ClinPGx through GeneFoundry

Search curated pharmacogenomics datasets, gene-drug clinical annotations, CPIC and PharmGKB dosing guidelines, and variant-level drug responses.

Research area
Gene–disease
Namespace
clinpgx
Listed tools
13
Upstream source
ClinPGx

Research tasks

  • Query gene-drug pairs and dosing guidelines (e.g. CYP2D6 and codeine)
  • Search pharmacogenomic variant assertions and CPIC clinical recommendations
  • Inspect curated snapshot datasets across drug response phenotypes

Start with tool discovery

The catalog lists clinpgx_search_records as a representative tool. After connecting your client, inspect the tools and input requirements returned by the service before submitting a query.

Identifiers to prepare

  • Gene symbol (e.g. CYP2D6, TPMT, DPYD)
  • Drug name or RxNorm identifier
  • CPIC guideline identifier
  • Variant or star allele (e.g. *4, *5)

Source version: v0.1.0 snapshot (120 curated datasets) / 2026 live API

All available tools (13)

The router surfaces these tools namespaced under clinpgx_*:

get_api_schemaDiscover exact allowlisted contracts; inventory-only routes are not callable.

Router invocation: clinpgx_get_api_schema()

Discover exact allowlisted contracts; inventory-only routes are not callable.

Input parameters

  • cursor(any) — Previous page cursor.
  • limit(integer) — Maximum operation entries.
  • namespace(string) — Website includes linked CPIC reference routes.
  • offset(integer) — Zero-based entry offset.
  • operation(any) — Exact operation ID; omit to list.
  • response_mode(string) — Detail mode; schemas remain reachable.
get_api_dataRead one allowlisted API operation; paginate its response without refetching.

Router invocation: clinpgx_get_api_data()

Read one allowlisted API operation; paginate its response without refetching.

Input parameters

  • cursor(any) — Immutable previous-page cursor.
  • form_parameters(any) — Verified Infobutton form only.
  • limit(integer) — Maximum returned rows.
  • offset(integer) — Offset in this retained response, not upstream corpus.
  • operation(string) [required] — Exact API operation from get_api_schema.
  • path_parameters(any) — Declared path fields only.
  • pointer(string) — RFC 6901 pointer in decoded source data.
  • pointers(any) — Ordered scalar RFC 6901 pointers for JSON data.
  • query_parameters(any) — Declared query fields only.
  • representation(string) — Verified source representation.
  • response_mode(string) — Detail mode; source content stays reachable.
get_website_dataRead verified site and linked CPIC reference routes with distinct provenance.

Router invocation: clinpgx_get_website_data()

Read verified site and linked CPIC reference routes with distinct provenance.

Input parameters

  • cursor(any) — Immutable previous-page cursor.
  • limit(integer) — Maximum returned rows.
  • offset(integer) — Offset in this retained response, not upstream corpus.
  • operation(string) [required] — Website or CPIC operation from get_api_schema.
  • path_parameters(any) — Declared path fields only.
  • pointer(string) — RFC 6901 pointer in decoded source data.
  • pointers(any) — Ordered scalar RFC 6901 pointers for JSON data.
  • query_parameters(any) — Declared query fields only.
  • response_mode(string) — Detail mode; source content stays reachable.
list_datasetsList datasets available in the installed snapshot catalog. Use response_mode='minimal' for concise overview.

Router invocation: clinpgx_list_datasets()

List datasets available in the installed snapshot catalog. Use response_mode='minimal' for concise overview.

Input parameters

  • cursor(any) — Snapshot-bound continuation cursor.
  • include_legacy(boolean) — Include datasets marked legacy or deprecated.
  • limit(integer) — Maximum datasets to return.
  • offset(integer) — Zero-based dataset offset.
  • query(any) — Case-insensitive dataset ID or file-name filter.
  • response_mode(string) — Response detail mode.
get_datasetInspect one installed dataset snapshot record. Member items include member_sha256.

Router invocation: clinpgx_get_dataset()

Inspect one installed dataset snapshot record. Member items include member_sha256.

Input parameters

  • cursor(any) — Snapshot-bound continuation cursor.
  • dataset_id(string) [required] — Exact installed dataset identifier.
  • limit(integer) — Maximum members to return.
  • member(any) — Exact installed member path to scope inspection.
  • offset(integer) — Zero-based member offset.
  • response_mode(string) — Response detail mode.
search_datasetSearch indexed rows within an installed snapshot dataset. Rows include member_sha256.

Router invocation: clinpgx_search_dataset()

Search indexed rows within an installed snapshot dataset. Rows include member_sha256.

Input parameters

  • cursor(any) — Snapshot-bound continuation cursor.
  • dataset_id(string) [required] — Exact installed dataset identifier.
  • filters(any) — ANDed filters: reserved lowercase canonical keys, or exact advertised source fields when member is explicit. For PharmCAT diplotype children, combine exact canonical gene and name (the diplotype string) filters.
  • include_fields(any) — Ordered profiled source fields to return.
  • limit(integer) — Maximum rows to return.
  • match(string) — Exact cells or declared member tokenization.
  • member(any) — Exact installed member path.
  • offset(integer) — Zero-based row offset.
  • parent_fields(any) — Ordered enclosing PharmCAT parent fields: gene and/or version.
  • query(any) — Literal token query.
  • response_mode(string) — Response detail mode.
get_dataset_record

Router invocation: clinpgx_get_dataset_record()

Input parameters

  • include_fields(any) — Ordered profiled source fields to return.
  • parent_fields(any) — Ordered enclosing PharmCAT parent fields: gene and/or version.
  • pointer(string) — RFC 6901 pointer in the normalized record.
  • pointers(any) — Ordered scalar RFC 6901 pointers.
  • record_id(string) [required] — Snapshot-bound record identity discovered with search_dataset.
  • response_mode(string) — Response detail mode.
search_recordsSearch exact live fields or installed dataset memberships.

