manifests/benchmarks.toml

# Registry metadata only. Raw data remain in their authoritative repositories.

[[sources]]
source_id = "mccloskey-2018"
title = "Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism"
primary_url = "https://doi.org/10.1038/s41467-018-06219-9"
accession = "s41467-018-06219-9"
revision = "2018-09-14"
license_id = "CC-BY-4.0"
license_verified = true
redistribution = "metadata_only"
notes = "Keep source assets remote until each supplementary file has a recorded checksum and redistribution review."

[[sources]]
source_id = "kochanowski-2021"
title = "Global coordination of metabolic pathways in Escherichia coli by active and passive regulation"
primary_url = "https://doi.org/10.15252/msb.202010064"
accession = "10.15252/msb.202010064"
revision = "2021-04-19"
license_id = "CC-BY-4.0"
license_verified = true
redistribution = "metadata_only"
notes = "Five supplementary workbooks are pinned below. Flux and metabolite conditions have explicit strain/effector keys; the ten absolute-protein limitation conditions still require a deterministic cross-modality mapping."
fully_mapped_condition_ids = []

[[artifacts]]
source_id = "kochanowski-2021"
artifact_id = "dataset-ev1"
url = "https://static-content.springer.com/esm/art%3A10.15252%2Fmsb.202010064/MediaObjects/44320_2021_BFMSB202010064_MOESM2_ESM.xlsx"
local_filename = "EV1.xlsx"
sha256 = "b873c20844964d4bc746a66f2e78668fcf69227f289cf8c0184a91036c53014a"
redistribution = "metadata_only"

[[artifacts]]
source_id = "kochanowski-2021"
artifact_id = "dataset-ev2-proteomics"
url = "https://static-content.springer.com/esm/art%3A10.15252%2Fmsb.202010064/MediaObjects/44320_2021_BFMSB202010064_MOESM3_ESM.xlsx"
local_filename = "EV2.xlsx"
sha256 = "6580db4aa14cb22a867debae877848ec94d178af809dcddecd0767606c3a07d2"
redistribution = "metadata_only"

[[artifacts]]
source_id = "kochanowski-2021"
artifact_id = "dataset-ev3-fluxes"
url = "https://static-content.springer.com/esm/art%3A10.15252%2Fmsb.202010064/MediaObjects/44320_2021_BFMSB202010064_MOESM4_ESM.xlsx"
local_filename = "EV3.xlsx"
sha256 = "7a84ead545821b75852c2b43808b64015b6567d41ec1ab1dbf99949798633486"
redistribution = "metadata_only"

[[artifacts]]
source_id = "kochanowski-2021"
artifact_id = "dataset-ev4-metabolomics"
url = "https://static-content.springer.com/esm/art%3A10.15252%2Fmsb.202010064/MediaObjects/44320_2021_BFMSB202010064_MOESM5_ESM.xlsx"
local_filename = "EV4.xlsx"
sha256 = "6d06cab98596990104c114e5a6daab186e2d2877323a707462f266824e974a71"
redistribution = "metadata_only"

[[artifacts]]
source_id = "kochanowski-2021"
artifact_id = "dataset-ev5-regulation"
url = "https://static-content.springer.com/esm/art%3A10.15252%2Fmsb.202010064/MediaObjects/44320_2021_BFMSB202010064_MOESM6_ESM.xlsx"
local_filename = "EV5.xlsx"
sha256 = "7242847200852886268076d9a765cd22c20221f3ef98d0e189be97cd5e1dd7b6"
redistribution = "metadata_only"

[kochanowski_condition_harmonization]
flux_metabolite_condition_count = 16
absolute_protein_condition_count = 10
joinable_modalities = ["13c_mfa_flux", "absolute_intracellular_metabolite"]
excluded_modalities = ["protein_spectral_count"]
flux_metabolite_condition_ids = [
  "kochanowski-2021|catabolic|NCM3722|3-MBA|0uM",
  "kochanowski-2021|catabolic|NCM3722|3-MBA|400uM",
  "kochanowski-2021|catabolic|NQ1243|3-MBA|400uM",
  "kochanowski-2021|catabolic|NQ1243|3-MBA|100uM",
  "kochanowski-2021|catabolic|NQ1243|3-MBA|0uM",
  "kochanowski-2021|catabolic|NQ1390|3-MBA|400uM",
  "kochanowski-2021|catabolic|NQ1390|3-MBA|100uM",
  "kochanowski-2021|catabolic|NQ1390|3-MBA|40uM",
  "kochanowski-2021|anabolic|NCM3722|IPTG|0uM",
  "kochanowski-2021|anabolic|NCM3722|IPTG|100uM",
  "kochanowski-2021|anabolic|NQ393|IPTG|100uM",
  "kochanowski-2021|anabolic|NQ393|IPTG|50uM",
  "kochanowski-2021|anabolic|NQ393|IPTG|40uM",
  "kochanowski-2021|anabolic|NQ393|IPTG|30uM",
  "kochanowski-2021|anabolic|NQ393|IPTG|20uM",
  "kochanowski-2021|anabolic|NQ393|IPTG|10uM",
]
fully_mapped_condition_ids = []
status = "blocked"
reason = "EV2 limitation conditions are labeled by growth rate while EV3 and EV4 use strain and effector concentration; an explicit source-backed mapping has not been validated."

