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James Malone
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2020 – today
- 2022
- [j31]Nicolas Matentzoglu
, James P. Balhoff
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022(2022) (2022) - 2021
- [i3]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:
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR abs/2112.07051 (2021)
2010 – 2019
- 2019
- [j30]Y. Amy Tang
Ten quick tips for biocuration. PLoS Comput. Biol. 15(5) (2019) - [j29]Robert Stevens, Phillip Lord, James Malone, Nicolas Matentzoglu
Measuring expert performance at manually classifying domain entities under upper ontology classes. J. Web Semant. 57 (2019) - [i2]Toshiaki Katayama
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8: 1677 (2019) - 2018
- [j28]Nicolas Matentzoglu
MIRO: guidelines for minimum information for the reporting of an ontology. J. Biomed. Semant. 9(1): 6:1-6:13 (2018) - [i1]Robert Stevens, Phillip Lord, James Malone, Nicolas Matentzoglu:
Measuring Expert Performance at Manually Classifying Domain Entities under Upper Ontology Classes. CoRR abs/1810.05093 (2018) - 2017
- [j27]Ian Harrow
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. J. Biomed. Semant. 8(1): 55:1-55:13 (2017) - [j26]Gautier Koscielny, Peter An, Denise Carvalho-Silva, Jennifer A. Cham
Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 45(Database-Issue): D985-D994 (2017) - 2016
- [j25]Sirarat Sarntivijai
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. J. Biomed. Semant. 7: 8 (2016) - [j24]Simon Jupp
Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates. J. Biomed. Semant. 7: 17 (2016) - [j23]Simon Jupp
The cellular microscopy phenotype ontology. J. Biomed. Semant. 7: 28 (2016) - [j22]James Malone, Robert Stevens, Simon Jupp
Ten Simple Rules for Selecting a Bio-ontology. PLoS Comput. Biol. 12(2) (2016) - [c19]Mélanie Courtot, James Malone, Chris Mungall:
Ten Simple Rules for Biomedical Ontology Development. ICBO/BioCreative 2016 - [c18]Ian Harrow, Ernesto Jiménez-Ruiz, Andrea Splendiani, Martin Romacker, Stefan Negru, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, Erfan Younesi, James Malone:
Introducing the disease and phenotype OAEI track. OM@ISWC 2016: 227-228 - [c17]Ian Harrow, Martin Romacker, Andrea Splendiani, Stefan Negru, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, Erfan Younesi, James Malone, Ernesto Jiménez-Ruiz:
Ontologies Guidelines for Best Practice and a Process to Evaluate Existing Ontologies Mapping Tools and Algorithms. ISWC (Posters & Demos) 2016 - [c16]Ian Harrow, Martin Romacker, Andrea Splendiani, Stefan Negru, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, Erfan Younesi, James Malone, Ernesto Jiménez-Ruiz:
Ontologies Guidelines and Evaluation of Ontologies Mapping Tools and Algorithms. SWAT4LS 2016 - [e2]James Malone, Robert Stevens, Kerstin Forsberg, Andrea Splendiani:
Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, Cambridge UK, December 7-10, 2015. CEUR Workshop Proceedings 1546, CEUR-WS.org 2016 [contents] - 2015
- [j21]Warren A. Kibbe
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 43(Database-Issue): 1071-1078 (2015) - [c15]James Malone, Robert Stevens, Kerstin Forsberg, Andrea Splendiani:
2015 SWAT4LS International Conference Editorial. SWAT4LS 2015: 1 - [c14]Simon Jupp, Danielle Welter, Tony Burdett, Helen E. Parkinson, James Malone:
Collaborative Ontology Development Using the Webulous Architecture and Google App. SWAT4LS 2015: 120-121 - 2014
- [j20]Simon Jupp
The EBI RDF platform: linked open data for the life sciences. Bioinform. 30(9): 1338-1339 (2014) - [j19]James Malone, Andy Brown, Allyson L. Lister
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. J. Biomed. Semant. 5: 25 (2014) - [j18]Sirarat Sarntivijai
CLO: The cell line ontology. J. Biomed. Semant. 5: 37 (2014) - [j17]Robert Petryszak
Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res. 42(Database-Issue): 926-932 (2014) - [c13]Simon Jupp, James Malone, Alasdair J. G. Gray:
Capturing Provenance for a Linkset of Convenience. LISC@ISWC 2014: 71-75 - 2013
- [j16]Jon C. Ison
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinform. 29(10): 1325-1332 (2013) - [j15]James Malone, Robert Stevens:
Measuring the level of activity in community built bio-ontologies. J. Biomed. Informatics 46(1): 5-14 (2013) - [j14]Gabriella Rustici
