R
Ralf Stephan
Researcher at Ontario Institute for Cancer Research
Publications - 16
Citations - 809
Ralf Stephan is an academic researcher from Ontario Institute for Cancer Research. The author has contributed to research in topics: Open Biomedical Ontologies & Class (set theory). The author has an hindex of 5, co-authored 16 publications receiving 268 citations.
Papers
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Journal ArticleDOI
The reactome pathway knowledgebase 2022.
Marc Gillespie,Marc Gillespie,Bijay Jassal,Ralf Stephan,Marija Milacic,Karen Rothfels,Andrea Senff-Ribeiro,Andrea Senff-Ribeiro,Johannes Griss,Johannes Griss,Cristoffer Sevilla,Lisa Matthews,Chuqiao Gong,Chuan Deng,Chuan Deng,Thawfeek M. Varusai,Eliot Ragueneau,Yusra Haider,Bruce May,Veronica Shamovsky,Joel Weiser,Timothy Brunson,Nasim Sanati,Liam Beckman,Xiang Shao,Antonio Fabregat,Konstantinos Sidiropoulos,Julieth Murillo,Guilherme Viteri,Justin Cook,Solomon Shorser,Gary D. Bader,Emek Demir,Chris Sander,Robin Haw,Guanming Wu,Lincoln Stein,Lincoln Stein,Henning Hermjakob,Henning Hermjakob,Peter D'Eustachio +40 more
TL;DR: The Reactome Knowledgebase as mentioned in this paper provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired disease processes, annotated as an ordered network of molecular transformations in a single consistent data model.
Journal ArticleDOI
The Gene Ontology: Enhancements for 2011
Judith A. Blake,Mary E. Dolan,H. Drabkin,David P. Hill,L. Ni,D. Sitnikov,Shane C. Burgess,Teresia Buza,Cathy R. Gresham,Fiona M. McCarthy,Lakshmi Pillai,Hui Wang,Seth Carbon,Suzanna E. Lewis,Christopher J. Mungall,P Gaudet,Rex L. Chisholm,Petra Fey,Warren A. Kibbe,S. Basu,Deborah A. Siegele,B. K. McIntosh,Daniel P. Renfro,Adrienne E. Zweifel,James C. Hu,Nicholas H. Brown,Susan Tweedie,Yasmin Alam-Faruque,Rolf Apweiler,A. Auchinchloss,Kristian B. Axelsen,Ghislaine Argoud-Puy,Benoit Bely,M. C. Blatter,Lydie Bougueleret,Emmanuel Boutet,S. Branconi-Quintaje,Lionel Breuza,Alan Bridge,Paul Browne,W. M. Chan,Elisabeth Coudert,Isabelle Cusin,E. Dimmer,P. Duek-Roggli,Ruth Y. Eberhardt,Anne Estreicher,L Famiglietti,S. Ferro-Rojas,M Feuermann,Malcolm J. Gardner,Arnaud Gos,Nadine Gruaz-Gumowski,Ursula Hinz,Chantal Hulo,Rachael P. Huntley,J. James,S. Jimenez,Florence Jungo,Guillaume Keller,Kati Laiho,Duncan Legge,P Lemercier,Damien Lieberherr,Michele Magrane,Maria Jesus Martin,Patrick Masson,M. Moinat,Claire O'Donovan,Ivo Pedruzzi,Klemens Pichler,Diego Poggioli,P. Porras Millán,Sylvain Poux,Catherine Rivoire,Bernd Roechert,Tony Sawford,Maria Victoria Schneider,H. Sehra,Eleanor J Stanley,Andre Stutz,Shyamala Sundaram,Michael Tognolli,Ioannis Xenarios,Rebecca E. Foulger,Jane Lomax,Paola Roncaglia,Evelyn Camon,Varsha K. Khodiyar,Ruth C. Lovering,Philippa J. Talmud,Marcus C. Chibucos,M. Gwinn Giglio,Kara Dolinski,Sven Heinicke,Michael S. Livstone,Ralf Stephan,Midori A. Harris,Stephen G. Oliver,Kim Rutherford,Valerie Wood,Jürg Bähler,Antonia Lock,Paul J. Kersey,Mark D. McDowall,Daniel M. Staines,Melinda R. Dwinell,Mary Shimoyama,Stan Laulederkind,Tom Hayman,Shur-Jen Wang,Victoria Petri,Timothy F. Lowry,P D'Eustachio,Lisa Matthews,C. D. Amundsen,Rama Balakrishnan,Gail Binkley,J. M. Cherry,Karen R. Christie,Maria C. Costanzo,Selina S. Dwight,Stacia R. Engel,Dianna G. Fisk,Jodi E. Hirschman,Benjamin C. Hitz,Eurie L. Hong,Kalpana Karra,Cynthia J. Krieger,Stuart R. Miyasato,Robert S. Nash,Julie Park,Marek S. Skrzypek,Shuai Weng,Edith D. Wong,Tanya Z. Berardini,Dong Li,Eva Huala,Donna K. Slonim,Heather C. Wick,Paul Thomas,Juancarlos Chan,Ranjana Kishore,Paul W. Sternberg,K. Van Auken,Douglas G. Howe,Monte Westerfield +146 more
TL;DR: The Gene Ontology (GO) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies and continues to expand and improve as a result of targeted ontology development.
