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2020 – today
- 2022
[j31]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). 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, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C. Munoz-Torres, Drashtti Vasant, Eleanor Williams, Melissa A. Haendel:
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, 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:
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8: 1677 (2019) - 2018
- [j28]Nicolas Matentzoglu, James Malone, Chris Mungall, Robert Stevens:
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, Ernesto Jiménez-Ruiz, Andrea Splendiani, Martin Romacker, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, James Malone, Arild Waaler:
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, 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:
Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 45(Database-Issue): D985-D994 (2017) - 2016
- [j25]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:
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. J. Biomed. Semant. 7: 8 (2016) - [j24]Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen E. Parkinson, James Malone:
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, James Malone, Tony Burdett, Jean-Karim Hériché, Eleanor Williams, Jan Ellenberg, Helen E. Parkinson, Gabriella Rustici:
The cellular microscopy phenotype ontology. J. Biomed. Semant. 7: 28 (2016) - [j22]James Malone, Robert Stevens, Simon Jupp, Tom Hancocks, Helen E. Parkinson, Catherine Brooksbank:
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, 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:
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, 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:
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, Jon C. Ison, Duncan Hull, Helen E. Parkinson, Robert Stevens:
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, 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:
CLO: The cell line ontology. J. Biomed. Semant. 5: 37 (2014) - [j17]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:
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, Matús Kalas, Inge Jonassen, Dan M. Bolser, Mahmut Uludag, Hamish McWilliam, James Malone, Rodrigo Lopez, Steve Pettifer, Peter M. Rice:
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, 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:
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, Eric Prud'hommeaux, Michael Miller, Jun Zhao, James Malone, Tomasz Adamusiak, Jamie P. McCusker, Sudeshna Das, Philippe Rocca-Serra, Ronan Fox, M. Scott Marshall:
Translating standards into practice - One Semantic Web API for Gene Expression. J. Biomed. Informatics 45(4): 782-794 (2012) - [j12]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:
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, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg:
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, 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:
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, Jun Zhao, Jamie P. McCusker, Ronan Fox, Eric Prud'hommeaux, James Malone, Sudeshna Das, Michael Miller, Tomasz Adamusiak, Philippe Rocca-Serra, M. Scott Marshall:
Translating standards into practice: one semantic web API for gene expression. SWAT4LS 2011: 6-7 - 2010
- [j7]James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, Helen E. Parkinson:
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, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen E. Parkinson, Alvis Brazma:
Gene Expression Atlas at the European Bioinformatics Institute. Nucleic Acids Res. 38(Database-Issue): 690-698 (2010)
2000 – 2009
- 2009
- [j4]Tim F. Rayner, Faisal Ibne Rezwan, Margus Lukk, Xiangqun Zheng Bradley, Anna Farne, Ele Holloway, James Malone, Eleanor Williams, Helen E. Parkinson:
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. Bioinform. 25(2): 279-280 (2009) - [j3]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:
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, Chris Bowerman:
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, Stefan Wermter, Chris Bowerman:
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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