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Glama

hgnc-link

Python 3.12+ CI Conformance License: MIT

An MCP (Model Context Protocol) server that grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset from genenames.org, served from a local index of HGNC's bulk downloads over Streamable HTTP or stdio.

IMPORTANT

Research use only. Not clinical decision support. Do not use for diagnosis, treatment, triage, or patient management.

Why

Every downstream genetics tool needs the same thing from HGNC: turn any gene symbol — current, outdated (previous), or alias — and any HGNC ID form into the canonical {hgnc_id, approved_symbol}, then pull cross-references.

HGNC does publish a REST API, but it is field-scoped (/fetch/{field}/{value}): the caller must already know whether a string is a current symbol, a previous symbol, an alias or an ID, and query the matching field — a network round-trip per guess. It will not tell you how a symbol matched, and it will not warn you that an alias belongs to several genes.

hgnc-link collapses that into one local call against a SQLite index of the bulk dumps. It runs the full cascade (HGNC ID → current → previous → alias → withdrawn redirect), returns the match provenance in match_type, and surfaces ambiguity as an ambiguous_query error with the candidate list rather than silently collapsing it to one gene.

Related MCP server: plant-genomics-mcp

Quick start

Hosted — no install:

claude mcp add --transport http hgnc https://hgnc-link.genefoundry.org/mcp

Local (Python 3.12+, uv). make data is mandatory — the server has no data until the HGNC dumps (~33 MB) are downloaded and the local index is built:

make install          # uv sync --group dev
make data             # download the HGNC dumps, build the local SQLite index
make dev              # unified REST + MCP on http://127.0.0.1:8000/mcp
make mcp-serve        # ...or a stdio MCP server, for Claude Desktop
claude mcp add --transport http hgnc-link --scope user http://127.0.0.1:8000/mcp

For stdio see claude-desktop-config.json. Keep the index fresh with make data-refresh from cron — it is conditional, so an unchanged dump costs one 304 and no rebuild (Deployment). Serving over HTTP behind a proxy requires adding the public hostname to the exact Host allowlist — read Configuration first.

Tools

Tool

Purpose

resolve_symbol

Start here. Any symbol/ID → {hgnc_id, approved_symbol, match_type} + candidates.

resolve_symbols_batch

Resolve many symbols/IDs at once; never fails the batch on a miss.

get_gene

Full HGNC record for one gene (alias- and previous-symbol aware).

search_genes

Full-text search over symbol, name, alias and previous symbols.

get_gene_cross_references

Gene → NCBI / Ensembl / UniProt / RefSeq / MANE / OMIM / … identifiers.

resolve_gene_by_xref

External ID → HGNC gene (the reverse mapping).

get_gene_group

Browse a gene family by group ID or name.

get_server_capabilities

Discovery surface: tools, signatures, workflows, vocabulary.

get_hgnc_diagnostics

Loaded release, record counts, freshness, data-source status.

serverInfo.name is hgnc-link, and leaf tool names are intentionally unprefixed per the GeneFoundry Tool-Naming Standard v1. The canonical gateway namespace token is hgnc: behind genefoundry-router these surface as hgnc_<tool> (e.g. hgnc_resolve_symbol).

Every response carries _meta.next_commands — a ready-to-call {tool, arguments} list, on success and on error — and honours response_mode ∈ {minimal, compact, standard, full} (default compact). See Usage.

Data & provenance

  • Source — the HGNC bulk downloads (hgnc_complete_set.json + withdrawn.txt) from genenames.org, built into a local SQLite index. Queries are served from that index; there are no per-request REST round-trips.

  • Refresh — HGNC publishes Tuesdays and Fridays. hgnc-link-data refresh is the cron entry point and is conditional (an unchanged dump returns 304, so no rebuild); the in-app scheduler is off by default. See Data.

  • Licence — HGNC data is released with no usage restrictions (effectively public domain / CC0). Attribution is requested but not required.

  • Citation — Seal RL, Braschi B, Gray K, Jones TEM, Tweedie S, Haim-Vilmovsky L, Bruford EA. Genenames.org: the HGNC resources in 2023. Nucleic Acids Res. 2023;51(D1):D1003-D1009. doi:10.1093/nar/gkac888. RRID:SCR_002827.

