Reactome launched - Bioinformatics.org

Geeta Joshi-Tope • June 4, 2004

Reactome launched

Today, we have launched Reactome, a curated database of biological processes in humans. This database, available at http://www.reactome.org is a dual-purpose project that can be used by the general biologist as an online textbook of biology, or by a bioinformaticist to make discoveries about biological pathways. This project is a NIH-funded collaboration between Lincoln Stein's laboratory at Cold Spring Harbor Laboratory, NY, and Ewan Birney's laboratory at the European Bioinformatics Institute, Hinxton, England.

The basic information in the Reactome database is provided by bench biologists who are experts in that domain of biology. The information is then managed by groups of curators at CSHL and EBI, peer-reviewed by other researchers and published on the web. It covers biological pathways ranging from the basic processes of metabolism to high-level processes such as hormonal signaling. While Reactome is targeted at human pathways, it also includes many individual biochemical reactions from non-human systems such as rat, mouse, puffer fish and zebra fish. This makes the database relevant to the large number of researchers who work on model organisms. All the information in Reactome is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity.

Reactome supersedes an earlier project called The Genome Knowledgebase and incorporates all the information previously available in its predecessor. Reactome sports a radically redesigned user interface in which the entire set of human pathways known to the database are represented as a series of constellations in a "starry sky." The starry sky can be used to navigate through the universe of human reactions and is invaluable to visualize connections between pathways, some of which will be surprising to biologists who are not familiar with pathways outside their domain of research. Reactome cross-references the online databases PubMed, SwissProt, LocusLink, Ensembl, and the Gene Ontology.

Since the first release of The Genome Knowledgebase a year ago, this project has covered the important topics of the mitotic cell cycle and its checkpoints, five different pathways for DNA Repair, DNA replication, metabolism of sugars, amino acids, lipids, and nucleotides, the tricarboxylic acid cycle, the central dogma comprising the transcription of coding genes, processing of mRNA and translation to proteins. Future releases, which occur at roughly quarterly intervals will include apoptosis, synaptic transmission, hemostasis, and hematopoeisis. Reactome covers almost 1000 proteins, which covers a substantial portion of human proteins in the SwissProt Database (UniProt).

The Reactome data and software are distributed under an open source license that allows for unrestricted reuse and redistribution. Author contributions to Reactome are citable, and we encourage the biology community to link to it.

Reactome gratefully acknowledges support from the National Human Genome Research Institute (NHGRI) and the Cell Migration Consortium (CMC) for their grant support, European Union Project Grant and the EBI Industry Program.

Discussion forums: Reactome launched

Expanded view | Monitor forum | Save place

Start a new thread:

You have to be to post a reply.