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.

Release 2.x:

• 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)

Reaction Matrix

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.

The bacterial Reactome Knowledge-base

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

You can also access the DB programatically. For more details, read about the Reactome Web Services. See also the pathway browser download page.

Ensembl Bacteria

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.