Microme is a resource for bacterial metabolism, whose aim is to support the large scale inference of metabolic flux directly from genome sequence. It is populated with data generated by direct import from external sources and by automatic inference from these seed data onto additional genomes; 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.
Microme also provides an infrastructure for the integration of a curated repository of reference pathways and reactions, genome-scale constraint-based models, and downstream applications in comparative genomics and biotechnology.
Microme and Ensembl Bacteria
Microme data is integrated into the Ensembl Bacteria dataset through the inclusion of data from its pathway-reaction data matrix. Pathway data is generated from information provided by EcoCyc and MetaCyc. The reactions in those pathways are correlated with reaction information from the Rhea reaction database, and associated with reaction catalysts from the UniProt Knowledgebase.
Since each of these UniProtKB proteins also corresponds to a translation in the Ensembl Bacteria dataset, this allows the source references from Rhea, MetaCyc, and other sources to be added to the "External references" detail of the corresponding transcripts. For example, see the Rhea and MetaCyc identifiers listed for hcaD-1 on E. coli K-12.
The Microme reaction matrix is rebuilt in tandem with the Ensembl Bacteria release cycle, allowing for updated cross references to be added to each new release.
MICROME is an EU Framework Programme 7 Collaborative Project. Grant Agreement Number 222886-2