ArrayExpress update - trends in database growth and links to data analysis tools. Nucleic Acids Res. 41(Database-Issue): 987-990 (2013) - [c12]James Malone, Tony Burdett, Jon C. Ison, Simon Jupp, Drashtti Vasant, Danielle Welter, Helen E. Parkinson:
Putting OWL into Production at the European Bioinformatics Institute. OWLED 2013 - 2012
- [j13]Helena F. Deus
Translating standards into practice - One Semantic Web API for Gene Expression. J. Biomed. Informatics 45(4): 782-794 (2012) - [j12]Misha Kapushesky, Tomasz Adamusiak
Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 40(Database-Issue): 1077-1081 (2012) - [c11]Maria Copeland, Andy Brown, Helen E. Parkinson, Robert Stevens, James Malone:
The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies. ICBO 2012 - [c10]Simon Jupp, Andrew Gibson, James Malone, Robert Stevens:
Taking a view on bio-ontologies. ICBO 2012 - [c9]Simon Jupp, Helen E. Parkinson, James Malone:
Semantic Web Atlas: Putting Gene Expression Data into Biological Context. SWAT4LS 2012 - 2011
- [j11]Mélanie Courtot
MIREOT: The minimum information to reference an external ontology term. Appl. Ontology 6(1): 23-33 (2011) - [j10]Robert Stevens, James Malone, Sandra Williams, Richard Power, Allan Third:
Automating generation of textual class definitions from OWL to English. J. Biomed. Semant. 2(S-2): S5 (2011) - [j9]Ravensara S. Travillian, Tomasz Adamusiak, Tony Burdett, Michael Gruenberger, John M. Hancock, Ann-Marie Mallon, James Malone, Paul N. Schofield, Helen E. Parkinson:
Anatomy ontologies and potential users: bridging the gap. J. Biomed. Semant. 2(S-4): S3 (2011) - [j8]Helen E. Parkinson
ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res. 39(Database-Issue): 1002-1004 (2011) - [c8]Chao Pang, Tomasz Adamusiak, Helen E. Parkinson, James Malone:
Rapid Development of an Ontology of Coriell Cell Lines. ICBO 2011 - [c7]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:
Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. ICBO 2011 - [c6]Ravensara S. Travillian, James Malone, Chao Pang, John M. Hancock, Peter W. H. Holland, Paul N. Schofield, Helen E. Parkinson:
The Vertebrate Bridging Ontology (VBO). ICBO 2011 - [c5]Helena F. Deus
Translating standards into practice: one semantic web API for gene expression. SWAT4LS 2011: 6-7 - 2010
- [j7]James Malone, Ele Holloway, Tomasz Adamusiak
Modeling sample variables with an Experimental Factor Ontology. Bioinform. 26(8): 1112-1118 (2010) - [j6]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.:
Modeling biomedical experimental processes with OBI. J. Biomed. Semant. 1(S-1): S7 (2010) - [j5]Misha Kapushesky, Ibrahim Emam
Gene Expression Atlas at the European Bioinformatics Institute. Nucleic Acids Res. 38(Database-Issue): 690-698 (2010)
2000 – 2009
- 2009
- [j4]Tim F. Rayner
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. Bioinform. 25(2): 279-280 (2009) - [j3]Helen E. Parkinson
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 37(Database-Issue): 868-872 (2009) - [c4]James Malone, Tomasz Adamusiak, Ele Holloway, Misha Kapushesky, Helen E. Parkinson:
Developing an Ontology from the Application Up. OWLED 2009 - 2008
- [c3]Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg:
The OWL of Biomedical Investigations. OWLED 2008 - [p1]James Malone:
Soft Computing in Bioinformatics: Genomic and Proteomic Applications. Soft Computing Applications in Industry 2008: 135-150 - [e1]Mukesh Doble, William Loging, James Malone, Vincent Shin-Mu Tseng:
International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, BCBGC-08, Orlando, Florida, USA , July 7-10, 2008. ISRST 2008, ISBN 978-1-60651-002-5 [contents] - 2006
- [j2]James Malone, Kenneth McGarry
Automated trend analysis of proteomics data using an intelligent data mining architecture. Expert Syst. Appl. 30(1): 24-33 (2006) - [j1]James Malone, Kenneth McGarry
Data mining using rule extraction from Kohonen self-organising maps. Neural Comput. Appl. 15(1): 9-17 (2006) - [c2]Gayathri Nadarajan, Yun-Heh Chen-Burger, James Malone:
Semantic Grid Services for Video Analysis. IAT Workshops 2006: 121-124 - [c1]Gayathri Nadarajan, Chuanjiang Yi, Yun-Heh Chen-Burger, Hai Jin, James Malone, Chengwei Wang:
Dynamic Access Control Prediction for Ordered Service Sequence in Grid Environment. Web Intelligence 2006: 145-151
Coauthor Index
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