Traxome™

Ask about any condition, gene, variant, drug or supplement — get one clear answer, traced to public databases, and reframed for patients, clinicians, or researchers.

Built for the Built with Claude — Life Sciences hackathon.

▶ Watch the 2-minute demo on YouTube

What it does

One search box. Type a condition (migraine), a gene (CACNA1A), a variant (BRCA1 R1699W), a pharmacogene pair (CYP2C19 clopidogrel), or anything you can take — drugs, supplements, herbs, peptides (advil, ashwagandha). Traxome identifies it and answers through the lens you pick:

• Patient — plain-language explainer, side effects and interactions in everyday words, trusted resources (MedlinePlus, Mayo, Cleveland, NHS), and where to find or afford a treatment.
• Clinician — full FDA-label detail, real-world safety signal (FAERS), pharmacogenomics (CPIC), and guideline + cash-price links.
• Researcher — evidence-ranked risk genes, genetic architecture, and click-through variant analysis with CSV/JSON export.

Every verdict is traceable: pathogenicity is scored by an explicit, toggleable ACMG rule engine, and every value links to its live source.

Other tools: a Gene Explorer with an interactive 3D protein structure (AlphaFold + PDB, export to PNG/PDF/PDB/XYZ); an interactive knowledge graph; a batch panel for gene panels and variant lists; a live literature feed merged from OpenAlex + Europe PMC + Crossref + arXiv; smart disambiguation (glp1, vitamin d) and typo-proof search.

Provable evidence layer

An optional deterministic layer that turns any answer into a citable, verifiable object. Each part is feature-flagged and off by default:

• Evidence Capsules — a resolved entity + its assertions, frozen with a SHA-256 hash and a content-addressed id you can cite and re-verify offline.
• Reclassification Radar — watch an entity; scheduled refetches diff the capsules and report exactly what changed (e.g. a ClinVar reclassification) — never a temporary outage as a "removal".
• Concordance & Completeness — agreement vs conflict across sources over their stated values, a present/absent evidence map, and transparent rules-only ranking.
• Evidence API + MCP — the deterministic tools, callable by any AI agent or lab pipeline (below).
• Private HPO workbench — phenotype→gene ranking that runs in your browser; only canonical IDs ever leave the device; exports a GA4GH Phenopacket.
• Conformance Lab — a public suite of 100+ mechanical invariants (python -m conformance) that gates every build.

Quickstart

./run.sh            # serves http://localhost:8069 (installs deps on first run)
./run.sh 9000       # or pick a port

No API key, no GPU, no config — click an example to start. The web app is backed by a REST API (POST /api/analyze {text} routes to the right stage; there are per-stage endpoints for variants, conditions, substances, pharmacogenomics, literature, batch, and the Gene Explorer). Every response carries a provenance block.

Evidence API + MCP

Make Traxome's deterministic evidence callable by any tool. One registry of read-only tools, exposed two ways — both off by default, enabled with an env flag.

REST

TRAXOME_EVIDENCE_API=1 ./run.sh

curl localhost:8069/api/v1/tools                       # the tool catalog (names + JSON-Schemas)
curl -X POST localhost:8069/api/v1/tools/get_variant_evidence \
  -H 'content-type: application/json' \
  -d '{"params": {"query": "BRCA1 R1699W"}}'

Every response carries provenance (sources + version). Failures are stable typed errors — ambiguous (409, returns candidates, never auto-picks), source-unavailable (503), rate-limited (429). Raw notes / VCFs / PHI are refused: it takes a canonical id or short query only.

Tools: resolve_entity · get_gene_evidence · get_variant_evidence · get_gene_disease_links · get_pharmacogenomic_guidance · get_controlled_status · search_literature · build_capsule · validate_capsule · compare_capsules.

MCP

The exact same tools over MCP, two ways.

Local (stdio) — a dependency-free server; plug into Claude Desktop, Cursor, or any MCP client:

TRAXOME_EVIDENCE_API=1 python -m evidence_api.mcp

{ "mcpServers": { "traxome": {
    "command": "python", "args": ["-m", "evidence_api.mcp"],
    "env": { "TRAXOME_EVIDENCE_API": "1" } } } }

Remote (hosted URL) — connect by URL, no install. In Claude → Settings → Connectors → Add custom connector, paste:

https://traxome.vercel.app/mcp

Leave the OAuth Client ID blank — the server runs an auto-approve OAuth 2.1 handshake (the tools are public/read-only), so it connects with no login. Deploy needs TRAXOME_EVIDENCE_API=1 set (and, recommended, TRAXOME_PUBLIC_ORIGIN=https://traxome.vercel.app + a random TRAXOME_OAUTH_SECRET). Works in Claude, Cursor, and any Streamable-HTTP MCP client.

New to it? docs/MCP_EXAMPLES.md is a starter guide — what to ask, organized by lens (patient → clinician → researcher), every question tested and working. A printable PDF is alongside it.

Feature flags

Flag	Enables
TRAXOME_CAPSULES=1	Evidence Capsules — POST /api/capsule
TRAXOME_RADAR=1	Reclassification Radar — /api/radar/*
TRAXOME_CONCORDANCE=1	Concordance & completeness — POST /api/concordance
TRAXOME_EVIDENCE_API=1	Evidence API + MCP — /api/v1/tools
TRAXOME_WORKBENCH=1	Private HPO workbench — /api/workbench/*

Live sources

ClinVar · gnomAD · dbNSFP (AlphaMissense/PolyPhen-2/SIFT/ClinPred/GERP) · UniProt · AlphaFold · RCSB/PDBe · Ensembl · Open Targets · CPIC · openFDA (labels + FAERS) · RxNorm · PubChem · HPO/MONDO · OpenAlex/PubMed/Europe PMC/Crossref/arXiv · ClinicalTrials.gov · MedlinePlus — all free, queried live, no key.

License & attribution

Code is MIT-licensed. Traxome re-presents public biomedical data and credits every source inline (see Live sources). Most sources are queried live; the small bundled HPO subgraph used by the workbench demo is derived from the Human Phenotype Ontology and is used under its license, with thanks to the HPO project. Each source remains subject to its own terms of use.

Not a diagnosis

Transparent decision-support only, not a certified classification. Confirm any interpretation with a qualified clinical geneticist.