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2020 – today
- 2022
- [c18]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
- [j54]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) - 2020
- [j53]Hamed Haselimashhadi, Jeremy C. Mason
, Violeta Muñoz-Fuentes
, Federico López-Gómez
, Kolawole O. Babalola
, Elif F. Acar, Vivek Kumar, Jacqui White, Ann M. Flenniken, Ruairidh King, Ewan Straiton
, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E. Christianson, Chih-Wei Hsu, Corey L. Reynolds, Denise G. Lanza
, Isabel Lorenzo, Jennie R. Green, Juan J. Gallegos, Ritu Bohat, Rodney C. Samaco, Surabi Veeraragavan, Jong Kyoung Kim
, Gregor Miller
, Helmut Fuchs, Lillian Garrett, Lore Becker
, Yeon Kyung Kang, David Clary, Soo Young Cho, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum
, Patrick T. Reilly, Nadine Spielmann, Holger Maier, Valérie Gailus-Durner, Tania Sorg
, Hiroshi Masuya, Yuichi Obata, Jason D. Heaney, Mary E. Dickinson, Wolfgang Wurst, Glauco P. Tocchini-Valentini, Kevin C. Kent Lloyd, Colin McKerlie, Je Kyung Seong, Yann Herault
, Martin Hrabé de Angelis
, Steve D. M. Brown, Damian Smedley, Paul Flicek
, Ann-Marie Mallon, Helen E. Parkinson
, Terrence F. Meehan
:
Soft windowing application to improve analysis of high-throughput phenotyping data. Bioinform. 36(5): 1492-1500 (2020) - [j52]Rachel Drysdale, Charles E. Cook
, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl
, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez
, Nicole Redaschi
, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman
, Alan Bridge, Guy Cochrane
, Robert D. Finn
, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata
, Per Oksvold, Sandra E. Orchard
, Christine A. Orengo, Helen E. Parkinson
, Bengt Persson, Pablo Porras
, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans
, Dietmar Schomburg, Ian Sillitoe, J. Dylan Spalding
, Mathias Uhlén, Sameer Velankar
, Juan Antonio Vizcaíno
, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates
, Niklas Blomberg
, Christine Durinx, Johanna R. McEntyre
:
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinform. 36(8): 2636-2642 (2020)
2010 – 2019
- 2019
- [j51]Annalisa Buniello
, Jacqueline A. L. MacArthur, Maria Cerezo
, Laura W. Harris, James D. Hayhurst
, Cinzia Malangone
, Aoife McMahon
, Joannella Morales
, Edward Mountjoy
, Elliot Sollis
, Daniel Suveges
, Olga Vrousgou, Patricia L. Whetzel, M. Ridwan Amode, Jose A. Guillen
, Harpreet Singh Riat, Stephen J. Trevanion
, Peggy Hall, Heather Junkins, Paul Flicek
, Tony Burdett
, Lucia A. Hindorff, Fiona Cunningham
, Helen E. Parkinson
:
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47(Database-Issue): D1005-D1012 (2019) - [j50]Nathalie Conte, Jeremy C. Mason
, Csaba Halmagyi
, Steven B. Neuhauser, Abayomi Mosaku
, Galabina Yordanova
, Aikaterini Chatzipli, Dale A. Begley, Debra M. Krupke, Helen E. Parkinson
, Terrence F. Meehan
, Carol C. Bult:
PDX Finder: A portal for patient-derived tumor xenograft model discovery. Nucleic Acids Res. 47(Database-Issue): D1073-D1079 (2019) - [j49]Mélanie Courtot
, Luca Cherubin
, Adam Faulconbridge
, Daniel Vaughan
, Matthew Green
, David Richardson
, Peter W. Harrison
, Patricia L. Whetzel
, Helen E. Parkinson
, Tony Burdett
:
BioSamples database: an updated sample metadata hub. Nucleic Acids Res. 47(Database-Issue): D1172-D1178 (2019) - 2018
- [j48]David Osumi-Sutherland
, Enrico Ponta, Mélanie Courtot
, Helen E. Parkinson
, Laura Badi:
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis. J. Biomed. Semant. 9(1): 10:1-10:10 (2018) - 2017
- [j47]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) - [j46]Ian Streeter, Peter W. Harrison, Adam Faulconbridge
, The HipSci Consortium, Paul Flicek
, Helen E. Parkinson
, Laura Clarke
:
The human-induced pluripotent stem cell initiative - data resources for cellular genetics. Nucleic Acids Res. 45(Database-Issue): D691-D697 (2017) - [j45]Jacqueline A. L. MacArthur
, Emily Bowler
, Maria Cerezo
, Laurent Gil, Peggy Hall, Emma Hastings
, Heather Junkins, Aoife McMahon
, Annalisa Milano
, Joannella Morales
, Zoë May Pendlington
, Danielle Welter
, Tony Burdett
, Lucia Hindorff, Paul Flicek
, Fiona Cunningham
, Helen E. Parkinson
:
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res. 45(Database-Issue): D896-D901 (2017) - [j44]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) - [c17]Simon Jupp, Thomas Liener, Sirarat Sarntivijai, Olga Vrousgou, Tony Burdett, Helen E. Parkinson:
OxO - A Gravy of Ontology Mapping Extracts. ICBO 2017 - 2016
- [j43]Anika Oellrich, Terrence F. Meehan
, Helen E. Parkinson
, Sirarat Sarntivijai
, Jacqueline K. White, Natasha A. Karp
:
Reporting phenotypes in mouse models when considering body size as a potential confounder. J. Biomed. Semant. 7: 2 (2016) - [j42]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) - [j41]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) - [j40]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) - [j39]Solomon Adebayo, Kenneth McLeod
, Ilinca Tudose
, David Osumi-Sutherland
, Tony Burdett
, Richard A. Baldock, Albert Burger, Helen E. Parkinson
:
PhenoImageShare: an image annotation and query infrastructure. J. Biomed. Semant. 7: 35 (2016) - [j38]Jon C. Ison
, Kristoffer Rapacki, Hervé Ménager
, Matús Kalas
, Emil Rydza, Piotr Chmura
, Christian Anthon
, Niall Beard
, Karel Berka
, Dan M. Bolser
, Tim Booth
, Anthony Bretaudeau, Jan Brezovsky
, Rita Casadio
, Gianni Cesareni, Frederik Coppens
, Michael Cornell, Gianmauro Cuccuru
, Kristian Davidsen, Gianluca Della Vedova
, Tunca Dogan
, Olivia Doppelt-Azeroual
, Laura Emery, Elisabeth Gasteiger
, Thomas Gatter, Tatyana Goldberg, Marie Grosjean
, Björn A. Grüning
, Manuela Helmer-Citterich
, Hans Ienasescu, Vassilios Ioannidis
, Martin Closter Jespersen, Rafael C. Jimenez
, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata
, Fabien Mareuil
, Ivan Micetic
, Rune Møllegaard Friborg, Sébastien Moretti
, Chris Morris
, Steffen Möller, Aleksandra Nenadic, Hedi Peterson
, Giuseppe Profiti
, Peter M. Rice, Paolo Romano
, Paola Roncaglia, Rabie Saidi
, Andrea Schafferhans
, Veit Schwämmle
, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger
, Radka Svobodová Vareková
, Silvio C. E. Tosatto
, Victor de la Torre, Paolo Uva
, Allegra Via, Guy Yachdav, Federico Zambelli
, Gert Vriend, Burkhard Rost, Helen E. Parkinson
, Peter Løngreen, Søren Brunak
:
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44(Database-Issue): 38-47 (2016) - [j37]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) - [j36]Marcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani
, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang
, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca
, Laura Huerta
, Maria Keays
, Y. Amy Tang
, Helen E. Parkinson
, Antonio Fabregat
, Sheldon J. McKay, Joel Weiser, Peter D'Eustachio
, Lincoln Stein, Robert Petryszak, Paul J. Kersey
, Pankaj Jaiswal, Doreen Ware:
Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res. 44(Database-Issue): 1133-1140 (2016) - [j35]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) - [c16]Olga Vrousgou, Tony Burdett, Helen E. Parkinson, Simon Jupp:
Biomedical Ontology Evolution in the EMBL-EBI Ontology Lookup Service. EDBT/ICDT Workshops 2016 - [c15]Senay Kafkas, Ian Dunham, Helen E. Parkinson, Johanna R. McEntyre:
Use of Text Mining for Experimental Factor Ontology Coverage Expansion in the Scope of Target Validation. ICBO/BioCreative 2016 - [c14]Mélanie Courtot, Alex L. Mitchell, Maxim Scheremetjew, Janet Piñero González, Laura I. Furlong, Robert D. Finn, Helen E. Parkinson:
Slim-o-matic: a Semi-Automated Way to Generate Gene Ontology Slims. SWAT4LS 2016 - 2015
