3 votes

Reactome – a knowledgebase of human biological pathways

Peter D’Eustachio¹, David Croft², Bernard de Bono², Gopal Gopinath³, Marc Gillespie⁴, Bijay Jassal², Lisa Matthews³, Esther Schmidt², Imre Vastrik², Guanming Wu³, Suzanna Lewis⁵, Ewan Birney² & Lincoln Stein³

Correspondence: (Login to view email address)

1. NYU School of Medicine - Biochemistry
2. European Bioinformatics Institute
3. Cold Spring Harbor Laboratory
4. Cold Spring Harbor Laboratory and St. John's University
5. Lawrence Berkeley National Laboratory

PDF (1.7 MB)

Document Type:

Poster

Date:

Received 30 October 2007 20:56 UTC; Posted 31 October 2007

Subjects:

Molecular Cell Biology, Bioinformatics

Tags:

• BioPax
• SBML
• pathway
• curation

Abstract:

Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is a manually curated human pathway knowledgebase describing a wide range of biological processes in a computationally accessible manner. The core unit of the Reactome data model is the Reaction, whose instances form a network of biological interactions through entities that are consumed, produced, or act as catalysts. Entities are distinguished by their molecular identities and cellular locations. Set objects allow grouping of related entities. Curation is based on communication between expert authors and staff curators, facilitated by freely available data entry tools. Manually curated data are subjected to quality control and peer review by a second expert. Reactome data are released quarterly. At release time, electronic orthology inference performed on human data produces reaction predictions in 22 species ranging from mouse to bacteria. Cross-references to a large number of publicly available databases are attached, providing multiple entry points into the database. The Reactome Mart allows query submission and data retrieval from Reactome and across other databases. The SkyPainter tool provides visualization and statistical analysis of user supplied data, e.g. from microarray experiments. Reactome data are freely available in a number of data formats (e.g. BioPax, SBML).

Presented at:

2nd International Biocuration Meeting, 25 October 2007

Discussion

Votes:

3 votes

(Login to vote)

Comments:

0 comments

(Login to post a comment)

Share:

(Login to share with a colleague)

Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 2.5 License

How to cite this document:

D’Eustachio, Peter, Croft, David, de Bono, Bernard, Gopinath, Gopal, Gillespie, Marc, Jassal, Bijay, Matthews, Lisa, Schmidt, Esther, Vastrik, Imre, Wu, Guanming, Lewis, Suzanna, Birney, Ewan, and Stein, Lincoln. Reactome – a knowledgebase of human biological pathways. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2007.1281.1> (2007)

Version info:

Other versions of this document in Nature Precedings

None.

Other versions of this document elsewhere on the web

None known.

Submit a new version link