Datasets:

lhallee
/

GEM-Integration

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.