GEM-Integration

This dataset is the redistribution-approved data package for the GEM-Atlas research platform. It contains harmonized tables derived from Kochanowski et al. (2021), explicit condition splits, schemas, checksums, and metadata-only source manifests.

Included values

• 16 EV3/EV4 strain-effector conditions.
• Source-derived 13C-MFA flux estimates from EV3.
• Absolute intracellular metabolite measurements from EV4.
• The separate EV2 protein series. It is not joined to EV3/EV4 because the source does not identify strain and effector for those columns.

Kochanowski source data are attributed to:

Kochanowski K, et al. Global coordination of metabolic pathways in Escherichia coli by active and passive regulation. Molecular Systems Biology 17:e10064 (2021). https://doi.org/10.15252/msb.202010064

These derived tables retain the source CC BY 4.0 license and accession metadata.

Deliberately excluded

• HeCaToS experimental values. Its BioStudies accessions are represented only by metadata, checksums, and deterministic retrieval recipes.
• Ecoli-GEM and Human-GEM model bytes. The manifests point to official pinned revisions instead.
• Atlas embedding or model tensors. They remain in their separately pinned Hub repository.
• Credentials and local cache paths.

The observation_mask column distinguishes experimentally observed values from inferred 13C-MFA values. Missing measurements remain null and are never encoded as observed zeroes.