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 gr

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 Do not submit patient information, confidential research questions, unpublished compound programs, or proprietary target hypotheses.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: 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 . One hop lookup Pin at least one endpoint and type both nodes: 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. Inspect saved provenance Rebuild a bounded summary without network access: 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](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) [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI) [Biolink Model](https://biolink.github.io/biolink model/)

ncats-arax