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Folklore Clinical Variant Interpretation MCP

by io.github.helena-bioinformatics

Get details for a PubMed publication

get_publication_details
Read-onlyIdempotent

Retrieve the complete public bibliographic record for one PMID from Folklore's PubMed-derived genetics corpus. Returns the full abstract, authors, journal metadata, publication and MeSH terms, gene and variant mentions, retraction status, and PubMed/PMC links. Use after literature search when a user asks to inspect a specific publication. This is read-only professional literature evidence and contains no patient context.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidYesOne PubMed identifier to look up in Folklore's current corpus, as 1 to 12 digits without a PMID prefix.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
publicationYes
usage_boundaryYes
contract_versionYes

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed2 schema fields changed
    • addedOutput schema / $defs / PublicAbstractReuse
      Added value: +{
+  "additionalProperties": false,
+  "properties": {
+    "allowed": {
+      "default": false,
+      "title": "Allowed",
+      "type": "boolean"
+    },
+    "evidence_url": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Evidence Url"
+    },
+    "license": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "License"
+    },
+    "source": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Source"
+    }
+  },
+  "title": "PublicAbstractReuse",
+  "type": "object"
+}
    • addedOutput schema / $defs / PublicPublicationDetails / properties / abstract_reuse
      Added value: +{
+  "$ref": "#/$defs/PublicAbstractReuse"
+}
  2. Changed1 schema field changed
    • addedInput schema / properties / pmid / description
      Added value: +"One PubMed identifier to look up in Folklore's current corpus, as 1 to 12 digits without a PMID prefix."
  3. Added

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, and destructiveHint=false. The description adds non-redundant context by noting the data is 'professional literature evidence and contains no patient context,' which is useful for privacy and sensitivity assessment. It also highlights that retraction status is included, a behavioral detail beyond what annotations cover.

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 tightly written sentences, each earning its place: the first states the action and scope, the second lists return contents, the third gives usage context and safety framing. It is front-loaded with the verb and resource and contains no filler.

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?

For a one-parameter, read-only, idempotent tool with an output schema and rich annotations, the description covers purpose, scope, return contents, usage trigger, and data sensitivity. There is no missing information an agent would need to invoke it correctly.

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%: the sole pmid parameter is fully documented with pattern, format, and prefix guidance. The description doesn't add any additional parameter-level semantics, so it does not exceed the 3-point baseline expected when structured schema already covers parameters completely.

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 opens with a specific verb ('Retrieve') and names a precise resource: 'complete public bibliographic record for one PMID from Folklore's PubMed-derived genetics corpus.' It then enumerates the returned fields (abstract, authors, journal, MeSH terms, gene/variant mentions, retraction status, links), which clearly separates it from the sibling search tools that return sets of results rather than a single record.

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 gives an explicit trigger: 'Use after literature search when a user asks to inspect a specific publication.' This clearly tells an agent when to invoke it, but it does not explicitly name alternatives or state when not to use it beyond the implied contrast with searching. It is clear context without formal exclusions, so not a 5.

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

All Folklore Clinical Variant Interpretation MCP toolsInspect
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TDQS

A4.3/5.0
Disambiguation4/5

Most tools have clearly distinct roles: evidence/classification, variant-specific literature, broad literature search, publication details, and an auxiliary support action. The main ambiguity is between search_literature_corpus and search_variant_literature, though their descriptions clarify that one is a general semantic search and the other resolves a specific variant's publications.

Naming Consistency5/5

All tool names follow a consistent snake_case verb_noun pattern: get_publication_details, search_literature_corpus, search_variant_evidence, search_variant_literature, and support_helena. The naming convention is uniform and predictable.

Tool Count5/5

Five tools is a well-scoped count for a clinical variant interpretation server. Each tool contributes to literature search, variant evidence, publication retrieval, or explicit support infrastructure, without unnecessary bloat.

Completeness4/5

The core workflow is covered: find literature, retrieve publication details, resolve a variant, obtain ACMG/AMP evidence, and find variant-specific publications. Minor gaps exist for batch variant handling or larger/structural variants, but within the stated GRCh38 SNV/indel scope the surface is reasonably complete.

Resources