Documentation

  • Usage — canonical workflows, response_mode, chaining, ambiguity and withdrawn-ID semantics, the hgnc:// resources.

  • Configuration — every HGNC_LINK_* variable, the transports, and the Host / Origin / CORS boundary.

  • Data — the bulk dumps, the index build, freshness, and the (unwired) live REST client.

  • Deployment — cron and systemd refresh, and the Docker path.

  • Architecture — the ingest → SQLite → service → MCP planes, and the schema.

  • Design spec — why it is shaped this way.

Contributing

See AGENTS.md for engineering conventions — the error taxonomy, the next_commands contract, and how to add a tool. make ci-local is the definition-of-done gate: format, lint, line budget, README standard, mypy strict, and tests.

License

MIT © hgnc-link contributors. HGNC data carries no usage restrictions (effectively CC0); the attribution cited above is requested but not required.

Available Tools

9 tools
get_geneGet Gene RecordA
Read-onlyIdempotent

Return the full HGNC record for a gene, resolved from an HGNC id, current symbol, previous symbol, or alias. Includes name, status, locus group/type, location, aliases/previous symbols, gene groups, and all cross-references. response_mode controls verbosity (compact drops dates/provenance; minimal keeps identity + anchor ids). Signature: get_gene(query, response_mode=).

ParametersJSON Schema
NameRequiredDescriptionDefault
queryYesA gene symbol (current/previous/alias, case-insensitive) or HGNC id (HGNC:1100 or 1100).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

TDQS

A4.5/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare read-only, open-world, idempotent, non-destructive. Description adds specifics: lists returned fields, explains response_mode effect (compact drops dates/provenance, minimal keeps identity+anchor ids). No contradictions.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences: first describes purpose and data, second gives signature. No unnecessary words, front-loaded with key info.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With 2 params fully described in schema and annotations, description covers return contents and response_mode variations. No output schema needed because description lists fields explicitly. Completeness excellent.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema covers both parameters with descriptions and examples. Description goes beyond schema by explaining that response_mode controls verbosity with concrete examples (compact drops dates/provenance, minimal keeps identity+anchor ids).

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Description clearly states it returns the full HGNC record for a gene, specifies input types (HGNC id, symbol, alias), and lists contents (name, status, location, cross-refs). Distinguishes from siblings like resolve_symbol and search_genes.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Describes when to use (get full record by various identifiers) and mentions response_mode verbosity levels. Lacks explicit when-not-to-use or comparison to all siblings, but context of sibling tools makes it clear.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_gene_cross_referencesGet Gene Cross-ReferencesA
Read-onlyIdempotent

Return external database cross-references for a gene (forward identifier mapping): NCBI Gene, Ensembl, UniProt, RefSeq, MANE Select, OMIM, UCSC, VEGA, CCDS, MGI, RGD, Orphanet, COSMIC, PubMed. response_mode sets the default field set: minimal=NCBI+Ensembl ids; compact (default)=the high-value ids (NCBI, Ensembl, UniProt, RefSeq, MANE Select, OMIM, CCDS); standard/full=every populated field. databases optionally filters to specific sources by field key OR friendly label (e.g. 'mane', 'ncbi', 'uniprot') and OVERRIDES the response_mode tier; an unknown key is rejected with invalid_input + did-you-mean. Resolve the gene from an id/symbol/alias first. Signature: get_gene_cross_references(query, databases=, response_mode=).