Journal ArticleDOI
Wikidata as a knowledge graph for the life sciences.
Andra Waagmeester,Gregory S. Stupp,Sebastian Burgstaller-Muehlbacher,Benjamin M. Good,Malachi Griffith,Obi L. Griffith,Kristina Hanspers,Henning Hermjakob,Toby S. Hudson,Kevin Hybiske,Sarah M. Keating,Magnus Manske,Michael Mayers,Daniel Mietchen,Elvira Mitraka,Alexander R. Pico,Timothy E. Putman,Anders Riutta,Núria Queralt-Rosinach,Lynn M. Schriml,Thomas Shafee,Denise Slenter,Ralf Stephan,Katherine Thornton,Ginger Tsueng,Roger Tu,Sabah Ul-Hasan,Egon Willighagen,Chunlei Wu,Andrew I. Su +29 more
TL;DR: The breadth and depth of the biomedical knowledge contained within Wikidata is described, and the open-source tools built to add information toWikidata and to synchronize it with source databases are discussed.
Journal ArticleDOI
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
Marek Ostaszewski,Anna Niarakis,Anna Niarakis,Alexander Mazein,Inna Kuperstein,Inna Kuperstein,Robert Phair,Aurelio Orta-Resendiz,Vidisha Singh,Sara Sadat Aghamiri,Marcio Luis Acencio,Enrico Glaab,Andreas Ruepp,Gisela Fobo,Corinna Montrone,Barbara Brauner,Goar Frishman,Luis Cristobal Monraz Gomez,Luis Cristobal Monraz Gomez,Julia Somers,Matti Hoch,Shailendra K. Gupta,Julia Scheel,Hanna Borlinghaus,Tobias Czauderna,Falk Schreiber,Falk Schreiber,Arnau Montagud,Miguel Ponce de Leon,Akira Funahashi,Yusuke Hiki,Noriko Hiroi,Takahiro G. Yamada,Andreas Dräger,Alina Renz,Muhammad Naveez,Muhammad Naveez,Zsolt Bocskei,Francesco Messina,Daniela Börnigen,Liam Fergusson,Marta Conti,Marius Rameil,Vanessa Nakonecnij,Jakob Vanhoefer,Leonard Schmiester,Leonard Schmiester,Muying Wang,Emily E. Ackerman,Jason E. Shoemaker,Jeremy Zucker,Kristie L. Oxford,Jeremy Teuton,Ebru Kocakaya,Gokce Yagmur Summak,Kristina Hanspers,Martina Kutmon,Susan L. Coort,Lars M. T. Eijssen,Lars M. T. Eijssen,Friederike Ehrhart,Friederike Ehrhart,D A B Rex,Denise Slenter,Marvin Martens,Nhung Pham,Robin Haw,Bijay Jassal,Lisa Matthews,M Orlic-Milacic,Andrea Senff Ribeiro,Andrea Senff Ribeiro,Karen Rothfels,Veronica Shamovsky,Ralf Stephan,Cristoffer Sevilla,Thawfeek M. Varusai,Jean-Marie Ravel,Rupsha Fraser,Vera Ortseifen,Silvia Marchesi,Piotr Gawron,Piotr Gawron,Ewa Smula,Laurent Heirendt,Venkata P. Satagopam,Guanming Wu,Anders Riutta,Martin Golebiewski,Stuart Owen,Carole Goble,Xiaoming Hu,Rupert W. Overall,Rupert W. Overall,Rupert W. Overall,Dieter Maier,Angela Bauch,Benjamin M. Gyori,John A. Bachman,Carlos Vega,Valentin Grouès,M. Vazquez,Pablo Porras,Luana Licata,Marta Iannuccelli,Francesca Sacco,Anastasia P. Nesterova,Anton Yuryev,Anita de Waard,Dénes Türei,Augustin Luna,Özgün Babur,Sylvain Soliman,Alberto Valdeolivas,Marina Esteban-Medina,Maria Peña-Chilet,Kinza Rian,Tomáš Helikar,Bhanwar Lal Puniya,Dezso Modos,Agatha Treveil,Marton Olbei,Bertrand De Meulder,Stephane Ballereau,Aurelien Dugourd,Aurelien Dugourd,Aurélien Naldi,Vincent Noël,Vincent Noël,Laurence Calzone,Laurence Calzone,Chris Sander,Emek Demir,Tamas Korcsmaros,Tom C. Freeman,Franck Augé,Jacques S. Beckmann,Jan Hasenauer,Olaf Wolkenhauer,Egon L Wilighagen,Alexander R. Pico,Chris T. Evelo,Marc Gillespie,Marc Gillespie,Lincoln Stein,Lincoln Stein,Henning Hermjakob,Peter D'Eustachio,Julio Saez-Rodriguez,Joaquín Dopazo,Alfonso Valencia,Alfonso Valencia,Hiroaki Kitano,Emmanuel Barillot,Emmanuel Barillot,Charles Auffray,Rudi Balling,Reinhard Schneider,Covid Disease Map Community +158 more
TL;DR: The COVID-19 Disease Map (C19DMap) as mentioned in this paper is a large-scale community effort to build an open access, interoperable and computable repository of COVID19 molecular mechanisms.
