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Reactome: a database of reactions, pathways and biological processes

D. Croft, G. O'Kelly, G. Wu, R. Haw, M. Gillespie, L. Matthews, M. Caudy, P. Garapati, G. Gopinath, B. Jassal, S. Jupe, I. Kalatskaya (+10 others)
2010 Nucleic Acids Research  
Reactome (http://www.reactome.org) is a collaboration among groups at the  ...  Development of the Reactome data model and fly and chicken databases is a collaborative project and this work benefited greatly from our interactions with Carl Schmidt, Mark Williams and Michael Ashburner  ...  ACKNOWLEDGEMENTS We are grateful to the many researchers who have volunteered to be external authors and reviewers.  ... 
doi:10.1093/nar/gkq1018 pmid:21067998 pmcid:PMC3013646 fatcat:yu7wdrauubeyji53uzmbqjmz5m

The Reactome BioMart

R. A. Haw, D. Croft, C. K. Yung, N. Ndegwa, P. D'Eustachio, H. Hermjakob, L. D. Stein
2011 Database: The Journal of Biological Databases and Curation  
Reactome is an open source, expert-authored, manually curated and peer-reviewed database of reactions, pathways and biological processes.  ...  The Reactome BioMart provides biologists and bioinformaticians with a single web interface for performing simple or elaborate queries of the Reactome database, aggregating data from different sources and  ...  Acknowledgements Development of the Reactome website, data model and data analysis tools described in this article is a result of concerted work of the Reactome curators and developers.  ... 
doi:10.1093/database/bar031 pmid:22012987 pmcid:PMC3197281 fatcat:7j3z3tpj55fvpnricsucwuxm2m

The Reactome pathway knowledgebase

David Croft, Antonio Fabregat Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani Garapati, Marc Gillespie, Maulik R. Kamdar, Bijay Jassal, Steven Jupe (+11 others)
2013 Nucleic Acids Research  
Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions.  ...  The data model has been extended to support annotation of disease processes due to infectious agents and to mutation.  ...  ACKNOWLEDGEMENTS The authors are grateful to the many expert scientists who have collaborated with us as external authors and reviewers of Reactome content.  ... 
doi:10.1093/nar/gkt1102 pmid:24243840 pmcid:PMC3965010 fatcat:k6erba6xa5htfn3zzadwhk3cme

Reactome enhanced pathway visualization

Konstantinos Sidiropoulos, Guilherme Viteri, Cristoffer Sevilla, Steve Jupe, Marissa Webber, Marija Orlic-Milacic, Bijay Jassal, Bruce May, Veronica Shamovsky, Corina Duenas, Karen Rothfels, Lisa Matthews (+8 others)
2017 Bioinformatics  
Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways.  ...  Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed  ...  The basic unit of a pathway database is a reaction in which molecules are transformed.  ... 
doi:10.1093/bioinformatics/btx441 pmid:29077811 pmcid:PMC5860170 fatcat:ypdq4ibaandhnbs6ysoegcgab4

The Reactome Pathway Knowledgebase

Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas Roca (+11 others)
2017 Nucleic Acids Research  
Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions.  ...  The data model has been extended to support annotation of disease processes due to infectious agents and to mutation.  ...  ACKNOWLEDGEMENTS The authors are grateful to the many expert scientists who have collaborated with us as external authors and reviewers of Reactome content.  ... 
doi:10.1093/nar/gkx1132 pmid:29145629 pmcid:PMC5753187 fatcat:2br73vnp4fbhbc3xlejyjmvyh4

The reactome pathway knowledgebase

2019 Nucleic Acids Research  
Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells  ...  data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.  ...  ACKNOWLEDGEMENTS We are grateful to the more than 800 expert scientists who have collaborated with us as external authors and reviewers of Reactome content since 2002.  ... 
doi:10.1093/nar/gkz1031 pmid:31691815 pmcid:PMC7145712 fatcat:5wzwts2srbcftp2pihewasxchq

The Reactome pathway Knowledgebase

Antonio Fabregat, Konstantinos Sidiropoulos, Phani Garapati, Marc Gillespie, Kerstin Hausmann, Robin Haw, Bijay Jassal, Steven Jupe, Florian Korninger, Sheldon McKay, Lisa Matthews, Bruce May (+10 others)
2015 Nucleic Acids Research  
A new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions.  ...  Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation catalogues  ...  ACKNOWLEDGEMENT We are grateful to Ewan Birney for his advice and support, and to the many expert scientists who have collaborated with us as external authors and reviewers of Reactome content.  ... 
doi:10.1093/nar/gkv1351 pmid:26656494 pmcid:PMC4702931 fatcat:ikxhcsslzrfeziyzq2p6qadvay

