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ncats-arax skill

by K-Dense-AI·K-Dense-AI/scientific-agent-skills·47k stars·MIT

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.

A100/100content scan

Is the ncats-arax skill safe?

Clean: nothing in its files matched our rules. We read 4 files in the folder on 2026-09-28.

No findings.

Install the ncats-arax skill

A skill is a folder. Copy it into your agent's skills folder and the agent loads it when the task matches its description. 

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills
mkdir -p ~/.claude/skills
cp -r /tmp/scientific-agent-skills/skills/ncats-arax ~/.claude/skills/ncats-arax
available in every project

In the Claude apps, zip the folder and upload it from the Skills settings. The folder on GitHub

The instructions your agent would load

SKILL.md as published, without the frontmatter. Read it on GitHub

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

caller metadata even when store=false is requested.

  • Use only public, nonsensitive research questions. ARAX status facilities may expose query and

programs, or proprietary target hypotheses.

  • Do not submit patient information, confidential research questions, unpublished compound

exists.

  • 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
  • Describe position as unscored response order, never rank.
  • Verify important candidates with literature and authoritative databases separately.

Workflow

failure or empty result.

  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

TRAPI payload.

  1. Inspect summary.json for bounded bindings and provenance and response.json for the exact
  1. 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-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

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

  • 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.

and source-record URL fields.

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

publications exist.

  • Treat publicationavailability: notreturned as missing metadata, not evidence that no

partial, unfamiliar, or scientifically surprising.

  • 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

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

  • ARAX documentation
  • ARAX production OpenAPI
  • ARAXi operation documentation
  • Translator Reasoner API
  • Biolink Model

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