ncats-arax – Coding skill for AI agents

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• Do not submit patient information, confidential research questions, unpublished compound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 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

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. The same applies

to a failed provider in lookup mode. An explicit non-success ARAX response status exits 6 with

the raw response retained; it must not be reported as a successful zero-result query.

Inspect saved provenance

Rebuild a bounded summary without network access:

python skills/ncats-arax/scripts/arax_client.py summarize \
  --request outputs/ivacaftor-cystic-fibrosis/request.json \
  --response outputs/ivacaftor-cystic-fibrosis/response.json \
  --format text

The inspector accepts only the same constrained request shapes and fixed operations that the live

commands generate. Use --format json for the normalized view on standard output.

Interpret results

• Follow each analysis's query-edge bindings; do not summarize every knowledge-graph edge.
• Preserve the physical edge subject, predicate, object, and qualifier values returned by ARAX.

Returned predicates or qualifier aspects may be more specific than the query constraint.

• Inspect all source objects, including primary, aggregator, supporting-data, upstream-resource,

and source-record URL fields.

• Trace aggregator edges to their primary/upstream sources and publications before claiming

corroboration. Multiple providers can redistribute the same record; report distinct primary

evidence, not provider count as confidence or independent replication.

• Treat publication_availability: not_returned as missing metadata, not evidence that no

publications exist.

• Treat missing auxiliary-graph references and provider failures as explicit warnings.
• Consult the raw response whenever the bounded summary omits detail or the service response is

partial, unfamiliar, or scientifically surprising.

Deliberate exclusions

The client has no raw-query, workflow, operation, overlay, ranking, inference, link-prediction,

Pathfinder, ARS, batch, all-provider, three-hop, cache, daemon, SDK, MCP, or

natural-language-to-TRAPI surface. Do not work around those limits with direct HTTP calls under

this skill.

Official references

Reviewed on 2026-09-30 against production ARAX 1.5.4 / TRAPI 1.5.0 (the URL still contains v1.4).

Live public smoke tests passed for preflight, normalization, qualified one-hop and endpoint-pinned

two-hop lookups, and RTX-KG2/MolePro federation. Results and provider availability can change.

The official introductory guide contains older response examples; use the deployed schema and

current ARAX source for field and operation contracts. No Python SDK is used by this client.

• [ARAX documentation](https://ncatstranslator.github.io/TranslatorTechnicalDocumentation/architecture/ara/arax/)
• [ARAX production OpenAPI](https://arax.transltr.io/api/arax/v1.4/openapi.json)
• [ARAXi operation documentation](https://github.com/RTXteam/RTX/blob/master/code/ARAX/Documentation/DSL_Documentation.md)
• [ARAX query execution and scoreless resultification](https://github.com/RTXteam/RTX/blob/master/code/ARAX/ARAXQuery/ARAX_query.py)
• [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI)
• [Biolink Model](https://biolink.github.io/biolink-model/)