ParametersJSON Schema
NameRequiredDescriptionDefault
queryYesA gene symbol (current/previous/alias, case-insensitive) or HGNC id (HGNC:1100 or 1100).
databasesNoOptional cross-reference filter: a list of field keys or friendly labels (e.g. 'ncbi', 'ensembl', 'uniprot', 'refseq', 'mane', 'omim', 'ucsc', 'vega', 'ccds', 'mgi', 'rgd', 'pubmed'). Overrides the response_mode tier; an unknown key is rejected with invalid_input + did_you_mean.
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

TDQS

A4.2/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already indicate read-only, idempotent, open-world. The description adds valuable behavioral details: unknown database keys yield invalid_input+did-you-mean, databases overrides response_mode, and the signature. No contradiction with annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is front-loaded with purpose and parameter highlights, but includes a signature line. Nearly all sentences add value; minor redundancy with schema examples. Overall efficient.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

No output schema is provided, but the description does not explain the return format (e.g., list of objects with fields). For a complex tool with three parameters, this gap reduces completeness. However, the description covers input and behavior well.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Parameters have 100% schema coverage. The description adds meaning beyond schema by listing database options, explaining response_mode tiers (minimal, compact, standard, full), and the override behavior with databases.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description explicitly states the tool returns external database cross-references for a gene, listing many databases and explaining response_mode and databases parameters. It differentiates from sibling tools like get_gene (gene details) and resolve_gene_by_xref (reverse mapping).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description mentions resolving the gene first and how parameters work, but does not explicitly compare to alternatives like resolve_gene_by_xref for reverse mapping. Usage context is clear but lack of when-not-to-use slightly lowers score.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_gene_groupGet Gene GroupA
Read-onlyIdempotent

Browse a HGNC gene group/family by numeric group id (e.g. '1157') or by name (e.g. 'RAF family'). Returns the member genes as symbol-ordered summaries. Members are paginated with limit + offset; the response carries member_count, returned, truncated, and next_offset, and (when truncated) a next_commands entry that fetches the next page. A name matching several groups returns the candidate groups so you can re-call with a specific id. Signature: get_gene_group(group, limit=, offset=, response_mode=).

ParametersJSON Schema
NameRequiredDescriptionDefault
groupYesGene group id (numeric) or group name.
limitNoMax members (default 200).
offsetNoSkip this many members for pagination (default 0).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

TDQS

A4.7/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations (readOnlyHint, idempotentHint) are reinforced by description detailing pagination, response fields (member_count, returned, truncated, next_offset, next_commands), and ambiguity resolution. No contradictions.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Single, well-structured paragraph with clear sentences. Front-loads the main action, then details pagination and edge cases. No wasted words.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite no output schema, the description fully explains pagination, ambiguity handling, and response structure. Covers all necessary behaviors for an AI agent to use the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema covers 100% parameters, but description adds meaning: group parameter examples, pagination behavior for limit/offset, and response_mode verbosity levels. Enhances understanding beyond schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'Browse' and the resource 'HGNC gene group/family', with specific input options (numeric id or name). It distinguishes from siblings like get_gene which handles individual genes.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicit usage context: browse groups by id or name. It describes how to handle ambiguous names by returning candidates for re-call with an id. Lacks explicit when-not-to-use, but sibling names provide context differentiation.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_hgnc_diagnosticsGet HGNC DiagnosticsA
Read-onlyIdempotent

Report the local HGNC index status: whether the data is built, the loaded release date, gene/withdrawn counts, schema version, and when it was built. Use this to confirm freshness or diagnose an unavailable-data error. Signature: get_hgnc_diagnostics().

ParametersJSON Schema
NameRequiredDescriptionDefault

No parameters

TDQS

A4.8/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, openWorldHint=true, idempotentHint=true, destructiveHint=false. The description adds that the tool reports status with no side effects and specifies the exact output fields and the fact that it takes no parameters, going beyond annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences plus a signature line. Extremely concise, with all key information front-loaded. No unnecessary words.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite no output schema, the description enumerates all returned fields: built status, release date, gene/withdrawn counts, schema version, built time. This is complete for a diagnostic tool and aligns with the stated use case of confirming freshness or diagnosing errors.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The tool has no parameters (0 params, schema coverage 100%). The description explicitly states 'Signature: get_hgnc_diagnostics()' confirming no arguments, which adds clarity beyond the empty schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool reports local HGNC index status with specific fields (built status, release date, counts, schema version, built time). It distinguishes from sibling tools which focus on gene lookup and cross-references, not diagnostics.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly says 'Use this to confirm freshness or diagnose an unavailable-data error', providing clear context for when to use. Does not explicitly mention alternatives like get_server_capabilities, but the use case is well-defined.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_server_capabilitiesGet Server CapabilitiesA
Read-onlyIdempotent

Return the hgnc-link discovery surface. detail='summary' (default) is light: identity/build/HGNC release, the tool list WITH call signatures, accepted argument aliases, response modes, recommended workflows, error taxonomy, and limits. detail='full' adds vocabularies (locus groups, status values, match types) and the cross-reference database catalogue. Call this first in a cold session, or read hgnc://tools / hgnc://capabilities. Signature: get_server_capabilities(detail=).

