James Malone

James Malone

Lead Ontologist - Parkinson team: Samples, Phenotypes and Ontologies

James Malone is a Lead Ontologist in the Samples, Phenotypes and Ontologies team at EMBL-EBI. His work focuses on the use of semantics in describing, sharing and integrating data across the life sciences. This touches on aspects of ontologies, RDF, semantic web and machine learning. Prior to joining EMBL-EBI in 2007, James was a Research Fellow working in AI at the University of Edinburgh. He holds a Masters degree in Bioinformatics from Oxford University, and a PhD in Bioinformatics and Machine Learning from the University of Sunderland. James writes a blog about ontologies.

ORCID iD: 0000-0002-1615-2899

Tel:+ 44 (0) 1223 494 676 / Fax:+ 44 (0) 1223 492 468



Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.
Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM.
Nucleic Acids Res Volume 43 (2015) p.d1071-8
DOI: 10.1093/nar/gku1011


Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.
Nucleic Acids Res Volume 42 (2014) p.d926-32
DOI: 10.1093/nar/gkt1270

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.
Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R.
J Biomed Semantics Volume 5 (2014) p.25
DOI: 10.1186/2041-1480-5-25

The EBI RDF platform: linked open data for the life sciences.
Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.
Bioinformatics Volume 30 (2014) p.1338-1339
DOI: 10.1093/bioinformatics/btt765


ArrayExpress update--trends in database growth and links to data analysis tools.
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.
Nucleic Acids Res Volume 41 (2013) p.d987-90
DOI: 10.1093/nar/gks1174

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.
Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P.
Bioinformatics Volume 29 (2013) p.1325-1332
DOI: 10.1093/bioinformatics/btt113

Measuring the level of activity in community built bio-ontologies.
Malone J, Stevens R.
J Biomed Inform Volume 46 (2013) p.5-14
DOI: 10.1016/j.jbi.2012.04.002