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.
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.
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Do not submit patient information, confidential research questions, unpublished compound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
Normalize free text separately, then review and report the proposed CURIE and category.
Choose a typed one-hop query or an exactly two-hop query with both endpoints pinned.
Use default RTX-KG2 lookup unless the user explicitly names two to five providers.
Acknowledge that the biomedical query is public and choose a new or empty output directory.
Run the client once. Do not silently change provider selection or expansion order after a
failure or empty result.
Inspect summary.json for bounded bindings and provenance and response.json for the exact
TRAPI payload.
Verify scientifically important paths outside ARAX.
Preflight
Check the production OpenAPI without making a biomedical query:
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:
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.
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:
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:
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 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.
