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Computational infrastructure for human biology.
Built from evidence.Designed to reason.
Biomedical knowledge is fragmented across papers, databases, models and ontologies. Catalyst is assembling a provenance-aware knowledge graph that turns literature into structured evidence today, and is building toward a research engine for computable mechanisms, followed by dynamic simulation and quantitative predictions. Every finding retains its source and study context; model-generated hypotheses and predictions will remain distinct from reported evidence.
One finding
Zn(2+) decreases Diarrhoea duration
“Twenty-four trials reported on the duration of diarrhoea, and the associated meta-analysis suggested that the duration of diarrhoea decreased significantly in the zinc group as compared to no zinc/placebo group (MD = −13.27 hours; 95% CI = −17.66, −8.89; 24 trials, 6249 participants, moderate certainty of evidence).”
Three readings of the same paths: from a substance, from a result, or from a place in the body.
What the literature reports, where it goes, and the molecule itself.
A measured endpoint, and everything reported to move it.
Where the graph reaches, and what has a transporter route there.
Every node is keyed by an external ontology. No serial integers, no internal names.
Every edge is one of 31 relations, and no others exist. That is what lets two compounds be compared instead of merely described.
Declared, not yet used
The vocabulary is fixed before the evidence arrives, not extended to fit it.
Evidence strength is derived from the study behind the claim, not asserted by whoever wrote it. These are the inputs it is derived from.
Strong
Randomised human trials or their synthesis, with the effect's size and interval recorded and no recorded weakness outstanding
Moderate
Human evidence with one recorded weakness, or capped at moderate by its design or by unread numbers
Limited
Human evidence with several recorded weaknesses, or a design that tops out at limited
Very limited
Human evidence with major recorded weaknesses, or non-human, uncontrolled or unverified evidence
Insufficient
Mechanistic inference, no evidence found, or evidence weakened below very limited
The two channels are independent. Evidence strength is drawn as line weight, opacity and dash; class is drawn as shape. Neither is a colour, so both survive greyscale. The full key.
Read it, query it, or take it. The same rows at every door, each with its paper and its quoted span on it.
A summary written for a model rather than a person: what the graph holds, what the counts mean, and which of them must never be added together.
Served now, at /llms.txt.
Traversal over 398,707 precomputed, degree-weighted paths. Findings and inferences are separable in every result.
Four read endpoints live: relations, sources, reactions and reach. The rest in development.
The whole graph, with provenance columns intact, under the licences of its upstream sources.
The file is in development; the page says what it will carry.
Request
GET /api/v1/relations?node=CHEBI:16919&class=bothResponse
{ "node": { "id": "CHEBI:16919", "label": "creatine", "type": "compound", "href": "/compounds/creatine" }, "class": "both", "tier": "core", "findings": [ { "id": "01M102QACN9CTAD98A1CX76S62", "assertion_class": "documented", "predicate": "affects", "direction": "increases", "evidence_strength": "moderate", "subject": { "id": "CHEBI:16919", "label": "creatine", "type": "compound", "href": "/compounds/creatine" }, "object": { "id": "CAT:outcome/serum-creatinine", "label": "Serum creatinine concentration", "type": "outcome", "href": "/outcomes/serum-creatinine" }, "sentence": "creatine increases Serum creatinine concentration", "evidence_type": "crossover", "n": null, "population": "children aged 5-18 years with facioscapulohumeral muscular dystrophy; safety outcome, not the primary endpoint", "dose_regimen": "creatine monohydrate ~100 mg/kg/day (2.5-10 g daily by weight band) for 12 weeks per crossover period", "duration_days": 84, "effect_size": 12.63, "effect_metric": "mean_difference", "ci_low": 1.14, "ci_high": 24.12, "replication_count": 3, "contradiction_count": 0, "curated_at": "2026-08-26T22:23:18.405823+00:00", "permalink": "https://catalystproject.ai/e/01M102QACN9CTAD98A1CX76S62", "source": { "id": "PMID:40366059", "title": "Effect of creatine monohydrate on motor function in children with facioscapulohumeral muscular dystrophy: A multicenter, randomized, double-blind placebo-controlled crossover trial.", "url": "https://doi.org/10.1002/phar.70025", "year": 2025, "retracted": false, "quote": "Specifically, there was an increase in serum creatinine (mean difference 12.63 μmol/L, 95% CI 1.14 to 24.12) and decrease in eGFR (−25.79 mL/min/1.73 m2, 95% CI −44.3 to −7.25) in individuals on creatine supplementation compared to placebo." } } ], "relations": [ { "id": "01M0DBCYMYNNH2W88V0PB5XNSE", "assertion_class": "inferred", "predicate": "transported_by", "direction": "modulates", "subject": { "id": "CHEBI:16919", "label": "creatine", "type": "compound", "href": null }, "object": { "id": "UNIPROT:Q6ZSM3", "label": "SLC16A12", "type": "protein", "href": "/proteins/slc16a12" }, "sentence": "creatine is transported by SLC16A12", "source": { "database": "rhea", "name": "Rhea", "record": "RHEA:73043", "url": "https://www.rhea-db.org/rhea/73043", "release": "2026-08-19", "license": "CC BY 4.0" } } ], "page": { "limit": 50, "offset": 0, "total_relations": 34, "total_findings": 35 }, "withheld": { "relations": 0, "sources": [] }}Trimmed to 1 of 35 findings, 1 of 34 relations.