---
pretty_name: GEM-Integration
license: other
language:
- en
tags:
- biology
- systems-biology
- metabolism
- flux-balance-analysis
- multi-omics
configs:
- config_name: kochanowski_conditions
  data_files:
  - split: full
    path: kochanowski_2021/conditions.parquet
- config_name: kochanowski_protein_conditions
  data_files:
  - split: full
    path: kochanowski_2021/protein_conditions.parquet
- config_name: kochanowski_flux
  data_files:
  - split: full
    path: kochanowski_2021/flux_evidence.parquet
- config_name: kochanowski_metabolites
  data_files:
  - split: full
    path: kochanowski_2021/metabolite_evidence.parquet
- config_name: kochanowski_proteins
  data_files:
  - split: full
    path: kochanowski_2021/protein_evidence.parquet
---

# 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.