ParametersJSON Schema
NameRequiredDescriptionDefault
detailNosummary (default, light) or full (adds vocabularies/xref dbs).summary

TDQS

A4.7/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare read-only and idempotent. The description adds detail on return structure and suggests it as a discovery surface, but does not disclose rate limits or auth requirements.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is front-loaded with purpose, efficiently details both detail modes, and provides a clear call to action. Every sentence is informative with no redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite no output schema, the description fully explains return contents for both detail levels and mentions alternative access. This is complete for a server capabilities tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema has 100% coverage with enum and default. The description adds semantic context by detailing what each detail level contains, going beyond the schema's short description.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool returns the 'hgnc-link discovery surface' with a specific verb and resource. It distinguishes from sibling gene-focused tools by addressing server metadata.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly advises 'Call this first in a cold session' and provides alternative access methods (hgnc://tools / hgnc://capabilities). Detail levels are contrasted to guide selection.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

resolve_gene_by_xrefResolve Gene by Cross-ReferenceA
Read-onlyIdempotent

Reverse identifier mapping: find the HGNC gene(s) for an external database id. source is the database (entrez_id/ncbi, ensembl_gene_id, uniprot, refseq, mane_select, omim, ucsc, vega, ccds, mgi, rgd) and value is the id (e.g. source='ensembl_gene_id', value='ENSG00000157764'). A version suffix is tolerated (ENSG00000012048.23 resolves like ENSG00000012048), and a MANE Select transcript (ENST…/NM_…) resolves back to its gene. Signature: resolve_gene_by_xref(source, value, response_mode=).

ParametersJSON Schema
NameRequiredDescriptionDefault
valueYesThe external identifier value to look up (a version suffix is fine).
sourceYesCross-reference database. Canonical keys: entrez_id, ensembl_gene_id, uniprot_ids, refseq_accession, mane_select, omim_id, ucsc_id, vega_id, ccds_id, ena, mgd_id, rgd_id. Common synonyms (ncbi, ensembl, uniprot, refseq, mane, omim, mgi, rgd) are also accepted.
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

TDQS

A4.2/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint, idempotentHint, and not destructive. The description adds behavioral context about version suffix handling and transcript resolution, which goes beyond annotations without contradiction.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two concise sentences plus a signature line. Every sentence is purposeful, no redundancy. The core purpose is front-loaded.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given no output schema, the description does not explain return format, but for a lookup tool with annotations, the input guidance is sufficient. Missing mention of multiple/no results is minor.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so baseline is 3. The description adds examples and explains source synonyms and version suffix handling, providing minor added value over the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it is a 'reverse identifier mapping' to 'find the HGNC gene(s) for an external database id', specifying verb and resource. It distinguishes from siblings like resolve_symbol (resolves symbols) and get_gene_cross_references (retrieves existing xrefs).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides clear usage context with examples of source and value, tolerates version suffixes and MANE Select transcripts. It implicitly differentiates from alternatives but lacks explicit when-not-to-use statements.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

resolve_symbolResolve Gene SymbolA
Read-onlyIdempotent

Resolve any gene symbol or HGNC id to its canonical record. Accepts a current symbol, a previous (withdrawn) symbol, an alias, or an HGNC id in either form (HGNC:1100 or 1100), case-insensitively. Returns {hgnc_id, approved_symbol, match_type (hgnc_id|current|previous|alias)}. An alias shared by several genes returns an ambiguous_query error with the candidate list (not silently picked); a withdrawn/merged symbol returns a not_found error that redirects to the successor record. Signature: resolve_symbol(query, response_mode=).

