/ncats-arax

name: ncats-arax
description: Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance. Do not use for inference, ranking, open-ended pathfinding, clinical guidance, or sensitive queries.
allowed-tools: Read Bash
license: MIT
compatibility: Requires Python 3.10+ and outbound HTTPS access to arax.transltr.io. The client uses only the Python standard library and needs no API key. Queries and caller metadata may be publicly visible; never submit sensitive or patient-specific content.
metadata:
  version: "1.0"
  skill-author: neuroepithelial

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](references/query-contract.md) before constructing a query. Read [output-schema.md](references/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• Do not submit patient information, confidential research questions, unpublished compound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 `/query`, and reports a supported TRAPI version. 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 "primary myelofibrosis" \
  --expected-category biolink:Disease \
  --max-synonyms 10 \
  --acknowledge-public-query \
  --output-dir outputs/normalize-myelofibrosis

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

Federation is explicit and accepts two to five named providers:

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 \
  --mode federated \
  --kp infores:rtx-kg2 \
  --kp infores:molepro \
  --acknowledge-public-query \
  --output-dir outputs/federated-imatinib-abl1

Federation defaults to the hard maximum of 50 results. Provider errors may coexist with useful results; such a run exits 7 after retaining its artifacts and is marked partial.

Inspect saved provenance

Rebuild a bounded summary without network access:

python skills/ncats