http://precedings.nature.com/tags/BioPax Recently posted documents tagged with 'BioPax' 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.2007.1311.1 The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely availablecollection of curated and peer-reviewed signaling pathways composed of humanbiomolecular interactions and cellular processes. Created in a collaboration between theU.S. National Cancer Institute and Nature Publishing Group, the database is a researchtool for cell biologists, biochemists, computational biologists and bioinformaticians.The PID offers a range of tools to facilitate pathway exploration. Users can browse thepre-defi ned set of pathways and also create interaction network maps centered ona single molecule of interest or an extensive list of molecules. In addition, users candownload complete data sets in extensible markup language (XML) and BiologicalPathway Exchange (BioPAX) Level 2 formats. The database is updated every month andsupplemented by a concise editorial section that provides synopses of recent noteworthypapers in cell signaling and specially commissioned articles on the practical uses ofother relevant online tools. Users can sign up for free email alerts or RSS feeds to receivedatabase updates. http://dx.doi.org/10.1038/npre.2007.1311.1 Mon, 12 Nov 2007 16:51:55 UTC The NCI-Nature Pathway Interaction Database: A cell signaling resource. doi:10.1038/npre.2007.1311.1 2007-11-12 Kira Anthony Nature Precedings 2007-11-12T16:51:55Z Poster Cancer Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ 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/