Abstract
The Reactome Knowledgebase is an online, manually curated resource that provides an integrated view of the molecular details of human biological processes that range from metabolism to DNA replication and repair to signaling cascades. Its data model allows these diverse processes to be represented in a consistent way to facilitate usage as online text and as a resource for data mining, modeling, and analysis of large-scale expression data sets over the full range of human biological processes.
Key words
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry. J. M., et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29.
The Gene Ontology Consortium. (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38, D331–D335.
The UniProt Consortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 38, D142–D148
de Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., et al. (2010) Chemical Entities of Biological Interest: an update. Nucleic Acids Res. 38, D249–D254.
Leinonen, R., Akhtar, R., Birney, E., Bonfield, J., Bower, L., Corbett, M., et al. (2010) Improvements to services at the European Nucleotide Archive. Nucleic Acids Res. 38, D39–D45.
Li, L., Stoeckert, C. J. Jr., and Roos, D. S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189.
Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A., Huber, W. (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21, 3439–3940.
Acknowledgments
The data, data model, and data analysis tools described in this chapter are the product of the collaborative work of curators and software developers at the Ontario Institute for Cancer Research (Lincoln Stein, Michael Caudy, Marc Gillespie, Robin Haw, Bruce May, Guanming Wu), the European Bioinformatics Institute (Ewan Birney, Henning Hermjakob, David Croft, Phani Garapati, Bijay Jassal, Steven Jupe, Gavin O’Kelly, Esther Schmidt) and the NYU School of Medicine (Peter D’Eustachio, Shahana Mahajan, Lisa Matthews). We are grateful to the many scientists who collaborated with us as authors and reviewers to build the content of the knowledgebase. Grants from the National Human Genome Research Institute/NIH (P41 HG003751) and the European Union 6th Framework Programme (LSHG-CT-2005-518254 “ENFIN” support development of the Knowledgebase.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
D’Eustachio, P. (2011). Reactome Knowledgebase of Human Biological Pathways and Processes. In: Wu, C., Chen, C. (eds) Bioinformatics for Comparative Proteomics. Methods in Molecular Biology, vol 694. Humana Press. https://doi.org/10.1007/978-1-60761-977-2_4
Download citation
DOI: https://doi.org/10.1007/978-1-60761-977-2_4
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-976-5
Online ISBN: 978-1-60761-977-2
eBook Packages: Springer Protocols