Section: New Results

Representation and curation of metabolic pathways: UniPathway

UniPathway (http://www.unipathway.org ) is a manually curated database for the representation and annotation of metabolic pathways developed in collaboration with the Swiss Institute of Bioinformatics (Swiss-Prot group). UniPathway provides explicit chemical representations of enzyme-catalysed and spontaneous chemical reactions, as well as a hierarchical representation of metabolic pathways. This hierarchy uses linear subpathways as the basic building block for the assembly of larger and more complex pathways, including species-specific pathway variants. All of the pathway data in UniPathway has been extensively cross-linked to existing pathway resources such as KEGG and MetaCyc , as well as sequence resources such as the UniProt KnowledgeBase (UniProtKB ). UniPathway has been used to provide a controlled vocabulary for pathway annotation within UniProtKB records since UniProt release 14.7 (January 2009). In release 2011_08 of UniProt , UniPathway provides annotation for 118,390 distinct Swiss-Prot protein records and 783,299 TrEMBL protein records. On the UniProtKB web site, each of these records is linked to the appropriate pathway description in the UniPathway web site. In 2011, the complete description of the UniPathway database has been published in Nucleic Acids Research (Jan. 2012 Database Issue) and has been chosen by the editors of Nucleic Acids Research to appear on the Featured Articles page (top 5% of NAR papers : http://www.oxfordjournals.org/our_journals/nar/featured_articles.html ) [16] .