Skip to main content
Glama

Pubmed Lookup Citation

pubmed_lookup_citation
Read-only

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
NameRequiredDescriptionDefault
citationsYesCitations to look up — an array of up to 25, or a single citation object. More fields = better match accuracy.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
resultsNoMatch results, one per input citation
totalMatchedNoNumber of citations with PMID matches
totalWarningsNoNumber of matched citations that carry at least one warning
totalSubmittedNoNumber of citations submitted

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed6 schema fields changed
    • addedInput schema / properties / citations / anyOf
      Added value: +[
      +  {
      +    "description": "Up to 25 citations, each matched independently.",
      +    "items": {
      +      "description": "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.",
      +      "properties": {
      +        "authorName": {
      +          "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
      +          "pattern": "^[^|\\r\\n]*$",
      +          "type": "string"
      +        },
      +        "firstPage": {
      +          "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
      +          "pattern": "^[^|\\r\\n]*$",
      +          "type": "string"
      +        },
      +        "journal": {
      +          "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
      +          "pattern": "^[^|\\r\\n]*$",
      +          "type": "string"
      +        },
      +        "key": {
      +          "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.",
      +          "type": "string"
      +        },
      +        "volume": {
      +          "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
      +          "pattern": "^[^|\\r\\n]*$",
      +          "type": "string"
      +        },
      +        "year": {
      +          "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
      +          "pattern": "^[^|\\r\\n]*$",
      +          "type": "string"
      +        }
      +      },
      +      "type": "object"
      +    },
      +    "maxItems": 25,
      +    "minItems": 1,
      +    "type": "array"
      +  },
      +  {
      +    "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.",
      +    "properties": {
      +      "authorName": {
      +        "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
      +        "pattern": "^[^|\\r\\n]*$",
      +        "type": "string"
      +      },
      +      "firstPage": {
      +        "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
      +        "pattern": "^[^|\\r\\n]*$",
      +        "type": "string"
      +      },
      +      "journal": {
      +        "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
      +        "pattern": "^[^|\\r\\n]*$",
      +        "type": "string"
      +      },
      +      "key": {
      +        "description": "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.",
      +        "type": "string"
      +      },
      +      "volume": {
      +        "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
      +        "pattern": "^[^|\\r\\n]*$",
      +        "type": "string"
      +      },
      +      "year": {
      +        "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
      +        "pattern": "^[^|\\r\\n]*$",
      +        "type": "string"
      +      }
      +    },
      +    "type": "object"
      +  }
      +]
    • changedInput schema / properties / citations / description
      Previous value: -"Citations to look up. More fields = better match accuracy."New value: +"Citations to look up — an array of up to 25, or a single citation object. More fields = better match accuracy."
    • removedInput schema / properties / citations / items
      Removed value: -{
      -  "description": "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.",
      -  "properties": {
      -    "authorName": {
      -      "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
      -      "pattern": "^[^|\\r\\n]*$",
      -      "type": "string"
      -    },
      -    "firstPage": {
      -      "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
      -      "pattern": "^[^|\\r\\n]*$",
      -      "type": "string"
      -    },
      -    "journal": {
      -      "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
      -      "pattern": "^[^|\\r\\n]*$",
      -      "type": "string"
      -    },
      -    "key": {
      -      "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.",
      -      "type": "string"
      -    },
      -    "volume": {
      -      "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
      -      "pattern": "^[^|\\r\\n]*$",
      -      "type": "string"
      -    },
      -    "year": {
      -      "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
      -      "pattern": "^[^|\\r\\n]*$",
      -      "type": "string"
      -    }
      -  },
      -  "type": "object"
      -}
    • removedInput schema / properties / citations / maxItems
      Removed value: -25
    • removedInput schema / properties / citations / minItems
      Removed value: -1
    • removedInput schema / properties / citations / type
      Removed value: -"array"
  2. Changed1 schema field changed
    • 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`: 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). Other values are possible when a failure originates below the handler."
  3. Changed11 schema fields changed
    • 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]*$"
    • changedInput schema / properties / citations / items / properties / year / description
      Previous value: -"Publication year (e.g., \"1991\")"New value: +"Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break."
    • addedInput schema / properties / citations / items / properties / year / pattern
      Added value: +"^[^|\\r\\n]*$"
  4. Changed6 schema fields changed
    • 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"
      -]
  5. Changed1 schema field changed
    • 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."
  6. Changed4 schema fields changed
    • changedInput schema / properties / citations / items / description
      Previous value: -"Citation to match against PubMed"New value: +"Citation to match against PubMed. Must include at least one bibliographic field (journal, year, volume, firstPage, or authorName)."
    • changedOutput schema / properties / results / items / properties / candidatePmids / description
      Previous value: -"PMIDs returned for AMBIGUOUS matches — candidate articles needing more citation fields to disambiguate. Parsed from the raw `AMBIGUOUS <csv>` detail string for programmatic consumption."New value: +"Candidate PMIDs returned when the citation matched ambiguously. Add more bibliographic fields and retry to disambiguate, or fetch each candidate via pubmed_fetch_articles to pick the intended one."
    • changedOutput schema / properties / results / items / properties / warnings / description
      Previous value: -"Non-fatal warnings about this match. ECitMatch weights journal+volume+page and tolerates author/year disagreement, so a returned PMID may not match the queried author or year — downstream code should key on `code` to decide whether to trust the PMID."New value: +"Non-fatal warnings about this match. A PMID may be returned even when the queried author or year disagrees with the matched article — verify before treating the PMID as authoritative."
    • changedOutput schema / properties / results / items / properties / warnings / items / properties / code / description
      Previous value: -"Machine-readable warning classifier for downstream filtering"New value: +"Machine-readable warning code"
  7. Changed5 schema fields changed
    • addedOutput schema / properties / results / items / properties / candidatePmids
      Added value: +{
      +  "description": "PMIDs returned for AMBIGUOUS matches — candidate articles needing more citation fields to disambiguate. Parsed from the raw `AMBIGUOUS <csv>` detail string for programmatic consumption.",
      +  "items": {
      +    "description": "PMID",
      +    "type": "string"
      +  },
      +  "type": "array"
      +}
    • addedOutput schema / properties / results / items / properties / matchedFirstAuthor
      Added value: +{
      +  "description": "First author of the matched article (e.g., \"Husain M\"). Useful eyeball signal for verifying a match.",
      +  "type": "string"
      +}
    • addedOutput schema / properties / results / items / properties / warnings
      Added value: +{
      +  "description": "Non-fatal warnings about this match. ECitMatch weights journal+volume+page and tolerates author/year disagreement, so a returned PMID may not match the queried author or year — downstream code should key on `code` to decide whether to trust the PMID.",
      +  "items": {
      +    "additionalProperties": false,
      +    "description": "Non-fatal warning about the match",
      +    "properties": {
      +      "code": {
      +        "description": "Machine-readable warning classifier for downstream filtering",
      +        "enum": [
      +          "author_mismatch",
      +          "year_mismatch"
      +        ],
      +        "type": "string"
      +      },
      +      "message": {
      +        "description": "Human-readable description of the warning",
      +        "type": "string"
      +      }
      +    },
      +    "required": [
      +      "code",
      +      "message"
      +    ],
      +    "type": "object"
      +  },
      +  "type": "array"
      +}
    • addedOutput schema / properties / totalWarnings
      Added value: +{
      +  "description": "Number of matched citations that carry at least one warning",
      +  "type": "number"
      +}
    • changedOutput schema / required
      Previous value: -[
      -  "results",
      -  "totalMatched",
      -  "totalSubmitted"
      -]New value: +[
      +  "results",
      +  "totalMatched",
      +  "totalSubmitted",
      +  "totalWarnings"
      +]
  8. Changed2 schema fields changed
    • addedInput schema / properties / citations / items / description
      Added value: +"Citation to match against PubMed"
    • addedOutput schema / properties / results / items / description
      Added value: +"Per-citation match result"
  9. Changed3 schema fields changed
    • addedOutput schema / properties / results / items / properties / detail
      Added value: +{
      +  "description": "Additional detail returned by ECitMatch for non-exact matches",
      +  "type": "string"
      +}
    • addedOutput schema / properties / results / items / properties / status
      Added value: +{
      +  "description": "Lookup outcome classification for this citation",
      +  "enum": [
      +    "matched",
      +    "not_found",
      +    "ambiguous"
      +  ],
      +  "type": "string"
      +}
    • changedOutput schema / properties / results / items / required
      Previous value: -[
      -  "key",
      -  "matched"
      -]New value: +[
      +  "key",
      +  "matched",
      +  "status"
      +]
  10. Added