- [j34]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) - [j33]Nikolay Kolesnikov, Emma Hastings
, Maria Keays
, Olga Melnichuk, Y. Amy Tang
, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova
, Marco Brandizi, Tony Burdett
, Karyn Megy
, Ekaterina Pilicheva, Gabriella Rustici
, Andrew Tikhonov, Helen E. Parkinson
, Robert Petryszak
, Ugis Sarkans
, Alvis Brazma
:
ArrayExpress update - simplifying data submissions. Nucleic Acids Res. 43(Database-Issue): 1113-1116 (2015) - [c13]David Osumi-Sutherland, Enrico Ponta, Mélanie Courtot, Helen E. Parkinson, Laura Badi:
Cell, Chemical and Anatomical Views of the Gene Ontology: Mapping to a Roche Controlled Vocabulary. SWAT4LS 2015: 84-93 - [c12]Simon Jupp, Tony Burdett, Catherine Leroy, Helen E. Parkinson:
A new Ontology Lookup Service at EMBL-EBI. SWAT4LS 2015: 118-119 - [c11]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
- [j32]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) - [j31]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) - [j30]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) - [j29]Adam Faulconbridge
, Tony Burdett
, Marco Brandizi, Mikhail Gostev, Rui Pedro Pereira, Drashtti Vasant, Ugis Sarkans
, Alvis Brazma
, Helen E. Parkinson
:
Updates to BioSamples database at European Bioinformatics Institute. Nucleic Acids Res. 42(Database-Issue): 50-52 (2014) - [j28]Gautier Koscielny, Gagarine Yaikhom, Vivek Iyer, Terrence F. Meehan
, Hugh Morgan, Julian Atienza-Herrero, Andrew Blake, Chao-Kung Chen, Richard Easty, Armida Di Fenza, Tanja Fiegel, Mark Grifiths, Alan Horne, Natasha A. Karp
, Natalja Kurbatova
, Jeremy C. Mason
, Peter Matthews
, Darren J. Oakley
, Asfand Qazi, Jack Regnart, Ahmad Retha
, Luis A. Santos
, Duncan J. Sneddon, Jonathan Warren
, Henrik Westerberg, Robert J. Wilson
, David G. Melvin, Damian Smedley, Steve D. M. Brown, Paul Flicek, William C. Skarnes, Ann-Marie Mallon, Helen E. Parkinson
:
The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Res. 42(Database-Issue): 802-809 (2014) - [j27]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) - [j26]Danielle Welter
, Jacqueline A. L. MacArthur
, Joannella Morales
, Tony Burdett
, Peggy Hall, Heather Junkins, Alan Klemm, Paul Flicek
, Teri Manolio, Lucia Hindorff, Helen E. Parkinson
:
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42(Database-Issue): 1001-1006 (2014) - 2013
- [j25]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) - [c10]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
- [j24]Vincent Xue, Tony Burdett
, Margus Lukk
, Julie Taylor, Alvis Brazma
, Helen E. Parkinson
:
MageComet - web application for harmonizing existing large-scale experiment descriptions. Bioinform. 28(10): 1402-1403 (2012) - [j23]Mikhail Gostev, Adam Faulconbridge
, Marco Brandizi
, Julio Fernandez-Banet
, Ugis Sarkans
, Alvis Brazma
, Helen E. Parkinson
:
The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res. 40(Database-Issue): 64-70 (2012) - [j22]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) - [c9]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 - [c8]Danielle Welter, Tony Burdett, Lucia Hindorff, Heather Junkins, Jackie MacArthur, Helen E. Parkinson:
GOCI: An Ontology-Driven Search and Curation Infrastructure for the NHGRI GWAS Catalog. ICBO 2012 - [c7]Simon Jupp, Helen E. Parkinson, James Malone:
Semantic Web Atlas: Putting Gene Expression Data into Biological Context. SWAT4LS 2012 - [c6]Sören Auer, Theodore Dalamagas
, Helen E. Parkinson, François Bancilhon, Giorgos Flouris, Dimitris Sacharidis
, Peter Buneman, Dimitris Kotzinos, Yannis Stavrakas, Vassilis Christophides, George Papastefanatos
, Kostas Thiveos:
Diachronic linked data: towards long-term preservation of structured interrelated information. WOD 2012: 31-39 - 2011
- [j21]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) - [j20]Tomasz Adamusiak
