Microme is a resource for bacterial metabolism and aims to support the large scale inference of metabolic flux directly from genome sequence. Microme includes integrated data from external sources and also projected data generated through the automatic inference of reference species onto additional genomes. The data is subject to quality assurance (i.e. for chemical balance, consistency of cross-references, and ultimately, for their ability to define a viable model mathematically and their consistency with experimental evidence), and revised manually as appropriate.

Data Integration

The first release integrates reactions and pathways for Escherichia coli K-12, combining data from the EcoCyc database with reactions derived from the metabolic model of iAF1260, Feist AM et al. The two reaction sets have been matched and integrated, corrected for errors and discrepencies and cross-referenced to other resources including  ChEBI, the dictionary of molecular entitites, and Rhea, the database of annotated reactions.

Projection

Once the integrated pathways and reactions are reviewed, a projection process is initiated to infer pathways and reaction in target species. Homologies between gene projects, used to support the inference, are constructed using the Ensembl Gene Trees algorithm, Vilella et al.

Genome sequence and annotations are available through a genome browser, using the Ensembl software platform. Reference and projected pathways can be viewed through a pathway browser, utlisizing the Reactome software infrastructure.

More information on the project's details are available here.