pubmed-mcp-server

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Pubmed Lookup Citation

pubmed_lookup_citation

Read-only

Convert partial bibliographic citations into PubMed IDs using deterministic ECitMatch matching. Provide journal, year, volume, page, or author to reliably find the PMID for a structured reference.

Instructions

Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`citations`	Yes	Citations to look up. More fields = better match accuracy.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`results`	No	Match results, one per input citation
`totalMatched`	No	Number of citations with PMID matches
`totalWarnings`	No	Number of matched citations that carry at least one warning
`totalSubmitted`	No	Number of citations submitted

Schema Changelog

Changes observed during successful MCP inspections.

Changed11 schema fields changedv2.10.12Sep 11, 2026

changedInput schema / properties / citations / items / properties / authorName / description

Previous value: -"Author name, typically \"lastname initials\" (e.g., \"mann bj\")"New value: +"Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break."

addedInput schema / properties / citations / items / properties / authorName / pattern
```
Added value: +"^[^|\\r\\n]*$"
```

changedInput schema / properties / citations / items / properties / firstPage / description

Previous value: -"First page number"New value: +"First page number. Cannot contain a pipe (\"|\") or a line break."

addedInput schema / properties / citations / items / properties / firstPage / pattern
```
Added value: +"^[^|\\r\\n]*$"
```

changedInput schema / properties / citations / items / properties / journal / description

Previous value: -"Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\")"New value: +"Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break."

addedInput schema / properties / citations / items / properties / journal / pattern
```
Added value: +"^[^|\\r\\n]*$"
```

changedInput schema / properties / citations / items / properties / key / description

Previous value: -"Arbitrary label to track this citation in results. Auto-assigned if omitted."New value: +"Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here."

changedInput schema / properties / citations / items / properties / volume / description

Previous value: -"Volume number"New value: +"Volume number. Cannot contain a pipe (\"|\") or a line break."

addedInput schema / properties / citations / items / properties / volume / pattern
```
Added value: +"^[^|\\r\\n]*$"
```

changedInput schema / properties / citations / items / properties / year / description

Previous value: -"Publication year (e.g., \"1991\")"New value: +"Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break."

addedInput schema / properties / citations / items / properties / year / pattern
```
Added value: +"^[^|\\r\\n]*$"
```

Changed6 schema fields changedv2.10.4Aug 28, 2026

changedInput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedInput schema / additionalProperties
```
Added value: +false
```

changedOutput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedOutput schema / anyOf

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "results",
+      "totalMatched",
+      "totalSubmitted",
+      "totalWarnings"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

addedOutput schema / properties / error

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "queue_full",
+            "ncbi_unreachable",
+            "ncbi_deadline_exceeded",
+            "ncbi_invalid_response",
+            "ncbi_resource_not_found"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

removedOutput schema / required

Removed value: -[
-  "results",
-  "totalMatched",
-  "totalSubmitted",
-  "totalWarnings"
-]

Changed1 schema field changedv2.9.1Jun 9, 2026

changedInput schema / properties / citations / items / description

Previous value: -"Citation to match against PubMed. Must include at least one bibliographic field (journal, year, volume, firstPage, or authorName)."New value: +"Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match."

Addedv2.7.6May 29, 2026
Removedv2.7.4May 24, 2026
Addedv2.3.2Apr 4, 2026

TDQS

A4.2/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and openWorldHint, so safety is covered. The description adds real behavioral context: deterministic citation matching via ECitMatch, primary-keying on journal+volume+page, and the guarantee that author-only or volume-only inputs yield no match — non-obvious traits an agent needs.

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?

Three sentences, front-loaded with the action and purpose before constraints. The dense parenthetical about ECitMatch keying is information-rich rather than wasteful, though slightly compact for quick parsing.

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 an output schema present, return values need no explanation. The description covers the matching mechanism, input requirements, and accuracy tradeoffs; combined with readOnly/openWorld annotations, an agent has everything needed 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% and the nested citation schema already documents each field plus the journal-or-year requirement and the primary-key behavior, so the description largely repeats structured content. It reinforces field-selection strategy ("more fields = better match accuracy") but adds little 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?

States a specific verb and resource (look up PubMed IDs from partial bibliographic citations) and clearly scopes the input shape (journal, year, volume, page, author). It also contrasts itself with free-text search for structured references, letting an agent distinguish it from pubmed_search_articles.

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?

"Useful when you have a reference ... and need the PMID" gives explicit when-to-use context and positions it against free-text search. It does not name the sibling (pubmed_search_articles) directly or state when-not to use it, so it falls short of a full 5.

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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