Simon Jupp

Publication Activity (10 Years)

Years Active: 2008-2023
Publications (10 Years): 21

Top Topics

Biologically Meaningful

Functional Genomics

Top Venues

J. Biomed. Semant.

Nucleic Acids Res.

Publications

Fuqi Xu, Nick S. Juty, Carole A. Goble, Simon Jupp, Helen E. Parkinson, Mélanie Courtot
Features of a FAIR vocabulary. J. Biomed. Semant. 14 (1) (2023)
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 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)
Fuqi Xu, Nick S. Juty, Carole A. Goble, Simon Jupp, Helen E. Parkinson, Mélanie Courtot
Features of a FAIR Vocabulary. SWAT4HCLS (2022)
Isuru Udara Liyanage, Tony Burdett, Bert Droesbeke, Karoly Erdos, Rolando Fernandez, Alasdair J. G. Gray, Muhammad Haseeb, Simon Jupp, Flavia Penim, Cyril Pommier, Philippe Rocca-Serra, Mélanie Courtot, Frederik Coppens
ELIXIR biovalidator for semantic validation of life science metadata. Bioinform. 38 (11) (2022)
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 (2021)
Maya Ghoussaini, Edward Mountjoy, Miguel Carmona, Gareth Peat, Ellen M. Schmidt, Andrew Hercules, Luca Fumis, Alfredo Miranda, Denise Carvalho-Silva, Annalisa Buniello, Tony Burdett, James D. Hayhurst, Jarrod Baker, Javier Ferrer, Asier Gonzalez-Uriarte, Simon Jupp, Mohd anisul Karim, Gautier Koscielny, Sandra Machlitt-Northen, Cinzia Malangone, Zoë May Pendlington, Paola Roncaglia, Daniel Suveges, Daniel Wright, Olga Vrousgou, Eliseo Papa, Helen E. Parkinson, Jacqueline A. L. MacArthur, John A. Todd, Jeffrey C. Barrett, Jeremy Schwartzentruber, David G. Hulcoop, David Ochoa, Ellen M. McDonagh, Ian Dunham
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. Nucleic Acids Res. 49 (Database-Issue) (2021)
Irene Papatheodorou, Pablo Moreno, Jonathan R. Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A. Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang, Laura Huerta, Haider Iqbal, Monica Jianu, Suhaib Mohammed, Lingyun Zhao, Andrew F. Jarnuczak, Simon Jupp, John C. Marioni, Kerstin B. Meyer, Robert Petryszak, Cesar Augusto Prada Medina, Carlos Talavera-López, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma
Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 48 (Database-Issue) (2020)
Kent A. Shefchek, Nomi L. Harris, Michael A. Gargano, Nicolas Matentzoglu, Deepak R. Unni, Matthew H. Brush, Dan Keith, Tom Conlin, Nicole A. Vasilevsky, Xingmin Aaron Zhang, James P. Balhoff, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington, Clare Pilgrim, Tim E. Putman, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 48 (Database-Issue) (2020)
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 (2019)
Henriette Harmse, Mélanie Courtot, Warren Read, Nicolas Matentzoglu, David Osumi-Sutherland, Simon Jupp
Where Does an Ontology Start? ICBO (2019)
Danielle Welter, Simon Jupp, David Osumi-Sutherland
Human Cell Atlas Ontology. ICBO (2018)
Edison Ong, Sirarat Sarntivijai, Simon Jupp, Helen E. Parkinson, Yongqun He
Comparison, alignment, and synchronization of cell line information between CLO and EFO. BMC Bioinform. 18 (S-17) (2017)
Simon Jupp, Thomas Liener, Sirarat Sarntivijai, Olga Vrousgou, Tony Burdett, Helen E. Parkinson
OxO - A Gravy of Ontology Mapping Extracts. ICBO (2017)
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 (2016)
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 (2016)
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 (2016)
Robert Petryszak, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Simon Jupp, Satu Koskinen, Oliver Mannion, Laura Huerta, Karine Megy, Catherine Snow, Eleanor Williams, Mitra Barzine, Emma Hastings, Hendrik Weisser, James C. Wright, Pankaj Jaiswal, Wolfgang Huber, Jyoti Choudhary, Helen E. Parkinson, Alvis Brazma
Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 44 (Database-Issue) (2016)
Olga Vrousgou, Tony Burdett, Helen E. Parkinson, Simon Jupp
Biomedical Ontology Evolution in the EMBL-EBI Ontology Lookup Service. EDBT/ICDT Workshops (2016)
Thomas Liener, Tony Burdett, Simon Jupp
Updates from the EMBL-EBI RDF platform. SWAT4LS (2016)
Mike Conway, Artem Khojoyan, Fariba Fana, William Scuba, Melissa Castine, Danielle L. Mowery, Wendy W. Chapman, Simon Jupp
Developing a web-based SKOS editor. J. Biomed. Semant. 7 (2016)
