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2020 – today
- 2024
[c23]Wytze J. Vlietstra, Matthias Albus, Nick Drummond, Simon Jupp, George Georghiou:
Vision for modular taxonomy production at Elsevier: The VOICE project. SWAT4HCLS 2024: 210-211- 2023
- [j24]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): 6 (2023) - 2022
- [j23]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) - [j22]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): 3141-3142 (2022) - [c22]Fuqi Xu, Nick S. Juty, Carole A. Goble, Simon Jupp, Helen E. Parkinson, Mélanie Courtot:
Features of a FAIR Vocabulary. SWAT4HCLS 2022: 118-148 - 2021
- [j21]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): D1311-D1320 (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) - 2020
- [j20]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): D704-D715 (2020) - [j19]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:
Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 48(Database-Issue): D77-D83 (2020)
2010 – 2019
- 2019
- [c21]Henriette Harmse, Mélanie Courtot, Warren Read, Nicolas Matentzoglu, David Osumi-Sutherland, Simon Jupp:
Where Does an Ontology Start? ICBO 2019: 1 - [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
- [c20]Danielle Welter, Simon Jupp, David Osumi-Sutherland:
Human Cell Atlas Ontology. ICBO 2018 - 2017
- [j18]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): 25-33 (2017) - [c19]Simon Jupp, Thomas Liener, Sirarat Sarntivijai, Olga Vrousgou, Tony Burdett, Helen E. Parkinson:
OxO - A Gravy of Ontology Mapping Extracts. ICBO 2017 - 2016
- [j17]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: 5 (2016) - [j16]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) - [j15]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) - [j14]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) - [j13]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): 746-752 (2016) - [j12]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) - [c18]Olga Vrousgou, Tony Burdett, Helen E. Parkinson, Simon Jupp:
Biomedical Ontology Evolution in the EMBL-EBI Ontology Lookup Service. EDBT/ICDT Workshops 2016 - [c17]Thomas Liener, Tony Burdett, Simon Jupp:
Updates from the EMBL-EBI RDF platform. SWAT4LS 2016 - 2015
- [c16]Simon Jupp, Tony Burdett, Catherine Leroy, Helen E. Parkinson:
A new Ontology Lookup Service at EMBL-EBI. SWAT4LS 2015: 118-119 - [c15]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
- [j11]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) - [j10]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) - [c14]Simon Jupp, James Malone, Alasdair J. G. Gray:
Capturing Provenance for a Linkset of Convenience. LISC@ISWC 2014: 71-75 - 2013
- [j9]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: 235 (2013) - [j8]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): 467-480 (2013) - [c13]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 - [e1]Mariano Rodriguez-Muro, Simon Jupp, Kavitha Srinivas:
Proceedings of the 10th International Workshop on OWL: Experiences and Directions (OWLED 2013) co-located with 10th Extended Semantic Web Conference (ESWC 2013), Montpellier, France, May 26-27, 2013. CEUR Workshop Proceedings 1080, CEUR-WS.org 2013 [contents] - 2012
- [j7]Simon Jupp, Robert Stevens, Robert Hoehndorf:
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. J. Biomed. Semant. 3(S-1): S3 (2012) - [j6]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): S5 (2012) - [j5]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): 219-228 (2012) - [c12]Simon Jupp, Andrew Gibson, James Malone, Robert Stevens:
Taking a view on bio-ontologies. ICBO 2012 - [c11]Simon Jupp, Helen E. Parkinson, James Malone:
Semantic Web Atlas: Putting Gene Expression Data into Biological Context. SWAT4LS 2012 - 2011
- [j4]Simon Jupp, Julie Klein, Joost Schanstra, Robert Stevens:
Developing a kidney and urinary pathway knowledge base. J. Biomed. Semant. 2(S-2): S7 (2011) - [c10]Robert Stevens, Simon Jupp, Julie Klein, Joost Schanstra:
Using semantic web technologies to manage complexity and change in biomedical data. EMBC 2011: 3708-3711 - [c9]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 - 2010
- [c8]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 - [i1]Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Robert Stevens, Katy Wolstencroft:
Populous: A tool for populating ontology templates. CoRR abs/1012.1745 (2010)
2000 – 2009
- 2009
- [j3]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): 14 (2009) - [j2]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) - [c7]Simon Jupp, Sean Bechhofer, Robert Stevens:
A Flexible API and Editor for SKOS. ESWC 2009: 506-520 - [c6]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: 50-53 - 2008
- [j1]Sean Bechhofer, Yeliz Yesilada, Robert Stevens, Simon Jupp, Bernard Horan:
Using Ontologies and Vocabularies for Dynamic Linking. IEEE Internet Comput. 12(3): 32-39 (2008) - [c5]Gayo Diallo, Patty Kostkova, Gawesh Jawaheer, Simon Jupp, Robert Stevens:
Process of Building a Vocabulary for the Infection Domain. CBMS 2008: 308-313 - [c4]Simon Jupp, Sean Bechhofer, Robert Stevens:
SKOS with OWL: Don't be Full-ish! OWLED 2008 - [c3]Simon Jupp, Sean Bechhofer, Robert Stevens:
A Flexible API and Editor for SKOS. ISWC (Posters & Demos) 2008 - [c2]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 - [c1]Simon Jupp, Robert Stevens, Sean Bechhofer, Yeliz Yesilada, Patty Kostkova:
Knowledge Representation for Web Navigation. SWAT4LS 2008
Coauthor Index
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