Bioinformatics publications

The Pathway Tools software allows a group of scientists to create, update, and publish on the Web an evolving knowledge resource describing the genome and biochemical networks of the organism.

We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers.

MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments.

Using the completed V.cholerae genome sequence and PathoLogic software, we created VchoCyc, a pathway-genome database that predicted 171 likely metabolic pathways in the bacterium.

Different biological notions of pathways are used in different pathway databases. Those pathway ontologies significantly impact pathway computations.

In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome.

The BioWarehouse is an open source data warehousing environment focused on supporting bioinformatics databases (DBs). BioWarehouse integrates public source DBs such as Swiss-Prot and GenBank into a unified normalized schema…

We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases.

The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli.

This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways…

We report on a new type of systematic annotation error in genome and pathway databases that results from the misinterpretation of partial Enzyme Commission (EC) numbers such as ‘1.1.1.-’.