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)
Simon Jupp, Tony Burdett, Catherine Leroy, Helen E. Parkinson
A new Ontology Lookup Service at EMBL-EBI. SWAT4LS (2015)
Simon Jupp, Danielle Welter, Tony Burdett, Helen E. Parkinson, James Malone
Collaborative Ontology Development Using the Webulous Architecture and Google App. SWAT4LS (2015)
Simon Jupp, James Malone, Alasdair J. G. Gray
Capturing Provenance for a Linkset of Convenience. LISC@ISWC (2014)
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) (2014)
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) (2014)
Katherine Wolstencroft, Stuart Owen, Matthew Horridge, Simon Jupp, Olga Krebs, Jacky L. Snoep, Franco B. du Preez, Wolfgang Müller, Robert Stevens, Carole A. Goble
Stealthy annotation of experimental biology by spreadsheets. Concurr. Comput. Pract. Exp. 25 (4) (2013)
Panagiotis Moulos, Julie Klein, Simon Jupp, Robert Stevens, Jean-Loup Bascands, Joost P. Schanstra
The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases. BMC Bioinform. 14 (2013)
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)
Simon Jupp, Andrew Gibson, James Malone, Robert Stevens
Taking a view on bio-ontologies. ICBO (2012)
Jens Kappes, Mathias Liewald, Simon Jupp, Christoph Pirchl, Roman Herstelle
Designing superplastic forming process of a developmental AA5456 using pneumatic bulge test experiments and FE-simulation. Prod. Eng. 6 (3) (2012)
Simon Jupp, Robert Stevens, Robert Hoehndorf
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. J. Biomed. Semant. 3 (S-1) (2012)
Simon Jupp, Helen E. Parkinson, James Malone
Semantic Web Atlas: Putting Gene Expression Data into Biological Context. SWAT4LS (2012)
Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens
Populous: a tool for building OWL ontologies from templates. BMC Bioinform. 13 (S-1) (2012)
Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens
Populous: A Tool for Populating an Ontology. ICBO (2011)
Simon Jupp, Julie Klein, Joost Schanstra, Robert Stevens
Developing a kidney and urinary pathway knowledge base. J. Biomed. Semant. 2 (S-2) (2011)
Robert Stevens, Simon Jupp, Julie Klein, Joost Schanstra
Using semantic web technologies to manage complexity and change in biomedical data. EMBC (2011)
Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens, Katy Wolstencroft
Populous: A Tool for Populating Templates for OWL Ontologies. SWAT4LS (2010)
Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens, Katy Wolstencroft
Populous: A tool for populating ontology templates CoRR (2010)
Simon Jupp, Sean Bechhofer, Robert Stevens
A Flexible API and Editor for SKOS. ESWC (2009)
Christopher Brewster, Simon Jupp, Joanne S. Luciano, David M. Shotton, Robert D. Stevens, Ziqi Zhang
Issues in learning an ontology from text. BMC Bioinform. 10 (S-5) (2009)
Ed de Quincey, Helen Oliver, Patty Kostkova, Gawesh Jawaheer, Gemma Madle, Gayo Diallo, Dimitra Alexopoulou, Michael Schroeder, Bianca Habermann, Khaled Khelif, Simon Jupp, Robert Stevens
Mining for Patterns of Semantic Link Usage: Do Domain Users Actually Like Semantic Browsing? Web Intelligence/IAT Workshops (2009)
Helen Oliver, Gayo Diallo, Ed de Quincey, Dimitra Alexopoulou, Bianca Habermann, Patty Kostkova, Michael Schroeder, Simon Jupp, Khaled Khelif, Robert Stevens, Gawesh Jawaheer, Gemma Madle
A user-centred evaluation framework for the Sealife semantic web browsers. BMC Bioinform. 10 (S-10) (2009)
Simon Jupp, Sean Bechhofer, Robert Stevens
A Flexible API and Editor for SKOS. ISWC (Posters & Demos) (2008)
Gayo Diallo, Patty Kostkova, Gawesh Jawaheer, Simon Jupp, Robert Stevens
Process of Building a Vocabulary for the Infection Domain. CBMS (2008)
Sean Bechhofer, Yeliz Yesilada, Robert Stevens, Simon Jupp, Bernard Horan
Using Ontologies and Vocabularies for Dynamic Linking. IEEE Internet Comput. 12 (3) (2008)
Gayo Diallo, Gemma Madle, Gawesh Jawaheer, Patty Kostkova, Dimitra Alexopoulou, Robert Stevens, Simon Jupp, Khaled Khelif
A User-Centred Evaluation Framework for the SeaLife Semantic Web Browsers. SWAT4LS (2008)
Simon Jupp, Robert Stevens, Sean Bechhofer, Yeliz Yesilada, Patty Kostkova
Knowledge Representation for Web Navigation. SWAT4LS (2008)
Simon Jupp, Sean Bechhofer, Robert Stevens
SKOS with OWL: Don't be Full-ish! OWLED (2008)