| ---
|
| pretty_name: GEM-Integration
|
| license: other
|
| language:
|
| - en
|
| tags:
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| - biology
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| - systems-biology
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| - 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.
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| - Absolute intracellular metabolite measurements from EV4.
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| - 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.
|
|
|
