Friday, April 24, 2015

A New Curated BioCyc Database for Clostridium difficile

Peptoclostridium (Clostridium) difficile (commonly nicknamed “Cdiff”) is a spore-forming bacterium that causes serious healthcare-associated infections. In the United States alone, it is estimated that Cdiff infections were responsible for more than 29,000 deaths in 20111. Antibiotic resistance and recurrent infections are common problems in treating Cdiff infections.

The BioCyc collection currently contains twelve Clostridium/Peptoclostridium difficile databases; all of them can be easily accessed from a new home page, We chose the database for a strain commonly used in the laboratory, Peptoclostridium difficile 630, for a pilot project to update the genome annotation and to add literature curation.

Wednesday, April 15, 2015

Querying Databases by Organism Properties

The latest release (version 19.0) of BioCyc includes PGDBs for 5500 different organisms, and we expect that number to grow with every future release. With such numbers, unless you already have a specific species and strain in mind, it becomes impractical to browse through the complete list of organisms. We already allow users of the BioCyc website to select organisms specifically by name or taxonomic class. We describe here extensions to that selection process that enable users to search for organisms based on a larger set of properties of the organism, such when and where the sample was collected and what kind of environment it lives in.