pubmed-mcp-server

Pubmed Convert Ids

pubmed_convert_ids

Read-only

Convert DOI, PMID, and PMCID identifiers for articles indexed in PubMed Central. Submit up to 50 IDs of one type to resolve them across formats.

Instructions

Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`ids`	Yes	Article identifiers to convert — one identifier per element, all of the same type. Each element is checked against `idType` before the request: `doi` starts with "10." and carries a "/" ("10.1093/nar/gks1195"); `pmid` is digits ("23193287"); `pmcid` is digits with an optional "PMC" prefix ("PMC3531190" or "3531190"). No element may contain a comma or whitespace — a packed value like "23193287,37952131" is rejected, so split it across elements.
`idType`	Yes	The type of IDs being submitted. Required so the API can unambiguously resolve them.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`records`	No	Conversion results, one per input ID
`totalConverted`	No	Number of IDs successfully converted
`totalSubmitted`	No	Number of IDs submitted

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedv2.10.19Sep 30, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `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). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `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). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "queue_full",
-  "ncbi_unreachable",
-  "ncbi_deadline_exceeded",
-  "ncbi_invalid_response",
-  "ncbi_resource_not_found",
-  "malformed_id"
-]New value: +[
+  "queue_full",
+  "ncbi_unreachable",
+  "ncbi_rate_limited",
+  "ncbi_deadline_exceeded",
+  "ncbi_invalid_response",
+  "ncbi_resource_not_found",
+  "malformed_id"
+]

Changed1 schema field changedv2.10.18Sep 23, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"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). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `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). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."

Changed3 schema fields changedv2.10.12Sep 11, 2026

changedInput schema / properties / ids / description

Previous value: -"Article identifiers to convert. All IDs must be the same type. DOIs: \"10.1093/nar/gks1195\", PMIDs: \"23193287\", PMCIDs: \"PMC3531190\" (the \"PMC\" prefix is optional — bare digits like \"3531190\" are also accepted)."New value: +"Article identifiers to convert — one identifier per element, all of the same type. Each element is checked against `idType` before the request: `doi` starts with \"10.\" and carries a \"/\" (\"10.1093/nar/gks1195\"); `pmid` is digits (\"23193287\"); `pmcid` is digits with an optional \"PMC\" prefix (\"PMC3531190\" or \"3531190\"). No element may contain a comma or whitespace — a packed value like \"23193287,37952131\" is rejected, so split it across elements."

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"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."New value: +"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). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "queue_full",
-  "ncbi_unreachable",
-  "ncbi_deadline_exceeded",
-  "ncbi_invalid_response",
-  "ncbi_resource_not_found"
-]New value: +[
+  "queue_full",
+  "ncbi_unreachable",
+  "ncbi_deadline_exceeded",
+  "ncbi_invalid_response",
+  "ncbi_resource_not_found",
+  "malformed_id"
+]

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": [
+      "records",
+      "totalConverted",
+      "totalSubmitted"
+    ]
+  },
+  {
+    "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: -[
-  "records",
-  "totalConverted",
-  "totalSubmitted"
-]

Changed1 schema field changedv2.10.2Jul 30, 2026

changedOutput schema / properties / records / items / properties / doi / description

Previous value: -"Digital Object Identifier; absent if no DOI is on record"New value: +"Digital Object Identifier, cased as the PMC ID Converter reports it; absent if no DOI is on record. DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ from a Europe PMC-sourced `doi` — compare the two case-insensitively."

Changed1 schema field changedv2.9.6Jun 19, 2026

changedInput schema / properties / ids / description

Previous value: -"Article identifiers to convert. All IDs must be the same type. DOIs: \"10.1093/nar/gks1195\", PMIDs: \"23193287\", PMCIDs: \"PMC3531190\"."New value: +"Article identifiers to convert. All IDs must be the same type. DOIs: \"10.1093/nar/gks1195\", PMIDs: \"23193287\", PMCIDs: \"PMC3531190\" (the \"PMC\" prefix is optional — bare digits like \"3531190\" are also accepted)."

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

TDQS

A4.5/5.0

Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is known. The description adds real behavioral context beyond that: the PMC-only resolution boundary and the single-type/50-ID batch constraint. It stops short of describing output or partial-resolution behavior, but that is largely carried by the output schema.

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 short sentences, each earning its place: purpose first, then the batch constraint, then the scope limitation and alternative. No redundancy or 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?

With an output schema present, return values need not be explained, and the description supplies the key operational facts an agent needs: what it converts, batch limits, and the PMC-indexing boundary plus the fallback tool. Nothing essential for correct invocation 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%, and the schema already documents the ID formats, the 50-item cap, and single-type requirement in far more detail than the description. The description's parameter mentions ('up to 50 IDs of a single type') merely restate constraints already fully specified, so the baseline 3 is appropriate.

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 ('Convert') and resource ('article identifiers (DOI, PMID, PMCID)'), making the tool's function unambiguous. It also signals scope via the PMC-only note, so an agent can distinguish it from the search/fetch siblings.

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 names a when-not condition ('Only resolves articles indexed in PubMed Central') and routes the agent to the correct alternative for those cases ('use pubmed_search_articles instead'). It also states the per-request limit of 50 single-type IDs.

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

Deploy Server

Pubmed Convert Ids

Instructions

Input Schema

Output Schema

Schema Changelog

TDQS

Other Tools