ParametersJSON Schema
NameRequiredDescriptionDefault
queryYesA gene symbol (current/previous/alias, case-insensitive) or HGNC id (HGNC:1100 or 1100).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

TDQS

A4.4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations declare readOnly, openWorld, idempotent, and non-destructive hints. The description adds case-insensitivity, return format {hgnc_id, approved_symbol, match_type}, and error behavior (ambiguous returns candidates, not_found redirects). No contradictions.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three concise sentences: purpose, input/output/error details, and signature. No wasted words; each sentence serves a distinct purpose.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Covers inputs, outputs, and error cases. With 2 parameters and 100% schema coverage, the description sufficiently explains behavior. Lacks definition of response_mode verbosity levels, but output schema is absent; still adequate for most agents.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, but the description adds meaning beyond schema: explains query parameter accepts symbols/aliases/HGNC ids, and lists response_mode enum values with default 'compact'. However, it does not detail what each verbosity level returns; output schema is absent but description compensates with return fields.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool resolves any gene symbol or HGNC id to canonical record, specifying input types (current, previous, alias, HGNC id) and output fields. It distinguishes from siblings like resolve_gene_by_xref and resolve_symbols_batch by focusing on symbol/HGNC resolution.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly lists accepted inputs and mentions error handling (ambiguous_query with candidate list, not_found redirect). However, it does not explicitly state when to use alternatives like search_genes or get_gene, but the sibling list provides context.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

resolve_symbols_batchResolve Gene Symbols (Batch)A
Read-onlyIdempotent

Resolve a batch of gene symbols / HGNC ids in one call (max 200). Each entry is resolved with the same current->previous->alias cascade as resolve_symbol; an individual miss or withdrawal never fails the batch (it is marked unresolved / obsolete in that entry). Returns per-query results plus resolved/unresolved counts. Signature: resolve_symbols_batch(queries, response_mode=).

ParametersJSON Schema
NameRequiredDescriptionDefault
queriesYesGene symbols and/or HGNC ids to resolve (max 200).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

TDQS

A4.7/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Discloses the resolution cascade, individual miss behavior (marked unresolved/obsolete), and returned counts. No contradictions with annotations (readOnlyHint, idempotentHint, etc.).

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three focused sentences with no redundancy. Front-loaded with purpose. Highly efficient.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Explains return values (per-query results + counts) despite no output schema. Could briefly describe what each response_mode yields, but overall sufficiently complete for a batch read tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema has 100% coverage, but description adds significant context: explains the cascade, batch safety, and that response_mode controls verbosity. Mentions signature for clarity.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Description clearly states it resolves a batch of gene symbols/HGNC IDs (max 200) with the same cascade as resolve_symbol. It specifies per-query results and counts, distinguishing it from sibling tools like resolve_symbol.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Provides clear context for batch usage (max 200) and behavior on misses/withdrawals. Implicitly suggests using resolve_symbol for single queries, but lacks an explicit when-not statement.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

search_genesSearch GenesA
Read-onlyIdempotent

Free-text search over gene symbols, names, aliases, and previous symbols (FTS, relevance-ranked). Returns ranked {hgnc_id, symbol, name, locus_type, score} summaries. Nomenclature-only: there is NO disease/phenotype semantics, so a descriptive query (e.g. 'polycystin kidney') only matches words present in a gene's nomenclature. Use resolve_symbol for an exact symbol/id; use this for partial names. Signature: search_genes(query, limit=, response_mode=).

ParametersJSON Schema
NameRequiredDescriptionDefault
limitNoMax hits (default 25).
queryYesFree-text query (symbol fragment, name, alias).
response_modeNoVerbosity: minimal | compact | standard | full (default compact).compact