[[sources]]
source_id = "ishii-2007"
title = "Multiple high-throughput analyses monitor the response of E. coli to perturbations"
primary_url = "https://doi.org/10.1126/science.1132067"
accession = "10.1126/science.1132067"
revision = "2007-03-02"
license_id = "custom-restricted"
license_verified = true
redistribution = "restricted"
notes = "Source-local legacy benchmark; do not redistribute."

[[sources]]
source_id = "hecatos"
title = "HeCaToS toxicogenomics project"
primary_url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC9663581/"
accession = "PMC9663581"
revision = "2022-11-17"
license_id = "EMBL-EBI-Terms-of-Use"
license_verified = true
redistribution = "metadata_only"
notes = "The descriptor article is CC-BY-4.0. The older BioStudies records have no accession-level license field and remain subject to EMBL-EBI Terms of Use. APAPII provides condition-matched processed RNA, protein, and ATP measurements."

[[artifacts]]
source_id = "hecatos"
artifact_id = "apapii-transcriptomics-rlog"
accession = "S-HECA259"
url = "https://www.ebi.ac.uk/biostudies/files/S-HECA259/u/genomics-data/RNA-Seq_Analysis_Hepatic_MaSigPro_Genedata/Results_Hecatos_Hepatic_01DMSO_APAP_MaSigPro_rlog/Hecatos_Hepat_01DMSO_APAP_rlog.csv"
local_filename = "Hecatos_APAP_rlog.csv"
sha256 = "7363f28bac922cbef95d18d1a7cca47f48061d361b751b8786b61f110208d447"
redistribution = "metadata_only"

[[artifacts]]
source_id = "hecatos"
artifact_id = "apapii-transcriptomics-samples"
accession = "S-HECA259"
url = "https://www.ebi.ac.uk/biostudies/files/S-HECA259/u/genomics-data/RNA-Seq_Analysis_Hepatic_MaSigPro_Genedata/Results_Hecatos_Hepatic_01DMSO_APAP_MaSigPro_rlog/Hecatos_Hepat_01DMSO_APAP_SampleAnnot.csv"
local_filename = "Hecatos_APAP_RNA_SampleAnnot.csv"
sha256 = "5f8de56bd7eb6bd4868c46bc4b2bdea659fd1d87ec4929f8b07c504b89ed2d6e"
redistribution = "metadata_only"

[[artifacts]]
source_id = "hecatos"
artifact_id = "apapii-proteomics-log2"
accession = "S-HECA292"
url = "https://www.ebi.ac.uk/biostudies/files/S-HECA292/u/proteomics-data/Proteomics_Analysis_Hepatic_FC_TxvsT0_revised_workflow_Genedata/Results_Hecatos_Hepatic_Px_APAP_FC/Hepatic_APAP_log2_norm.txt"
local_filename = "Hepatic_APAP_protein_log2_norm.txt"
sha256 = "218b67dda6df63d6fedc4951bce1a7650dd391aa44a2bbe174b57f48891a24a2"
redistribution = "metadata_only"

[[artifacts]]
source_id = "hecatos"
artifact_id = "apapii-proteomics-samples"
accession = "S-HECA292"
url = "https://www.ebi.ac.uk/biostudies/files/S-HECA292/u/proteomics-data/Proteomics_Analysis_Hepatic_FC_TxvsT0_revised_workflow_Genedata/Results_Hecatos_Hepatic_Px_APAP_FC/Hepatic_APAP_SampleAnnot.txt"
local_filename = "Hepatic_APAP_protein_SampleAnnot.txt"
sha256 = "5122cc93e20eaea1f5679d88e34bcb998c397617b6c868e493a291f2d26ba5d1"
redistribution = "metadata_only"

[[artifacts]]
source_id = "hecatos"
artifact_id = "apapii-atp"
accession = "S-HECA8"
url = "https://www.ebi.ac.uk/biostudies/files/S-HECA8/Roche-sample-list/18OC002_ACETAMINOPHEN_ATP%20measurements.xlsx"
local_filename = "APAPII_ATP.xlsx"
sha256 = "48170fc6cc1040728c8323929526b4260b7d5c7592d75c4c35350ec7f716ee62"
redistribution = "metadata_only"

[hecatos_apapii_condition_harmonization]
condition_count = 10
primary_benchmark_condition_count = 9
training_condition_count = 7
heldout_condition_count = 2
joined_modalities = ["transcriptomics", "proteomics", "atp"]
training_condition_ids = [
  "apap_baseline_000h",
  "apap_therapeutic_024h",
  "apap_toxic_024h",
  "apap_therapeutic_072h",
  "apap_toxic_072h",
  "apap_therapeutic_168h",
  "apap_toxic_168h",
]
heldout_condition_ids = ["apap_therapeutic_240h", "apap_toxic_240h"]
excluded_condition_ids = ["apap_therapeutic_336h"]
split_method = "time-blocked test at T240 for both therapeutic and toxic doses; unpaired T336 excluded"
endpoint_limit = "ATP is a measured viability/metabolic phenotype, not a direct steady-state flux. A model-to-ATP observation map is required before reporting GEM predictive RMSE."

[[sources]]
source_id = "nci-60"
title = "NCI-60 multi-omics and exchange benchmark"
primary_url = "https://discover.nci.nih.gov/cellminer/"
accession = "CellMiner-NCI-60"
revision = "unresolved"
license_id = "unresolved"
license_verified = false
redistribution = "unresolved"
notes = "Omics campaigns are not condition-matched; resolve exact releases and terms before use."