Download Microme Data
Note: we will soon provide additional downloads, e.g. draft metabolic networks and models for a selection of species in release 2 dataset.
- genome-protein-reaction associations for ~3K organisms (bacteria/archaea)
- an initial set of 10 tested constraint-based models
- reactome data (24 bacterial species)
Release 1.0: reactome data (24 bacterial species)
Download data about the genome-protein-reaction associations inferred for thousands of genomes (bacteria and archaea):
- Flat file dumps of the database in tab-delimeted format
- JSON dumps of the database
The database can also be accessed programmatically or by using a MySQL client. For more details, go to the FTP site.
A number of downloads are available for the reactions and pathways of the 24 priority species:
- Events (reactions and pathways) in BioPax Level 2 and 3 format
- Events (reactions) in SBML level 2 format
- UniProt to pathway mappings
- Protein-protein interaction data (PSI-MITAB and tab-delimited)
- MySQL dumps of the whole knowledge-base, for local installation
A number of downloads are available for the genomic sequences of the 24 priority species:
- FASTA sequence databases of Ensembl gene, transcript and protein model predictions
- Flat files for more extensive sequence annotation
- MySQL dumps of the Ensembl Bacteria databases
- Gene sets for each species (GTF), including annotations of both coding and non-coding genes
- EMF flatfile dumps (variation and comparative data)
The database can also be accessed programmatically, using the Ensembl API. For more details, look at the API documentation page.