TDQS

A4.2/5.0
Behavior4/5

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

Annotations already mark the operation as read-only and open-world, and the description adds meaningful behavioral detail beyond that: it explains ECitMatch primary-key behavior, states that author-only or volume-only inputs guarantee no match, and notes that more fields improve accuracy. This gives the agent a realistic model of how matching behaves.

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, when to use, and matching constraints. The core action is front-loaded and there is no redundant or filler content.

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?

Given the single parameter, rich input schema, output schema presence, and read-only/open-world annotations, the description covers what the tool does, when to use it, and the key matching constraints an agent needs to invoke it correctly. Nothing critical is missing.

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% and the schema thoroughly documents the 'citations' parameter, so the baseline is 3. The description adds practical value on top by framing the input as 'partial bibliographic citations' and emphasizing that more fields improve match accuracy, which helps the agent decide how much information to include.

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

Purpose4/5

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

The description opens with a specific verb and resource: 'Look up PubMed IDs from partial bibliographic citations.' It also signals how this differs from free-text search by emphasizing deterministic citation matching, though it never names a sibling tool explicitly, so it stops just short of full sibling differentiation.

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 clearly states when the tool is useful: when you have structured reference data and need a PMID. It also compares favorably against free-text search for structured references, but does not explicitly explain when NOT to use it or name the alternative tool, so the guidance is strong but not exhaustive.

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

Try in Browser

Glama MCP Gateway

Add one secure layer between your agents and this server.