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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 Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness.  ...  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

The reactome pathway knowledgebase

2019 Nucleic Acids Research  
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular  ...  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, 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 Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness.  ...  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

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 overview module allows the visualization of analysis results on a genome-wide Reactome pathway hierarchy using a single screen page.  ...  The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations  ...  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

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  
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  ...  curated pathways.  ...  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

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.  ...  The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level  ...  The development of Reactome is supported by grants R01 HG002639 from the NHGRI at the US NIH and LSHG-CT-2003-503269 from EU (6th Framework Programme) and a subcontract from the NIH-funded Cell Migration  ... 
doi:10.1142/18609475730012 fatcat:nwbnqlqzzndz5hwhe77clluvp4

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.  ...  The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level  ...  The development of Reactome is supported by grants R01 HG002639 from the NHGRI at the US NIH and LSHG-CT-2003-503269 from EU (6th Framework Programme) and a subcontract from the NIH-funded Cell Migration  ... 
doi:10.1142/1860947573_0012 fatcat:hde26m55c5hlhe26k37fu4qxvq

A case study in pathway knowledgebase verification

Stephen A Racunas, Nigam H Shah, Nina V Fedoroff
2006 BMC Bioinformatics  
We then use this logic to formulate tests for desirable properties (such as completeness, consistency, and well-formedness) for pathways stored in Reactome.  ...  We develop an explicit formal language from the language implicit in the Reactome data format and specify a logic to evaluate models expressed using this language.  ...  Acknowledgements We acknowledge the help of Geeta Joshi-Tope for explaining the Reactome data format, Imre Vastrik for explaining the working of the Reactome database, Peter D'Eustachio for explaining  ... 
doi:10.1186/1471-2105-7-196 pmid:16603083 pmcid:PMC1522024 fatcat:dabtcgogznh65lzyueasg3lmny

Installing a Local Copy of the Reactome Web Site and Knowledgebase

Sheldon J. McKay, Joel Weiser
2015 Current Protocols in Bioinformatics  
The Reactome project builds, maintains, and publishes a knowledgebase of biological pathways.  ...  The information in the knowledgebase is gathered from the experts in the field, peer reviewed, and edited by Reactome editorial staff and then published to the Reactome Web site, http:// www.reactome.org  ...  Acknowledgments The Literature Cited  ... 
doi:10.1002/0471250953.bi0910s50 pmid:26087747 pmcid:PMC4615588 fatcat:cea7j4msljhrhke7ibydeq72w4

Reactome – a knowledgebase of human biological pathways

Peter D'Eustachio, Lisa Matthews, Ewan Birney, Lincoln Stein, Esther Schmidt, Imre Vastrik, Guanming Wu, David Croft, Bernard de Bono, Gopal Gopinath, Suzanna Lewis, Marc Gillespie (+1 others)
2007 Nature Precedings  
Acknowledgements The development of Reactome is supported by a grant from the US National Institutes of Health (P41 HG003751) and a grant from the EBI Industry Programme.  ...  We also acknowledge the OrthoMCL group at the University of Pennsylvania, USA for providing orthology data.  ...  Bijay Jassal bj1@ebi.ac.uk European Bioinformatics Institute Abstract Reactome is a manually curated knowledgebase, created and peer-reviewed by experts in their field.  ... 
doi:10.1038/npre.2007.1281.1 fatcat:ux3n3qxu3zalho3t65cp4jh3mm

Reactome – a knowledgebase of human biological pathways

Bijay Jassal, Phani Garapati, Gopal Gopinath, Michael Caudy, Marc Gillespie, Alexander Kanapin, Steven Jupe, Bruce May, Gavin O'Kelly, Shahana Mahajan, Ewan Birney, Peter D'Eustachio (+7 others)
2009 Nature Precedings  
Acknowledgements The development of Reactome is supported by a grant from the US National Institutes of Health (P41 HG003751) and a grant from the EBI Industry Programme.  ...  We also acknowledge the OrthoMCL group at the University of Pennsylvania, USA for providing orthology data.  ...  Bijay Jassal bj1@ebi.ac.uk European Bioinformatics Institute Abstract Reactome is a manually curated knowledgebase, created and peer-reviewed by experts in their field.  ... 
doi:10.1038/npre.2009.3200.1 fatcat:7sazzcqf5ff3bgzjavxyi5lw2y

Reactome graph database: Efficient access to complex pathway data

Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marin-Garcia, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob, Timothée Poisot
2018 PLoS Computational Biology  
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways.  ...  Author summary To better support genome analysis, modeling, systems biology and education, we now offer our knowledgebase of biomolecular pathways as a graph database.  ...  Like most biomolecular pathway knowledgebases, Reactome has relied on a relational database to store its content.  ... 
doi:10.1371/journal.pcbi.1005968 pmid:29377902 pmcid:PMC5805351 fatcat:7znckpg5a5cnrfeekcmakdieyy

Reactome Knowledgebase of Human Biological Pathways and Processes [chapter]

Peter D'Eustachio
2010 Msphere  
ACKNOWLEDGEMENTS We are grateful to many scientists who collaborated with us as authors and reviewers to build the content of the knowledgebase, and for the helpful comments of the reviewers of this manscript  ...  Changes in the Reactome data model. These have been minimized, to facilitate data curation and use of the knowledgebase.  ...  ABSTRACT Reactome (http://www.reactome.org) is an expertauthored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook.  ... 
doi:10.1007/978-1-60761-977-2_4 pmid:21082427 fatcat:mrdugzz6zzal5e6guxopyt6dwe

Reactome knowledgebase of human biological pathways and processes

L. Matthews, G. Gopinath, M. Gillespie, M. Caudy, D. Croft, B. de Bono, P. Garapati, J. Hemish, H. Hermjakob, B. Jassal, A. Kanapin, S. Lewis (+8 others)
2009 Nucleic Acids Research  
Reactome (http://www.reactome.org) is an expertauthored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current  ...  ACKNOWLEDGEMENTS We are grateful to many scientists who collaborated with us as authors and reviewers to build the content of the knowledgebase, and for the helpful comments of the reviewers of this manscript  ...  Changes in the Reactome data model. These have been minimized, to facilitate data curation and use of the knowledgebase.  ... 
doi:10.1093/nar/gkn863 pmid:18981052 pmcid:PMC2686536 fatcat:6oo2ou6qabaexb4zwngwpgp27y

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

2019 Nucleic Acids Research  
Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project.  ...  The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR)  ...  We acknowledge Robin Haw, Joel Weiser, Guanming Wu, and Lisa Matthews from the human Reactome project and the Ontario Institute for Cancer Research for providing access to the Reactome central curation  ... 
doi:10.1093/nar/gkz996 pmid:31680153 pmcid:PMC7145600 fatcat:ykzfjhf4hvgs7keopndswr5req
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