Search 800+ HNF1B clinical cases with phenotypes, genetic variants, and publications. The definitive resource for MODY5 and RCAD research.
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Last probed Nov 3, 2026 · mcp.hnf1b.org
13tools discovered
For AI agents — MCPBundles Directory API
For MCP client apps (human connect):
MCP connect URL: https://mcp.hnf1b.org/
Skill page: https://www.mcpbundles.com/skills/hnf1b-mcp-090b2c0fc2
Explore capabilities (13)
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Hnf1b
13
HNF1B: Capabilities & Tool Inventory
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hnf1b_get_capabilities
Return server capabilities, tool inventory, and operational metadata.
Discover what the HNF1B MCP server can do: canonical workflows, the
full tool inventory with per-tool summaries, supported payload modes
with character budgets, pagination limits, citation contract, error
codes, data-class taxonomy, v1 exclusions, and safety notices.
Calling this is RECOMMENDED for orientation in a new/cold session but
is OPTIONAL: tools with enum-constrained filters advertise them in
`filterable_fields`, so
Description may be truncated on the public preview.
HNF1B: Capabilities & Tool Inventory — Return server capabilities, tool inventory, and operational metadata.
Discover what the HNF1B MCP server can do: canonical workflows, the
full tool inventory with per-tool summaries, supported payload modes
with character budgets, pagination limits, citation contract, error
codes, data-class taxonomy, v1 exclusions, and safety notices.
Calling this is RECOMMENDED for orientation in a new/cold session but
is OPTIONAL: tools with enum-constrained filters advertise them in
`filterable_fields`, so
Search HNF1B-db (Discovery) — Unified discovery search — returns typed ID hits.
Searches across individuals, variants, and publications in HNF1B-db
and returns a list of typed ID hits only. Use the typed
``hnf1b_get_individual``, ``hnf1b_get_variant``, or
``hnf1b_get_publications`` tools to fetch authoritative content for any
returned ID.
Get HNF1B Individual (phenopacket) — Retrieve the full phenopacket record for a single individual.
Fetches by phenopacket_id.
Fetches authoritative curated data for one HNF1B-db individual from the
``/phenopackets/{phenopacket_id}`` endpoint and returns a compact shaped
record. Use ``hnf1b_get_individuals`` to retrieve multiple records in a
single call, or ``hnf1b_find_individuals_by_phenotype`` to discover
individuals sharing a given HPO phenotype.
Get/List HNF1B Individuals — Retrieve a list of HNF1B-db individuals by IDs or with optional filters.
When ``ids`` is provided the batch endpoint is used for efficient
multi-record retrieval. Otherwise the discovery list endpoint is
queried and each individual is optionally fetched in full when
``expand=True``. Use ``hnf1b_find_individuals_by_phenotype`` to first
discover individuals sharing a given HPO term before fetching them.
Find Individuals by HPO Phenotype — Cohort discovery: find individuals sharing one or more HPO phenotype terms.
Queries the ``/phenopackets/search`` discovery endpoint once per
supplied HPO term ID, collects the matching phenopacket IDs, then
aggregates them according to ``match_mode`` before fetching
authoritative content for the resulting cohort via the batch endpoint.
Suitable for building HPO-matched cohorts for downstream analysis.
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Search 800+ HNF1B clinical cases with phenotypes, genetic variants, and publications. The definitive resource for MODY5 and RCAD research.
How do I connect HNF1B Database to my AI agent?
Use the MCP endpoint listed on this page in your MCP client configuration. One-click install pills support Claude, Cursor, VS Code, and other hosts. Copy the remote MCP URL if your client needs a manual entry.
How many tools does HNF1B Database provide?
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Search HNF1B Variants — Browse HNF1B variant records with optional filters.
Returns a paginated list of HNF1B-db variants shaped with canonical
fields (``variant_id``, ``label``, ``classification``, ``consequence``,
``hg38``, ``carrier_count``, ``uri``, etc.). Filter by pathogenicity
classification, molecular consequence, protein domain, gene, or a
free-text query.
Get HNF1B Variant — Fetch the full authoritative record for a single HNF1B variant.
Returns the complete curated variant record — ``classification``
(pathogenicity), molecular ``consequence``, ``label``, ``hg38``,
``transcript``, ``protein``, ``structural_type``, ``gene_symbol`` and
``carrier_count`` — together with a ``carriers`` list of phenopacket IDs.
Pass those ``carriers`` IDs to ``hnf1b_get_individuals`` for per-carrier
phenotype detail. ``carrier_count`` counts DISTINCT carrier individuals
(phenopackets) f
Get HNF1B Gene Context — Return gene reference data including transcripts and protein domains.
Fetches the canonical gene record for *gene_symbol* from the HNF1B-db
reference API (``/reference/genes/{gene_symbol}``). Optionally
enriches the result with transcript isoforms and annotated protein
domains from the two sub-endpoints.
The payload carries a stable ``hnf1b://gene/{gene_symbol}`` URI that
can be used to anchor citations or cross-tool references.
Token discipline: outside ``full`` mode the payload is summariz
Get HNF1B Publications — Browse and search the local HNF1B publication cache.
Returns paginated publications from the HNF1B-db local cache, or
performs a reverse lookup to discover which individuals (phenopackets)
cite a given publication.
Set ``citing_pmid`` for reverse lookup — all other filters are ignored
when that parameter is supplied. Without ``citing_pmid``, use ``q``,
``year``, ``has_doi``, and ``page_size`` to filter/paginate the
publication list.
This tool NEVER calls the live PubMed metadata endpoint; it
Search Publication Passages (RAG) — Retrieve ranked passages from publication full text for a query (RAG).
Searches stored, license-gated open-access passages with hybrid
retrieval: PostgreSQL full-text search (always) fused with optional
semantic (pgvector) search via Reciprocal Rank Fusion. Returns the
most relevant passages, each with a stable ``passage_id`` and the
publication's verbatim ``recommended_citation``.
Use this to ground answers in the actual text of HNF1B publications
(abstracts + open-access body sections). For
Get HNF1B Cohort Statistics — Fetch aggregate statistics for the HNF1B phenopacket cohort.
Returns pre-computed aggregate statistics over the entire HNF1B-db
phenopacket cohort. Choose a *metric* to select the statistic; for
``survival`` also supply a *comparison* grouping variable.
Available metrics:
- ``summary`` — cohort-level counts and completeness overview.
- ``sex_distribution`` — breakdown of sex across all individuals.
- ``age_of_onset`` — distribution of renal age-of-onset bins.
- ``by_disease`` — case counts g
Resolve HPO / Vocabulary Terms — Resolve ontology or controlled-vocabulary terms against the HNF1B-db API.
Look up HPO phenotype terms or controlled-vocabulary values used by
HNF1B-db. For HPO, performs a free-text autocomplete search returning
matching HPO identifiers with labels and descriptions. For named
controlled vocabularies (sex, interpretation-status, progress-status,
allelic-state, evidence-code), retrieves the full vocabulary list and
optionally filters by *text* (case-insensitive substring match),
returning at mo
Compare Phenotypes Across Variants — Compare HPO phenotype frequencies across carriers of several variants.
A genotype-phenotype analytical primitive: instead of fetching each
variant's carriers and tallying HPO terms by hand, this returns per-HPO
observed / excluded / unknown counts for each variant group in one call.
Pass canonical ``variant_id`` values (GA4GH VRS / CNV descriptor) and/or
the friendly ``simple_id`` (e.g. ``"Var6"``) returned by
``hnf1b_search_variants`` / ``hnf1b_get_variant`` — both are accepted and
resolved t
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