, Tony Burdett
, Natalja Kurbatova
, K. Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki
, Misha Kapushesky, Helen E. Parkinson
, Morris A. Swertz
:
OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinform. 12: 218 (2011) - [j19]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) - [c5]Chao Pang, Tomasz Adamusiak, Helen E. Parkinson, James Malone:
Rapid Development of an Ontology of Coriell Cell Lines. ICBO 2011 - [c4]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 - [c3]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 - 2010
- [j18]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) - [j17]Ravi Shankar, Helen E. Parkinson
, Tony Burdett
, Emma Hastings
, Junmin Liu, Michael Miller, Rashmi Srinivasa, Joseph White, Alvis Brazma
, Gavin Sherlock
, Christian J. Stoeckert Jr., Catherine A. Ball:
Annotare - a tool for annotating high-throughput biomedical investigations and resulting data. Bioinform. 26(19): 2470-2471 (2010) - [j16]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) - [j15]Morris A. Swertz
, Martijn Dijkstra, Tomasz Adamusiak
, K. Joeri van der Velde, Alexandros Kanterakis
, Erik T. Roos, Joris Lops, Gudmundur A. Thorisson
, Danny Arends
, George Byelas, Juha Muilu
, Anthony J. Brookes, Engbert O. de Brock, Ritsert C. Jansen, Helen E. Parkinson
:
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinform. 11(S-12): S12 (2010) - [j14]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
- [j13]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) - [j12]Audrey Kauffmann, Tim F. Rayner
, Helen E. Parkinson
, Misha Kapushesky, Margus Lukk
, Alvis Brazma
, Wolfgang Huber
:
Importing ArrayExpress datasets into R/Bioconductor. Bioinform. 25(16): 2092-2094 (2009) - [j11]Helen E. Parkinson
, Misha Kapushesky, Nikolay Kolesnikov
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:
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 37(Database-Issue): 868-872 (2009) - [c2]James Malone, Tomasz Adamusiak, Ele Holloway, Misha Kapushesky, Helen E. Parkinson:
Developing an Ontology from the Application Up. OWLED 2009 - 2007
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:
ArrayExpress - a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35(Database-Issue): 747-750 (2007) - 2006
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The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinform. 22(7): 866-873 (2006) - [j8]Tim F. Rayner
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:
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform. 7: 489 (2006) - 2005
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:
The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinform. 21(8): 1495-1501 (2005) - [j6]Helen E. Parkinson
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ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 33(Database-Issue): 553-555 (2005) - [c1]Kevin L. Garwood, Phillip W. Lord, Helen E. Parkinson, Norman W. Paton, Carole A. Goble:
Pedro Ontology Services: A Framework for Rapid Ontology Markup. ESWC 2005: 578-591 - 2003
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The European Bioinformatics Institute's data resources. Nucleic Acids Res. 31(1): 43-50 (2003) - [j4]Alvis Brazma
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ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31(1): 68-71 (2003) - 2002
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EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database. Bioinform. 18(5): 763-764 (2002) - [j2]Catherine A. Ball, Gavin Sherlock
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An open letter to the scientific journals. Bioinform. 18(11): 1409 (2002) - 2001
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The EMBL nucleotide sequence database. Nucleic Acids Res. 29(1): 17-21 (2001)