Simon Jupp

According to our database, Simon Jupp authored at least 46 papers between 2008 and 2023.

Collaborative distances:

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

2023

Features of a FAIR vocabulary.

Fuqi Xu, Nick S. Juty, Carole A. Goble, Simon Jupp, Helen E. Parkinson, Mélanie Courtot

J. Biomed. Semant., December, 2023

2022

ELIXIR biovalidator for semantic validation of life science metadata.

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

Bioinform., 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

2021

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.

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

Nucleic Acids Res., 2021

2020

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

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

Nucleic Acids Res., 2020

Expression Atlas update: from tissues to single cells.

Irene Papatheodorou, Pablo A. 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

Nucleic Acids Res., 2020

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

Where Does an Ontology Start?

Henriette Harmse, Mélanie Courtot, Warren Read, Nicolas Matentzoglu, David Osumi-Sutherland, Simon Jupp

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019

2018

Human Cell Atlas Ontology.

Danielle Welter, Simon Jupp, David Osumi-Sutherland

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

2017

Comparison, alignment, and synchronization of cell line information between CLO and EFO.

Edison Ong, Sirarat Sarntivijai, Simon Jupp, Helen E. Parkinson, Yongqun He

BMC Bioinform., 2017

OxO - A Gravy of Ontology Mapping Extracts.

Simon Jupp, Thomas Liener, Sirarat Sarntivijai, Olga Vrousgou, Tony Burdett, Helen E. Parkinson

Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 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

Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants.

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

Nucleic Acids Res., 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

Developing a web-based SKOS editor.

Mike Conway, Artem Khojoyan, Fariba Fana, William Scuba, Melissa Castine, Danielle L. Mowery, Wendy W. Chapman, Simon Jupp

J. Biomed. Semant., 2016

Updates from the EMBL-EBI RDF platform.

Thomas Liener, Tony Burdett, Simon Jupp

Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

Biomedical Ontology Evolution in the EMBL-EBI Ontology Lookup Service.

Olga Vrousgou, Tony Burdett, Helen E. Parkinson, Simon Jupp

Proceedings of the Workshops of the EDBT/ICDT 2016 Joint Conference, 2016

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

A new Ontology Lookup Service at EMBL-EBI.

Simon Jupp, Tony Burdett, Catherine Leroy, Helen E. Parkinson

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

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

Stealthy annotation of experimental biology by spreadsheets.

Katherine Wolstencroft, Stuart Owen, Matthew Horridge, Simon Jupp, Olga Krebs, Jacky L. Snoep, Franco B. du Preez, Wolfgang Müller, Robert Stevens, Carole A. Goble

Concurr. Comput. Pract. Exp., 2013

The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases.

Panagiotis Moulos, Julie Klein, Simon Jupp, Robert Stevens, Jean-Loup Bascands, Joost P. Schanstra

BMC 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

Designing superplastic forming process of a developmental AA5456 using pneumatic bulge test experiments and FE-simulation.

Jens Kappes, Mathias Liewald, Simon Jupp, Christoph Pirchl, Roman Herstelle

Prod. Eng., 2012

Populous: a tool for building OWL ontologies from templates.

Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens

BMC Bioinform., 2012

Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.

Simon Jupp, Robert Stevens, Robert Hoehndorf

J. Biomed. Semant., 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

2011

Developing a kidney and urinary pathway knowledge base.

Simon Jupp, Julie Klein, Joost Schanstra, Robert Stevens

J. Biomed. Semant., 2011

Populous: A Tool for Populating an Ontology.

Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens

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

Using semantic web technologies to manage complexity and change in biomedical data.

Robert Stevens, Simon Jupp, Julie Klein, Joost Schanstra

Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011

2010

Populous: A tool for populating ontology templates

Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens, Katy Wolstencroft

CoRR, 2010

Populous: A Tool for Populating Templates for OWL Ontologies.

Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens, Katy Wolstencroft

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, 2010

2009

A user-centred evaluation framework for the Sealife semantic web browsers.

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

BMC Bioinform., 2009

Issues in learning an ontology from text.

Christopher Brewster, Simon Jupp, Joanne S. Luciano, David M. Shotton, Robert D. Stevens, Ziqi Zhang

BMC Bioinform., 2009

Mining for Patterns of Semantic Link Usage: Do Domain Users Actually Like Semantic Browsing?

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

Proceedings of the 2009 IEEE/WIC/ACM International Conference on Web Intelligence and International Conference on Intelligent Agent Technology, 2009

A Flexible API and Editor for SKOS.

Simon Jupp, Sean Bechhofer, Robert Stevens

Proceedings of the Semantic Web: Research and Applications, 2009

2008

Using Ontologies and Vocabularies for Dynamic Linking.

Sean Bechhofer, Yeliz Yesilada, Robert Stevens, Simon Jupp, Bernard Horan

IEEE Internet Comput., 2008

Knowledge Representation for Web Navigation.

Simon Jupp, Robert Stevens, Sean Bechhofer, Yeliz Yesilada, Patty Kostkova

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

A User-Centred Evaluation Framework for the SeaLife Semantic Web Browsers.

Gayo Diallo, Gemma Madle, Gawesh Jawaheer, Patty Kostkova, Dimitra Alexopoulou, Robert Stevens, Simon Jupp, Khaled Khelif

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

SKOS with OWL: Don't be Full-ish!

Simon Jupp, Sean Bechhofer, Robert Stevens

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

Process of Building a Vocabulary for the Infection Domain.

Gayo Diallo, Patty Kostkova, Gawesh Jawaheer, Simon Jupp, Robert Stevens

Proceedings of the Twenty-First IEEE International Symposium on Computer-Based Medical Systems, 2008