Tier 0 · open
Corpus atlas
The honest inventory: not only what the corpus can do, but what it cannot express. Coverage gaps are reported as findings, because a gap is a research target rather than an embarrassment.
- 15,717organism models
- 1,755canonical metabolites (MetaNetX)
- 1,535median reactions per model
- 10,276openly redistributable
Sources
Models come from eight sources: published collections, automated reconstructions from genome databases, and the APOLLO-595 pan-archaeal set. Source mix is declared because it sets the floor on what any discovery result can claim.
| Source | Models | Share |
|---|---|---|
| embl_gems | 5,574 | 35% |
| AGORA2 | 4,672 | 30% |
| CarveMe | 4,326 | 28% |
| AGORA | 601 | 4% |
| APOLLO-595 | 366 | 2% |
| BiGG | 91 | 1% |
| PARADIGM | 77 | 0% |
| SysBioChalmers | 9 | 0% |
What the corpus can do
Capability is measured from model exchange reactions, not asserted from literature. The counts below show how many models can grow on a minimal defined feedstock without organic growth factors — the rest require rich media (gap-filled).
| Feedstock (defined medium) | Models that grow | Share |
|---|---|---|
| sucrose | 3,389 | 22% |
| fructose | 3,348 | 21% |
| cellobiose | 3,336 | 21% |
| arabinose | 3,252 | 21% |
| glucose | 3,131 | 20% |
| sulfate+glc | 3,058 | 19% |
| formate | 2,973 | 19% |
| syngas | 2,962 | 19% |
Anaerobic-capable:11,601 models (74%) can grow under anaerobic conditions.
Oxygen niche
| Niche | Models | Share |
|---|---|---|
| facultative | 2,294 | 15% |
| anaerobe | 1,428 | 9% |
| aerobe | 871 | 6% |
| microaerophile | 435 | 3% |
| nanaerobe | 224 | 1% |
| aerotolerant | 4 | 0% |
O2 annotation covers 5,256 of 15,717 models; the remainder have no annotation in the source metadata.
Hazard degradation capability
Models with a confirmed metabolic route to consume known environmental hazards — measured by exchange-reaction presence, not by literature curation.
| Hazard | Models with degradation route | Share |
|---|---|---|
| nitrite | 10,890 | 69% |
| benzoate | 10,096 | 64% |
| catechol | 7,584 | 48% |
| toluene | 7,541 | 48% |
| formaldehyde | 7,223 | 46% |
| cyanide | 5,295 | 34% |
| phenol | 245 | 2% |
Quality and coverage
Quality is graded by canonical-identifier coverage — how many exchange metabolites map to a MetaNetX universal ID. Full coverage (>99%) enables cross-model comparisons with no disambiguation step.
| Coverage tier | Models | Share |
|---|---|---|
| Full canonical coverage (>99%) | 10,089 | 64% |
| High coverage (>90%) | 2,863 | 18% |
| Mid coverage (>80%) | 2,590 | 16% |
| Low coverage (<80%) | 459 | 3% |
| QC gate | Models |
|---|---|
| Passed (discovery-ready) | 15,636 |
| Exploratory (draft / unverified) | 79 |
Biosafety
BSL annotation is from DSMZ / ATCC metadata where available. Models without a verified annotation are listed as unverified — a missing annotation is not an implicit BSL-1 clearance.
| Biosafety tier | Models |
|---|---|
| unverified | 7,724 |
| BSL1 | 5,133 |
| BSL2 | 2,860 |
| BSL3 | 8 |
Of 15,717 models, 1,737 carry a human-pathogen annotation. Discovery runs flag these automatically and exclude them from unsupervised proposals.
Licensing
License status is tracked at the model level. Redistributable models may be published as part of a derived corpus; link-only models require fetching from the source repository. The Data page has the full breakdown by source with citation links.
| License class | Models | Share |
|---|---|---|
| Openly redistributable | 10,276 | 65% |
| Link-only (access from source) | 5,441 | 35% |
What this corpus cannot express
Gap-filled reconstructions. Most models are auto-reconstructed with gap-filling, which adds transporters and reactions to make the model biomass-viable on rich media. This inflates apparent metabolic capacity: a gap-filled transporter is a computational assumption, not a measured fact. Discovery results are candidates, not confirmations.
Eukaryotes. The current corpus is bacteria and archaea. Plant, algal, and fungal models are in development. Rhizobia–legume nitrogen fixation is the near-term priority.
Defined-medium viability. Most models require organic growth factors that do not exist in a minimal mineral medium. Obligate cross-feeding dependencies that rely on one partner supplying these factors cannot be confirmed in situ with gap-filled models; they are confirmed instead by the thermodynamic gate on specific energy reactions.
Corpus version
- Versionv0.3.0
- Content hash3574ed92836e…
- Released2026-08-03
- Models15,717
- Redistributable10,276
- Zenodo DOIpending (see Data page)