Reactome - A knowledgebase of biological pathways

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; Guanming Wu

doi:10.1007/11915034_95

Reactome - A knowledgebase of biological pathways

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, Guanming Wu

Research output: Contribution to journal › Conference article › peer-review

5 Scopus citations

Abstract

Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format. The data is provided by experts in the field and subject to a peer review process. The core unit of the Reactome data model is the reaction. The entities participating in reactions form a network of biological interactions. Reactions are grouped into pathways. Reactome data are cross-referenced to a wide selection of publically available databases (such as UniProt, Ensembl, GO, PubMed), facilitating overall integration of biological data. In addition to the manually curated, mainly human reactions, electronically inferred reactions to a wide range of other species, are presented on the website. All Reactome reactions are displayed as arrows on a Reactionmap. The Skypainter tool allows visualisation of user-supplied data by colouring the Reactionmap. Reactome data are freely available and can be downloaded in a number of formats.

Original language	English (US)
Pages (from-to)	710-719
Number of pages	10
Journal	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4277 LNCS - I
DOIs	https://doi.org/10.1007/11915034_95
State	Published - 2006
Externally published	Yes
Event	OTM 2006 Workshops - OTM Confederated International Workshops - Montpellier, France Duration: Oct 29 2006 → Nov 3 2006

Keywords

Biological processes
Knowledgebase
Pathways

ASJC Scopus subject areas

Theoretical Computer Science
Computer Science(all)

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10.1007/11915034_95

Cite this

Schmidt, E., Birney, E., Croft, D., De Bono, B., D'Eustachio, P., Gillespie, M., Gopinath, G., Jassal, B., Lewis, S., Matthews, L., Stein, L., Vastrik, I., & Wu, G. (2006). Reactome - A knowledgebase of biological pathways. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4277 LNCS - I, 710-719. https://doi.org/10.1007/11915034_95

Schmidt, E, Birney, E, Croft, D, De Bono, B, D'Eustachio, P, Gillespie, M, Gopinath, G, Jassal, B, Lewis, S, Matthews, L, Stein, L, Vastrik, I & Wu, G 2006, 'Reactome - A knowledgebase of biological pathways', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4277 LNCS - I, pp. 710-719. https://doi.org/10.1007/11915034_95

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abstract = "Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format. The data is provided by experts in the field and subject to a peer review process. The core unit of the Reactome data model is the reaction. The entities participating in reactions form a network of biological interactions. Reactions are grouped into pathways. Reactome data are cross-referenced to a wide selection of publically available databases (such as UniProt, Ensembl, GO, PubMed), facilitating overall integration of biological data. In addition to the manually curated, mainly human reactions, electronically inferred reactions to a wide range of other species, are presented on the website. All Reactome reactions are displayed as arrows on a Reactionmap. The Skypainter tool allows visualisation of user-supplied data by colouring the Reactionmap. Reactome data are freely available and can be downloaded in a number of formats.",

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author = "Esther Schmidt and Ewan Birney and David Croft and {De Bono}, Bernard and Peter D'Eustachio and Marc Gillespie and Gopal Gopinath and Bijay Jassal and Suzanna Lewis and Lisa Matthews and Lincoln Stein and Imre Vastrik and Guanming Wu",

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AU - Schmidt, Esther

AU - Birney, Ewan

AU - Croft, David

AU - De Bono, Bernard

AU - D'Eustachio, Peter

AU - Gillespie, Marc

AU - Gopinath, Gopal

AU - Jassal, Bijay

AU - Lewis, Suzanna

AU - Matthews, Lisa

AU - Stein, Lincoln

AU - Vastrik, Imre

AU - Wu, Guanming

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N2 - Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format. The data is provided by experts in the field and subject to a peer review process. The core unit of the Reactome data model is the reaction. The entities participating in reactions form a network of biological interactions. Reactions are grouped into pathways. Reactome data are cross-referenced to a wide selection of publically available databases (such as UniProt, Ensembl, GO, PubMed), facilitating overall integration of biological data. In addition to the manually curated, mainly human reactions, electronically inferred reactions to a wide range of other species, are presented on the website. All Reactome reactions are displayed as arrows on a Reactionmap. The Skypainter tool allows visualisation of user-supplied data by colouring the Reactionmap. Reactome data are freely available and can be downloaded in a number of formats.

AB - Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format. The data is provided by experts in the field and subject to a peer review process. The core unit of the Reactome data model is the reaction. The entities participating in reactions form a network of biological interactions. Reactions are grouped into pathways. Reactome data are cross-referenced to a wide selection of publically available databases (such as UniProt, Ensembl, GO, PubMed), facilitating overall integration of biological data. In addition to the manually curated, mainly human reactions, electronically inferred reactions to a wide range of other species, are presented on the website. All Reactome reactions are displayed as arrows on a Reactionmap. The Skypainter tool allows visualisation of user-supplied data by colouring the Reactionmap. Reactome data are freely available and can be downloaded in a number of formats.

KW - Biological processes

KW - Knowledgebase

KW - Pathways

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Y2 - 29 October 2006 through 3 November 2006

ER -

Reactome - A knowledgebase of biological pathways

Abstract

Keywords

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