http://precedings.nature.com/users/ba0ab426088546c5a9acf014a722fdd5/ Documents posted by Peter Deustachio Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2007.1281.1 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). http://dx.doi.org/10.1038/npre.2007.1281.1 Wed, 31 Oct 2007 21:20:37 UTC Reactome – a knowledgebase of human biological pathways doi:10.1038/npre.2007.1281.1 2009-05-07 Peter D'Eustachio Nature Precedings 2007-10-31T21:20:37Z Poster Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2009.3200.1 Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2921 human proteins, 2871 reactions and 4167 literature citations. This curated dataset is integrated with a functional interaction network assembled computationally from non-curated sources of information including protein-protein interactions, gene co-expression, and gene ontology annotations, providing access. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets.Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome’s data content and software can all be freely used and redistributed under open source terms. Reactome instances are cross-referenced to corresponding ones in databases including EntrezGene, OMIM, Ensembl, UniProt, the UCSC Genome Browser, KEGG, ChEBI, and Gene Ontology. http://dx.doi.org/10.1038/npre.2009.3200.1 Sun, 03 May 2009 15:44:21 UTC Reactome – a knowledgebase of human biological pathways doi:10.1038/npre.2009.3200.1 2009-05-07 Bijay Jassal Nature Precedings 2009-05-03T15:44:21Z Poster Chemistry Genetics & Genomics Immunology Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/