TDQS

A4.7/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already show readOnlyHint, idempotentHint, etc. The description adds beyond them by specifying FTS relevance-ranked search, return fields, and the nomenclature-only constraint, giving full behavioral context without contradiction.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three sentences, each earning its place: purpose, limitation, usage guidance. Front-loaded with key action and return format. No wasted words.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite no output schema, the description specifies return fields and structure. Covers search behavior, limitations, and usage context. With sibling list and robust annotations, no important context is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so baseline is 3. The description reiterates parameter roles (e.g., query is free-text) and adds a signature line, but does not significantly extend parameter meaning beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states 'Free-text search over gene symbols, names, aliases, and previous symbols' with a specific verb and resource. It distinguishes from siblings by directing to resolve_symbol for exact matches and highlighting nomenclature-only scope.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly tells when to use this tool ('use this for partial names') and when to use alternatives ('use resolve_symbol for an exact symbol/id'). Also clarifies that descriptive queries only match nomenclature words, providing clear usage boundaries.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. 9 tool updatesv2.1.0
    • Changedget_gene1 field changed
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "alias_symbol": {
        -      "type": "array"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "ensembl_gene_id": {
        -      "type": "string"
        -    },
        -    "entrez_id": {
        -      "type": "string"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "gene_group": {
        -      "type": "array"
        -    },
        -    "gene_group_id": {
        -      "type": "array"
        -    },
        -    "hgnc_id": {
        -      "type": "string"
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "location": {
        -      "type": "string"
        -    },
        -    "locus_group": {
        -      "type": "string"
        -    },
        -    "locus_type": {
        -      "type": "string"
        -    },
        -    "mane_select": {
        -      "type": "array"
        -    },
        -    "match_type": {
        -      "type": "string"
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "name": {
        -      "type": "string"
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "omim_id": {
        -      "type": "array"
        -    },
        -    "prev_symbol": {
        -      "type": "array"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "refseq_accession": {
        -      "type": "array"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "requested_query": {
        -      "type": "string"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "status": {
        -      "type": "string"
        -    },
        -    "success": {
        -      "type": "boolean"
        -    },
        -    "symbol": {
        -      "type": "string"
        -    },
        -    "uniprot_ids": {
        -      "type": "array"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
    • Changedget_gene_cross_references4 fields changed
      • changedInput schema / properties / databases / description
        Previous value: -"Optional database filter, e.g. ['ensembl','uniprot','omim']."New value: +"Optional cross-reference filter: a list of field keys or friendly labels (e.g. 'ncbi', 'ensembl', 'uniprot', 'refseq', 'mane', 'omim', 'ucsc', 'vega', 'ccds', 'mgi', 'rgd', 'pubmed'). Overrides the response_mode tier; an unknown key is rejected with invalid_input + did_you_mean."
      • addedInput schema / properties / databases / examples
        Added value: +[
        +  [
        +    "ensembl",
        +    "uniprot",
        +    "omim"
        +  ],
        +  [
        +    "mane"
        +  ]
        +]
      • addedInput schema / properties / databases / items
        Added value: +{
        +  "enum": [
        +    "ccds",
        +    "ccds_id",
        +    "cosmic",
        +    "ena",
        +    "ensembl",
        +    "ensembl_gene_id",
        +    "ensg",
        +    "entrez",
        +    "entrez_id",
        +    "gene_id",
        +    "mane",
        +    "mane select",
        +    "mane_select",
        +    "mgd_id",
        +    "mgi",
        +    "mim",
        +    "ncbi",
        +    "ncbi gene",
        +    "ncbi_gene",
        +    "ncbi_gene_id",
        +    "omim",
        +    "omim_id",
        +    "orphanet",
        +    "pubmed",
        +    "pubmed_id",
        +    "refseq",
        +    "refseq_accession",
        +    "rgd",
        +    "rgd_id",
        +    "ucsc",
        +    "ucsc_id",
        +    "uniprot",
        +    "uniprot_id",
        +    "uniprot_ids",
        +    "vega",
        +    "vega_id"
        +  ],
        +  "type": "string"
        +}
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "cross_references": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "database_count": {
        -      "type": "integer"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "hgnc_id": {
        -      "type": "string"
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "match_type": {
        -      "type": "string"