Posted ContentDOI
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
Marek Ostaszewski,Anna Niarakis,Anna Niarakis,Alexander Mazein,Inna Kuperstein,Inna Kuperstein,Robert Phair,Aurelio Orta-Resendiz,Aurelio Orta-Resendiz,Vidisha Singh,Sara Sadat Aghamiri,Marcio Luis Acencio,Enrico Glaab,Andreas Ruepp,Gisela Fobo,Corinna Montrone,Barbara Brauner,Goar Frishman,Julia Somers,Matti Hoch,Shailendra K. Gupta,Julia Scheel,Hanna Borlinghaus,Tobias Czauderna,Falk Schreiber,Falk Schreiber,Arnau Montagud,Miguel Ponce de Leon,Akira Funahashi,Yusuke Hiki,Noriko Hiroi,Takahiro G. Yamada,Andreas Dräger,Alina Renz,Muhammad Naveez,Muhammad Naveez,Zsolt Bocskei,Daniela Börnigen,Liam Fergusson,Marta Conti,Marius Rameil,Vanessa Nakonecnij,Jakob Vanhoefer,Leonard Schmiester,Muying Wang,Emily E. Ackerman,Jason E. Shoemaker,Jeremy Zucker,Kristie L. Oxford,Jeremy Teuton,Ebru Kocakaya,Gokce Yagmur Summak,Kristina Hanspers,Martina Kutmon,Susan L. Coort,Lars M. T. Eijssen,Lars M. T. Eijssen,Friederike Ehrhart,Friederike Ehrhart,D A B Rex,Denise Slenter,Marvin Martens,Nhung Pham,Robin Haw,Bijay Jassal,Lisa Matthews,M Orlic-Milacic,Andrea Senff-Ribeiro,Karen Rothfels,Veronica Shamovsky,Ralf Stephan,Cristoffer Sevilla,Thawfeek M. Varusai,Jean-Marie Ravel,Vera Ortseifen,Silvia Marchesi,Piotr Gawron,Piotr Gawron,Ewa Smula,Laurent Heirendt,Venkata P. Satagopam,Guanming Wu,Anders Riutta,Martin Golebiewski,Stuart Owen,Carole Goble,Xiaoming Hu,Rupert W. Overall,Rupert W. Overall,Dieter Maier,Angela Bauch,Benjamin M. Gyori,John A. Bachman,Carlos Vega,Valentin Grouès,M. Vazquez,Pablo Porras,Luana Licata,Marta Iannuccelli,Francesca Sacco,Dénes Türei,Augustin Luna,Özgün Babur,Sylvain Soliman,Alberto Valdeolivas,Marina Esteban-Medina,Maria Peña-Chilet,Kinza Rian,Tomáš Helikar,Bhanwar Lal Puniya,Anastasia P. Nesterova,Anton Yuryev,Anita de Waard,Dezso Modos,Agatha Treveil,Marton Olbei,Bertrand De Meulder,Aurélien Naldi,Aurelien Dugourd,Aurelien Dugourd,Laurence Calzone,Laurence Calzone,Chris Sander,Emek Demir,Tamas Korcsmaros,Tom C. Freeman,Franck Augé,Jacques S. Beckmann,Jan Hasenauer,Olaf Wolkenhauer,Egon Willighagen,Alexander R. Pico,Chris T. Evelo,Lincoln Stein,Henning Hermjakob,Julio Saez-Rodriguez,Joaquín Dopazo,Alfonso Valencia,Hiroaki Kitano,Emmanuel Barillot,Emmanuel Barillot,Charles Auffray,Rudi Balling,Reinhard Schneider +143 more
TL;DR: A large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the CO VID-19 Disease Map is described and the analytical and computational modelling approaches that can be applied to the contents of the COVID the Disease Map for mechanistic data interpretation and predictions are described.