Router invocation: clinpgx_search_records()

Search exact live fields or installed dataset memberships.

Input parameters

  • cursor(any) — Opaque continuation returned for the same selectors and source identity.
  • entity_type(string) [required] — Entity family to search in the selected source.
  • filters(any) — ANDed canonical filters (annotation_id, chemical, gene, id, name, resource_id, source, variant); API choices vary by entity.
  • limit(integer) — Maximum rows returned on this page.
  • offset(integer) — Zero-based offset; cannot accompany cursor.
  • query(any) — Literal AND-token local text query; unavailable for API searches.
  • response_mode(string) — Response detail preference; does not change source identity.
  • source(string) — Source policy: auto routes exact filters to API and broad queries locally.
  • view(string) — ClinPGx upstream projection for live API reads.
get_recordGet one exact entity without changing source; use source='website' for guideline URLs.

Router invocation: clinpgx_get_record()

Get one exact entity without changing source; use source='website' for guideline URLs.

Input parameters

  • entity_type(string) [required] — Entity family owning the requested identifier.
  • pointer(string) — RFC 6901 pointer in decoded API data or the normalized local record.
  • pointers(any) — Ordered scalar RFC 6901 pointers; mutually exclusive with pointer.
  • record_id(string) [required] — Exact ClinPGx identifier or returned local record_id; numeric-detail families reuse the decimal id returned by search_records.
  • response_mode(string) — Response detail preference; does not change source identity.
  • source(string) — Exact source to query; this tool never silently switches.
  • view(string) — ClinPGx upstream projection for live API reads.
get_related_recordsUse known IDs for live reports or joins. Guideline URLs live under source='website'.

Router invocation: clinpgx_get_related_records()

Use known IDs for live reports or joins. Guideline URLs live under source='website'.

Input parameters

  • cursor(any) — Opaque continuation returned for the same selectors and source identity.
  • entity_type(string) — Object class owning record_id; documentation-only and cursor-bound, not sent upstream as a pair filter.
  • limit(integer) — Maximum rows returned on this page.
  • offset(integer) — Zero-based offset; cannot accompany cursor.
  • other_id(any) — Second exact ClinPGx ID; when supplied, selects live API pair mode.
  • other_type(string) — Target connected-object type sent upstream without other_id; documentation-only and cursor-bound in pair mode, not an upstream pair filter.
  • record_id(string) [required] — Exact ClinPGx identifier or returned local record_id; numeric-detail families reuse the decimal id returned by search_records.
  • response_mode(string) — Response detail preference; does not change source identity.
  • result_type(string) [required] — Use relationship without other_id for API connected-object mode; API pair mode requires other_id and a mapped result type published by capabilities.
  • source(string) — Exact live connected/pair or installed join source.
  • view(string) — API pair upstream projection; not sent upstream in connected-object mode, but remains cursor-bound.
get_diagnosticsInspect source configuration and pinned data without revealing local paths or secrets.

Router invocation: clinpgx_get_diagnostics()

Inspect source configuration and pinned data without revealing local paths or secrets.

Input parameters

  • probe_upstream(boolean) — Request fixed gene evidence; cached hits are identified.
  • response_mode(string) — Response detail mode.
get_server_capabilitiesDiscover tools and source limits; non-full modes use api_contract_defaults, while full expands every API row.

Router invocation: clinpgx_get_server_capabilities()

Discover tools and source limits; non-full modes use api_contract_defaults, while full expands every API row.

Input parameters

  • response_mode(string) — Response detail mode; full expands shared API-row defaults.
get_source_contentRead retained source content in digest-bound, progressing chunks.

Router invocation: clinpgx_get_source_content()

Read retained source content in digest-bound, progressing chunks.

Input parameters

  • content_ref(string) [required] — Opaque reference returned by a source tool; pass it unchanged. content: identifies retained source or derived content, while asset: identifies snapshot-retained archive/member bytes. A pointer addresses JSON within that referenced content, not another representation.
  • length(integer) — Maximum units to return; structure may use a smaller bounded page.
  • pointer(string) — RFC 6901 pointer for JSON reads; base64 requires an empty pointer.
  • representation(string) — Structure discovers JSON values and includes short scalar values through 256 UTF-8 bytes; text reads strings; base64 returns exact original bytes.
  • response_mode(string) — Response detail mode; provenance and all selected content remain reachable.
  • start(integer) — Zero-based character, byte or child offset.

Database & release provenance

Data mode
none
Attestation
unhosted
Release version
v0.1.0
Container image:ghcr.io/berntpopp/clinpgx-link@sha256:29300d3229685997d7429db2b8dbf76a6d87ed099ad9d399725b4e2b3937fc4b

Inspect canonical provenance artifact: genefoundry.org/provenance (JSON)

Review the response

Keep the source record link and submitted identifiers with your notes. Record the dataset version and retrieval date when available. This page does not contain a captured ClinPGx response.

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