synthetic-sciences 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=falseis 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 - Do not submit patient information, confidential research questions, unpublished compound programs, or proprietary target hypotheses.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.jsonfor bounded bindings and provenance andresponse.jsonfor the exact TRAPI payload. - 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_returnedas 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.