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Journal Articles
- 2023
[j61]Déborah Caucheteur
, Zoë May Pendlington, Paola Roncaglia, Julien Gobeill, Luc Mottin, Nicolas Matentzoglu, Donat Agosti, David Osumi-Sutherland, Helen E. Parkinson, Patrick Ruch:
COVoc and COVTriage: novel resources to support literature triage. Bioinform. 39(1) (2023)- [j60]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) - [j59]Elliot Sollis, Abayomi Mosaku, Ala Abid, Annalisa Buniello, Maria Cerezo, Laurent Gil, Tudor Groza, Osman Nuri Günes, Peggy Hall, James D. Hayhurst, Arwa Ibrahim, Yue Ji, Sajo John, Elizabeth Lewis, Jacqueline A. L. MacArthur, Aoife McMahon, David Osumi-Sutherland, Kalliope Panoutsopoulou, Zoë May Pendlington, Santhi Ramachandran, Raymund Stefancsik, Jonathan Stewart, Patricia L. Whetzel, Robert J. Wilson, Lucia Hindorff, Fiona Cunningham, Samuel A. Lambert, Michael Inouye, Helen E. Parkinson, Laura W. Harris:
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51(D1): 977-985 (2023) - [j58]Tudor Groza, Federico López-Gómez, Hamed Haseli Mashhadi, Violeta Muñoz-Fuentes, Osman Nuri Günes, Robert J. Wilson, Pilar Cacheiro, Anthony Frost, Piia Keskivali-Bond, Bora Vardal, Aaron McCoy, Tsz Kwan Cheng, Luis A. Santos, Sara Wells, Damian Smedley, Ann-Marie Mallon, Helen E. Parkinson:
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. Nucleic Acids Res. 51(D1): 1038-1045 (2023) - [j57]Zinaida Perova, Mauricio Martínez, Tushar Mandloi, Federico López-Gómez, Csaba Halmagyi, Alex Follette, Jeremy C. Mason, Steven Newhauser, Dale A. Begley, Debra M. Krupke, Carol J. Bult, Helen E. Parkinson, Tudor Groza:
PDCM Finder: an open global research platform for patient-derived cancer models. Nucleic Acids Res. 51(D1): 1360-1366 (2023) - 2022
- [j56]Mallory Ann Freeberg, Lauren A. Fromont, Teresa D'altri, Anna Foix Romero, Jorge Izquierdo Ciges, Aina Jene, Giselle Kerry, Mauricio Moldes, Roberto Ariosa, Silvia Bahena, Daniel Barrowdale, Marcos Casado Barbero, Dietmar Fernández-Orth, Carles Garcia-Linares, Emilio Garcia-Rios, Frédéric Haziza, Bela Juhasz, Oscar Martinez Llobet, Gemma Milla, Anand Mohan, Manuel Rueda, Aravind Sankar, Dona Shaju, Ashutosh Shimpi, Babita Singh, Coline Thomas, Sabela de la Torre, Umuthan Uyan, Claudia Vasallo, Paul Flicek, Roderic Guigó, Arcadi Navarro, Helen E. Parkinson, Thomas M. Keane, Jordi Rambla:
The European Genome-phenome Archive in 2021. Nucleic Acids Res. 50(D1): 980-987 (2022) - [j55]Timothee Cezard, Fiona Cunningham, Sarah E. Hunt, Baron Koylass, Nitin Kumar, Gary Saunders, April Shen, Andres f Silva, Kirill Tsukanov, Sundararaman Venkataraman, Paul Flicek, Helen E. Parkinson, Thomas M. Keane:
The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res. 50(D1): 1216-1220 (2022) - 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 J. 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) - 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) - 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. Jiménez, 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) - 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) - 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) - 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) - 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) - 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) - 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, 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) - 2007
- [j10]Helen E. Parkinson, Misha Kapushesky, Mohammadreza Shojatalab, Niran Abeygunawardena, Richard Coulson, Anna Farne, Ele Holloway, Nikolay Kolesnykov, P. Lilja, Margus Lukk, Roby Mani, Tim F. Rayner, Anjan Sharma, E. William, Ugis Sarkans, Alvis Brazma:
ArrayExpress - a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35(Database-Issue): 747-750 (2007) - 2006
- [j9]Patricia L. Whetzel, Helen E. Parkinson, Helen C. Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Laurence Game, Mervi Heiskanen, Norman Morrison, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris F. Taylor, Joseph White, Christian J. Stoeckert Jr.:
The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinform. 22(7): 866-873 (2006) - [j8]Tim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert Jr., Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen E. Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma:
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform. 7: 489 (2006) - 2005
- [j7]Ugis Sarkans, Helen E. Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, Sergio Contrino, Ele Holloway, Philippe Rocca-Serra, Gaurab Mukherjee, Mohammadreza Shojatalab, Misha Kapushesky, Susanna-Assunta Sansone, Anna Farne, Tim F. Rayner, Alvis Brazma:
The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinform. 21(8): 1495-1501 (2005) - [j6]Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Niran Abeygunawardena, Sergio Contrino, Richard Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Misha Kapushesky, P. Lilja, Gaurab Mukherjee, Ahmet Oezcimen, Tim F. Rayner, Philippe Rocca-Serra, Anjan Sharma, Susanna-Assunta Sansone, Alvis Brazma:
ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 33(Database-Issue): 553-555 (2005) - 2003
- [j5]Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola J. Mulder, Claire O'Donovan, Helen E. Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron:
The European Bioinformatics Institute's data resources. Nucleic Acids Res. 31(1): 43-50 (2003) - [j4]Alvis Brazma, Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, Susanna-Assunta Sansone:
ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31(1): 68-71 (2003) - 2002
- [j3]Vincent Lombard, E. B. Camon, Helen E. Parkinson, Pascal Hingamp, Guenter Stoesser, Nicole Redaschi:
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, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank C. P. Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald C. Taylor, Alvis Brazma, John Quackenbush:
An open letter to the scientific journals. Bioinform. 18(11): 1409 (2002) - 2001
- [j1]Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Evelyn Camon, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Vincent Lombard, Rodrigo Lopez, Helen E. Parkinson, Nicole Redaschi, Peter Sterk, Peter Stoehr, Mary Ann Tuli:
The EMBL nucleotide sequence database. Nucleic Acids Res. 29(1): 17-21 (2001)
Conference and Workshop Papers
- 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 - 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
- [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
- [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 - 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
- [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
- [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 - 2009
- [c2]James Malone, Tomasz Adamusiak, Ele Holloway, Misha Kapushesky, Helen E. Parkinson:
Developing an Ontology from the Application Up. OWLED 2009 - 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
Coauthor Index
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