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "success": {
        -      "type": "boolean"
        -    },
        -    "symbol": {
        -      "type": "string"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
    • Changedget_gene_group1 field changed
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "ambiguous": {
        -      "type": "boolean"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "group_id": {
        -      "type": "string"
        -    },
        -    "group_name": {
        -      "type": "string"
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "limit": {
        -      "type": "integer"
        -    },
        -    "match_count": {
        -      "type": "integer"
        -    },
        -    "matches": {
        -      "type": "array"
        -    },
        -    "member_count": {
        -      "type": "integer"
        -    },
        -    "members": {
        -      "type": "array"
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "next_offset": {
        -      "type": [
        -        "integer",
        -        "null"
        -      ]
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "offset": {
        -      "type": "integer"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "returned": {
        -      "type": "integer"
        -    },
        -    "score": {
        -      "type": "number"
        -    },
        -    "success": {
        -      "type": "boolean"
        -    },
        -    "truncated": {
        -      "type": "boolean"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
    • Changedget_hgnc_diagnostics1 field changed
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "built_utc": {
        -      "type": "string"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "data_available": {
        -      "type": "boolean"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "gene_count": {
        -      "type": "integer"
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "live_fallback_enabled": {
        -      "type": "boolean"
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "release": {
        -      "type": "string"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "source_last_modified": {
        -      "type": "string"
        -    },
        -    "success": {
        -      "type": "boolean"
        -    },
        -    "symbol_lookup_rows": {
        -      "type": "integer"
        -    },
        -    "withdrawn_count": {
        -      "type": "integer"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
    • Changedget_server_capabilities1 field changed
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "error_codes": {
        -      "type": "array"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "hgnc_release": {
        -      "type": "string"
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "response_modes": {
        -      "type": "array"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "server": {
        -      "type": "string"
        -    },
        -    "server_version": {
        -      "type": "string"
        -    },
        -    "success": {
        -      "type": "boolean"
        -    },
        -    "tools": {
        -      "type": "array"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
    • Changedresolve_gene_by_xref6 fields changed
      • changedInput schema / properties / source / description
        Previous value: -"Cross-reference database, e.g. entrez_id, ensembl_gene_id, uniprot."New value: +"Cross-reference database. Canonical keys: entrez_id, ensembl_gene_id, uniprot_ids, refseq_accession, mane_select, omim_id, ucsc_id, vega_id, ccds_id, ena, mgd_id, rgd_id. Common synonyms (ncbi, ensembl, uniprot, refseq, mane, omim, mgi, rgd) are also accepted."
      • addedInput schema / properties / source / enum
        Added value: +[
        +  "ccds",
        +  "ccds_id",
        +  "ena",
        +  "ensembl",
        +  "ensembl_gene_id",
        +  "ensg",
        +  "entrez",
        +  "entrez_id",
        +  "gene_id",
        +  "mane",
        +  "mane_select",
        +  "mgd_id",
        +  "mgi",
        +  "mim",
        +  "ncbi",
        +  "ncbi_gene",
        +  "ncbi_gene_id",
        +  "omim",
        +  "omim_id",
        +  "refseq",
        +  "refseq_accession",
        +  "rgd",
        +  "rgd_id",
        +  "ucsc",
        +  "ucsc_id",
        +  "uniprot",
        +  "uniprot_id",
        +  "uniprot_ids",
        +  "vega",
        +  "vega_id"
        +]
      • addedInput schema / properties / source / examples
        Added value: +[
        +  "ensembl_gene_id",
        +  "refseq",
        +  "mane_select"
        +]
      • changedInput schema / properties / value / description
        Previous value: -"The external identifier value to look up."New value: +"The external identifier value to look up (a version suffix is fine)."
      • addedInput schema / properties / value / examples
        Added value: +[
        +  "ENSG00000157764",
        +  "NM_004333.6",
        +  "P15056"
        +]
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "count": {
        -      "type": "integer"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "results": {
        -      "type": "array"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "source": {
        -      "type": "string"
        -    },
        -    "source_label": {
        -      "type": "string"
        -    },
        -    "success": {
        -      "type": "boolean"
        -    },
        -    "value": {
