Database Constraints Applied to Metabolic Pathway Reconstruction Tools

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly iden...

The MetaCyc Metabolic Pathway Database

MetaCyc is a metabolic-pathway database (DB) that describes 445 pathways and 1115 enzymes occurring in 158 organisms. As a general reference source on metabolic pathways, MetaCyc serves several purposes in metabolic engineering. It provides an encyclopedic listing of enzymes and their properties to allow a metabolic engineer to find an enzyme whose characteristics solve an engineering problem a...

MetaboDB: a database for metabolic reconstruction

In silico metabolic reconstruction consists of deducing strain-specific metabolic pathways and other cellular characteristics only from the whole genome sequence. This task depends directly on: (i) the quality of the annotations to manage mining for enzymes in genomic data and (ii) the accurate description of metabolic pathways to be reconstructed. Here we present MetaboDB, a relational databas...

Parsing Tools Applied to ELANM

Screening Tools for Data Quality and Outlier Detection Applied to the Airbase Ambient Air Pollution Database

Systematic collection of long term mesoto large-scale datasets of ambient air quality provides an indispensible means for air pollution monitoring. However, the quality of these monitoring data depends on the chosen method of measurements and the QA/QC procedures applied. We present a consolidated screening tool for the automatic detection of outliers in large data volume air quality monitoring...