarry, Stefan Wermter, Chris Bowerman

Neural Comput. Appl., 2006

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

James Malone, Kenneth McGarry, Chris Bowerman

Expert Syst. Appl., 2006

Dynamic Access Control Prediction for Ordered Service Sequence in Grid Environment.

Gayathri Nadarajan, Chuanjiang Yi, Yun-Heh Chen-Burger, Hai Jin, James Malone, Chengwei Wang

Proceedings of the 2006 IEEE / WIC / ACM International Conference on Web Intelligence (WI 2006), 2006

Semantic Grid Services for Video Analysis.

Gayathri Nadarajan, Yun-Heh Chen-Burger, James Malone

Proceedings of the 2006 IEEE/WIC/ACM International Conference on Intelligent Agent Technology, 2006