        -      "type": "string"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
    • Changedresolve_symbol1 field changed
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "ambiguous": {
        -      "type": "boolean"
        -    },
        -    "approved_symbol": {
        -      "type": [
        -        "string",
        -        "null"
        -      ]
        -    },
        -    "candidate_count": {
        -      "type": "integer"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "hgnc_id": {
        -      "type": [
        -        "string",
        -        "null"
        -      ]
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "location": {
        -      "type": [
        -        "string",
        -        "null"
        -      ]
        -    },
        -    "locus_type": {
        -      "type": [
        -        "string",
        -        "null"
        -      ]
        -    },
        -    "match_type": {
        -      "type": [
        -        "string",
        -        "null"
        -      ]
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "name": {
        -      "type": [
        -        "string",
        -        "null"
        -      ]
        -    },
        -    "note": {
        -      "type": "string"
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "other_matches": {
        -      "type": "array"
        -    },
        -    "query": {
        -      "type": "string"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "status": {
        -      "type": [
        -        "string",
        -        "null"
        -      ]
        -    },
        -    "success": {
        -      "type": "boolean"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
    • Changedresolve_symbols_batch2 fields changed
      • addedInput schema / properties / queries / examples
        Added value: +[
        +  [
        +    "BRCA1",
        +    "TP53",
        +    "HGNC:1100"
        +  ]
        +]
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "query_count": {
        -      "type": "integer"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "resolved_count": {
        -      "type": "integer"
        -    },
        -    "results": {
        -      "type": "array"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "success": {
        -      "type": "boolean"
        -    },
        -    "unresolved_count": {
        -      "type": "integer"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
    • Changedsearch_genes2 fields changed
      • addedInput schema / properties / query / examples
        Added value: +[
        +  "BRCA",
        +  "kinase",
        +  "TP53"
        +]
      • changedOutput schema / (root)
        Previous value: -{
        -  "additionalProperties": true,
        -  "properties": {
        -    "_meta": {
        -      "additionalProperties": true,
        -      "type": "object"
        -    },
        -    "allowed_values": {
        -      "type": "array"
        -    },
        -    "candidates": {
        -      "type": "array"
        -    },
        -    "count": {
        -      "type": "integer"
        -    },
        -    "error_code": {
        -      "type": "string"
        -    },
        -    "field": {
        -      "type": "string"
        -    },
        -    "hint": {
        -      "type": "string"
        -    },
        -    "message": {
        -      "type": "string"
        -    },
        -    "obsolete": {
        -      "type": "boolean"
        -    },
        -    "query": {
        -      "type": "string"
        -    },
        -    "recovery_action": {
        -      "type": "string"
        -    },
        -    "replaced_by": {
        -      "type": "array"
        -    },
        -    "results": {
        -      "type": "array"
        -    },
        -    "retryable": {
        -      "type": "boolean"
        -    },
        -    "success": {
        -      "type": "boolean"
        -    }
        -  },
        -  "type": "object"
        -}New value: +null
  2. 9 tool updatesv1.0.2
    • First observedget_gene
    • First observedget_gene_cross_references
    • First observedget_gene_group
    • First observedget_hgnc_diagnostics
    • First observedget_server_capabilities
    • First observedresolve_gene_by_xref
    • First observedresolve_symbol
    • First observedresolve_symbols_batch
    • First observedsearch_genes

TDQS

A4.6/5.0
Disambiguation5/5

All nine tools have clearly distinct purposes: gene retrieval, cross-references, group browsing, diagnostics, capabilities, reverse lookup, single/batch symbol resolution, and free-text search. There is no overlap or ambiguity between any two tools.

Naming Consistency5/5

Tool names follow a consistent verb_noun pattern (e.g., get_gene, resolve_symbol, search_genes). The verbs are either get, resolve, or search, each clearly indicating the action, and the nouns specify the target. No mixing of conventions.

Tool Count5/5

With 9 tools, the server is well-scoped for the HGNC nomenclature domain. Each tool serves a distinct and necessary function (lookup, batch, search, cross-references, etc.), and the count is neither too sparse nor overwhelming.

Completeness5/5

The tool surface covers all core operations for a gene nomenclature service: single and batch resolution, forward and reverse cross-reference mapping, group browsing, free-text search, and server diagnostics/capabilities. There are no obvious missing operations for the stated purpose.

Maintenance

ActivityActive
ResponsivenessWithin a week

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