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pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

get_text_mined_terms

Read-onlyIdempotent

Extract text-mined entities such as genes, diseases, chemicals, and organisms from PubMed/PMC articles. Filter by semantic type.

Instructions

Get text-mined annotations from Europe PMC.

Returns entities extracted from the article text including genes, diseases, chemicals, organisms, and more. source is exactly one PMID or PMCID.

Args: source: {"kind":"pmid","value":"12345678"} or {"kind":"pmcid","value":"PMC7096777"}. semantic_type: Filter by entity type. Options: - "GENE_PROTEIN": Genes and proteins - "DISEASE": Diseases and conditions - "CHEMICAL": Drugs and chemicals - "ORGANISM": Species and organisms - "GO_TERM": Gene Ontology terms - None: Return all types (default)

Returns: List of text-mined entities with counts and sections.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sourceYes
output_formatNomarkdown
semantic_typeNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed8 schema fields changedv0.7.2
    • addedInput schema / $defs
      Added value: +{
+  "PMCIDSource": {
+    "additionalProperties": false,
+    "description": "An explicit PubMed Central identifier.",
+    "properties": {
+      "kind": {
+        "const": "pmcid",
+        "title": "Kind",
+        "type": "string"
+      },
+      "value": {
+        "maxLength": 23,
+        "pattern": "^PMC[1-9][0-9]{0,19}$",
+        "title": "Value",
+        "type": "string"
+      }
+    },
+    "required": [
+      "kind",
+      "value"
+    ],
+    "title": "PMCIDSource",
+    "type": "object"
+  },
+  "PMIDSource": {
+    "additionalProperties": false,
+    "description": "An explicit PubMed identifier.",
+    "properties": {
+      "kind": {
+        "const": "pmid",
+        "title": "Kind",
+        "type": "string"
+      },
+      "value": {
+        "maxLength": 20,
+        "pattern": "^[1-9][0-9]{0,19}$",
+        "title": "Value",
+        "type": "string"
+      }
+    },
+    "required": [
+      "kind",
+      "value"
+    ],
+    "title": "PMIDSource",
+    "type": "object"
+  }
+}
    • addedInput schema / additionalProperties
      Added value: +false
    • removedInput schema / properties / pmcid
      Removed value: -{
-  "anyOf": [
-    {
-      "type": "string"
-    },
-    {
-      "type": "integer"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "title": "Pmcid"
-}
    • removedInput schema / properties / pmid
      Removed value: -{
-  "anyOf": [
-    {
-      "type": "string"
-    },
-    {
-      "type": "integer"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "title": "Pmid"
-}
    • changedInput schema / properties / semantic_type / anyOf
      Previous value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "enum": [
+      "GENE_PROTEIN",
+      "DISEASE",
+      "CHEMICAL",
+      "ORGANISM",
+      "GO_TERM",
+      "EFO"
+    ],
+    "type": "string"
+  },
+  {
+    "type": "null"
+  }
+]
    • addedInput schema / properties / source
      Added value: +{
+  "discriminator": {
+    "mapping": {
+      "pmcid": "#/$defs/PMCIDSource",
+      "pmid": "#/$defs/PMIDSource"
+    },
+    "propertyName": "kind"
+  },
+  "oneOf": [
+    {
+      "$ref": "#/$defs/PMIDSource"
+    },
+    {
+      "$ref": "#/$defs/PMCIDSource"
+    }
+  ],
+  "title": "Source"
+}
    • addedInput schema / required
      Added value: +[
+  "source"
+]
    • changedOutput schema / (root)
      Previous value: -{
-  "properties": {
-    "result": {
-      "title": "Result",
-      "type": "string"
-    }
-  },
-  "required": [
-    "result"
-  ],
-  "title": "get_text_mined_termsOutput",
-  "type": "object"
-}New value: +null
  2. First observedv0.5.16

TDQS

A3.7/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, and openWorldHint, so safety and repeatability are covered structurally. The description adds the useful constraint that `source` is exactly one PMID or PMCID (a scope limit not visible in annotations), but says nothing about rate limits, coverage gaps, or behavior for articles without mined terms.

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 purpose and scope constraint are front-loaded in the first three lines, and the Args/Returns block is compact and scannable. Some redundancy exists between the prose entity list ('genes, diseases, chemicals, organisms') and the later semantic_type enumeration, costing a little efficiency.

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?

With no output schema, the description correctly spends a line on return shape ('List of text-mined entities with counts and sections'). It is complete enough to call correctly, with the minor gaps of the undocumented output_format parameter and the missing EFO option.

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 description coverage is 0%, so the description carries the burden and largely does: it spells out the PMID/PMCID shape and enumerates the semantic_type options. It omits the `output_format` parameter entirely and omits the EFO value present in the schema enum, but the substantive parameters are well documented.

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?

States a specific verb and resource ('Get text-mined annotations from Europe PMC') and enumerates the entity types returned, which no sibling tool provides. An agent can distinguish this from get_article_figures, fetch_article_details, or get_fulltext without opening a schema.

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

Usage Guidelines2/5

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

The description explains what is returned but gives no when-to-use or when-not-to-use guidance and names no alternative sibling (e.g., get_fulltext for raw text). The agent must infer that this tool is for entity extraction rather than full-text or figure retrieval.

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

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