NCATS ARAX

Use ARAX as a constrained knowledge-graph lookup service. Submit reviewed CURIEs and explicit Biolink types, preserve the exact TRAPI exchange, inspect query-edge bindings and provenance, and treat every returned path as a candidate for subsequent verification.

Read query-contract.md before constructing a query. Read output-schema.md when interpreting saved artifacts, warnings, provenance, or partial results.

Safety boundary

• Use only public, nonsensitive research questions. ARAX status facilities may expose query and caller metadata even when store=false is requested.
• Do not submit patient information, confidential research questions, unpublished compound programs, or proprietary target hypotheses.
• Do not present a returned path as a validated mechanism or clinical recommendation.
• Report a zero as "not returned under these constraints," never as evidence that no relationship exists.
• Describe position as unscored response order, never rank.
• Verify important candidates with literature and authoritative databases separately.

Workflow

1. Normalize free text separately, then review and report the proposed CURIE and category.
2. Choose a typed one-hop query or an exactly two-hop query with both endpoints pinned.
3. Use default RTX-KG2 lookup unless the user explicitly names two to five providers.
4. Acknowledge that the biomedical query is public and choose a new or empty output directory.
5. Run the client once. Do not silently change provider selection or expansion order after a failure or empty result.
6. Inspect summary.json for bounded bindings and provenance and response.json for the exact TRAPI payload.
7. Verify scientifically important paths outside ARAX.

Preflight

Check the production OpenAPI without making a biomedical query:

python skills/ncats-arax/scripts/arax_client.py preflight

The client verifies that the service identifies itself as ARAX, exposes POST /query and GET /entity, and reports a supported TRAPI version. It reads info.x-trapi.version, falling back to the title for older OpenAPI documents. A nonproduction endpoint or untested TRAPI series requires an explicit override; neither override changes the fixed query shapes or operations.

Normalize an entity

Normalization is review-only and never triggers a graph query:

python skills/ncats-arax/scripts/arax_client.py normalize "ivacaftor" \
  --expected-category biolink:SmallMolecule \
  --max-synonyms 10 \
  --acknowledge-public-query \
  --output-dir outputs/normalize-ivacaftor

Review the canonical identifier, name, category, and synonym preview before using a CURIE. Report all CURIEs and categories regardless of query outcome. A category warning or zero result is a reason to curate the identifier, not to chain automatically to /query.

One-hop lookup

Pin at least one endpoint and type both nodes:

python skills/ncats-arax/scripts/arax_client.py one-hop \
  --subject-id CHEBI:31690 \
  --subject-category biolink:SmallMolecule \
  --predicate biolink:affects \
  --object-id NCBIGene:25 \
  --object-category biolink:Gene \
  --qualifier biolink:object_aspect_qualifier=activity_or_abundance \
  --qualifier biolink:object_direction_qualifier=decreased \
  --acknowledge-public-query \
  --output-dir outputs/imatinib-abl1

Lookup mode is the default and fixes expansion to infores:rtx-kg2. It defaults to 20 results. Use --result-limit N to request 1-50 results; 50 is the hard cap in either mode.

Endpoint-pinned two-hop lookup

Use exactly one typed, unpinned intermediate node:

python skills/ncats-arax/scripts/arax_client.py two-hop \
  --subject-id CHEBI:66901 \
  --subject-category biolink:SmallMolecule \
  --predicate-1 biolink:affects \
  --intermediate-category biolink:Gene \
  --predicate-2 biolink:associated_with \
  --object-id MONDO:0009061 \
  --object-category biolink:Disease \
  --qualifier-1 biolink:object_aspect_qualifier=activity_or_abundance \
  --qualifier-1 biolink:object_direction_qualifier=increased \
  --expand-order right-first \
  --acknowledge-public-query \
  --output-dir outputs/ivacaftor-cystic-fibrosis

Right-first expansion is the default. If an empty result merits another attempt, run a new query explicitly with --expand-order left-first and keep the runs separate.

Selected-provider federation

…