ncats-arax

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• Do not submit patient information, confidential research questions, unpublished compound programs, or proprietary target hypotheses.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 /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

• 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.
• 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

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

Agent operating procedure

1. Check the environment. Confirm network access, API keys (if required) and the database's current API documentation and rate limits.
2. Pin down the inputs. Confirm formats, identifiers and parameters from the data or the user. Ask rather than guess any value that changes the result.
3. Run a small version first. Fetch a single known record and check the response format before bulk queries.
4. Execute the full task using the instructions and references above.
5. Validate the result. Identifiers resolve, record counts are reported, and the database version or access date is recorded.
6. Report. State what was run (versions, commands, parameters), what was checked, and what is still uncertain.

If this happens	Do this
HTTP 429 or 5xx errors	Respect rate limits with backoff, batch requests, and report partial results honestly.
A function, flag or endpoint in these instructions is missing in the installed version	Check the installed version's own documentation (help(), --help, official docs), adapt, and tell the user. Never invent an API.
A required input, identifier or parameter is ambiguous	Ask the user, or state the assumption explicitly before running.

Integrity rules

• Never fabricate results, parameters, identifiers, citations or statistics. If something cannot be run or verified, say so plainly.
• Never invent accession numbers, IDs or records; report 'not found' instead.
• Treat version-specific details here as possibly outdated: confirm them against the official documentation for the installed version.
• Ask before actions that cost money, consume shared GPUs or cloud quota, touch personal or patient data, or cannot be undone.