REACTOME: A KNOWLEDGEBASE OF BIOLOGICAL PATHWAYS

Lincoln Stein, Peter D'Eustachio, Gopal Gopinathrao, Marc Gillespie, Lisa Matthews, Guanming Wu, Imre Vastrik, Esther Schmidt, Bernard de Bono, Bijay Jassal, David Croft, Ewan Birney (+1 others)
2006 Computational Systems Bioinformatics  
The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways.  ...  Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes.  ...  ACKNOWLEDGEMENTS We are grateful to our external authors and peer-reviewers who help us to maintain a high quality of data in Reactome.  ... 
doi:10.1142/9781860947575_0009 fatcat:yk445f4ienairev4uebdmrgaca

Reactome: a knowledgebase of biological pathways

G. Joshi-Tope
2004 Nucleic Acids Research  
The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways.  ...  Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes.  ...  ACKNOWLEDGEMENTS We are grateful to our external authors and peer-reviewers who help us to maintain a high quality of data in Reactome.  ... 
doi:10.1093/nar/gki072 pmid:15608231 pmcid:PMC540026 fatcat:uboftol32jaqrdsrk4i2kiiqku

REACTOME: A KNOWLEDGEBASE OF BIOLOGICAL PATHWAYS

Lincoln Stein, Peter D'Eustachio, Gopal Gopinathrao, Marc Gillespie, Lisa Matthews, Guanming Wu, Imre Vastrik, Esther Schmidt, Bernard de Bono, Bijay Jassal, David Croft, Ewan Birney (+1 others)
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways.  ...  Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes.  ...  ACKNOWLEDGEMENTS We are grateful to our external authors and peer-reviewers who help us to maintain a high quality of data in Reactome.  ... 
doi:10.1142/1860947573_0012 fatcat:hde26m55c5hlhe26k37fu4qxvq

Reactome: A database of biological pathways

David Croft, David Croft
2010 Nature Precedings  
Where Reactome's Data Comes From• Expert and curator create outline of new pathway • Expert fills in details • Curator enters information into database • Reviewer (another expert) checks biological correctness  ...  are trying to capture are reactions and pathways • Re-branded as Reactome June 2004 27.02.08 3 Reactome Data Model Events: • ReactionsPathways Entities: • Proteins • Complexes • Small  ... 
doi:10.1038/npre.2010.5025.1 fatcat:dld4g3orhjcwzjxdygyzukulda

The reactome pathway knowledgebase 2022

Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai (+23 others)
2021 Nucleic Acids Research  
Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic  ...  The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans  ...  ACKNOWLEDGEMENTS We are grateful to the more than 800 expert scientists who have collaborated with us as external authors and reviewers of Reactome content since 2002.  ... 
doi:10.1093/nar/gkab1028 pmid:34788843 pmcid:PMC8689983 fatcat:gszsloaqnffptgjwf32yaieq3q

Reactome – A Knowledgebase of Biological Pathways [chapter]

Esther Schmidt, Ewan Birney, David Croft, Bernard de Bono, Peter D'Eustachio, Marc Gillespie, Gopal Gopinath, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Lincoln Stein, Imre Vastrik (+1 others)
2006 Lecture Notes in Computer Science  
The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways.  ...  Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes.  ...  ACKNOWLEDGEMENTS We are grateful to our external authors and peer-reviewers who help us to maintain a high quality of data in Reactome.  ... 
doi:10.1007/11915034_95 fatcat:mhi75mdnrzhddiaccuq6viyebq

REACTOME: A KNOWLEDGEBASE OF BIOLOGICAL PATHWAYS

Lincoln Stein, Peter D'Eustachio, Gopal Gopinathrao, Marc Gillespie, Lisa Matthews, Guanming Wu, Imre Vastrik, Esther Schmidt, Bernard de Bono, Bijay Jassal, David Croft, Ewan Birney (+1 others)
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways.  ...  Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes.  ...  ACKNOWLEDGEMENTS We are grateful to our external authors and peer-reviewers who help us to maintain a high quality of data in Reactome.  ... 
doi:10.1142/18609475730012 fatcat:nwbnqlqzzndz5hwhe77clluvp4

Reactome Pengine: a web-logic API to the Homo sapiens reactome

Samuel R Neaves, Sophia Tsoka, Louise A C Millard, Oliver Stegle
2018 Bioinformatics  
Full terms of use are available: Abstract Summary: Existing ways of accessing data from the Reactome database are limited.  ...  Reactome Pengine is a web service providing a logic programming-based API to the human reactome.  ...  Introduction Reactome (Fabregat et al., 2016) is a web service that includes a database of the molecular details of cellular processes and is a leading tool for bioinformaticans working with biological  ... 
doi:10.1093/bioinformatics/bty181 pmid:29617950 pmcid:PMC6084589 fatcat:suo5ixv3yfbgfpygzcycd57ene
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