Noodle Biomedical Literature Discovery MCP

Working · 40 ms

io.github.helena-bioinformatics/noodlev0.2.1

Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.

Research & Knowledge

Source Website Registry entry

Maintain this server? Claim it

Try it

Call this server's tools from your browser. Nothing to install.

https://api.helena.bio/noodle/v1/mcp

Requests go through mcptry because browsers can't call most MCP servers directly. Header values are sent to the server for that request only and are never stored or logged.

Tool list from our last check. Connect live to refresh it.

get_corpus_summary Read-only

Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.

This tool takes no arguments.

Tools (7)

get_corpus_summary

Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.

read-only

No arguments.

Input schema (JSON)

{
  "type": "object",
  "title": "GetCorpusSummaryArguments",
  "properties": {},
  "additionalProperties": false
}

get_publication_details

Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.

read-only

Argument	Type	Description
pmid*	string	One PubMed identifier to look up in Noodle's current public corpus, as 1 to 12 digits without a PMID prefix.

Input schema (JSON)

{
  "type": "object",
  "title": "GetPublicationDetailsArguments",
  "required": [
    "pmid"
  ],
  "properties": {
    "pmid": {
      "type": "string",
      "title": "Pmid",
      "pattern": "^[0-9]{1,12}$",
      "description": "One PubMed identifier to look up in Noodle's current public corpus, as 1 to 12 digits without a PMID prefix."
    }
  },
  "additionalProperties": false
}

get_publication_neighborhood

Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.

read-only

Argument	Type	Description
pmid*	string	One PubMed identifier, as 1 to 12 digits.
from_work_id	any	Optional prior work ID for a reversible graph path.

Input schema (JSON)

{
  "type": "object",
  "title": "GetPublicationNeighborhoodArguments",
  "required": [
    "pmid"
  ],
  "properties": {
    "pmid": {
      "type": "string",
      "title": "Pmid",
      "pattern": "^[0-9]{1,12}$",
      "description": "One PubMed identifier, as 1 to 12 digits."
    },
    "from_work_id": {
      "anyOf": [
        {
          "type": "string",
          "pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$"
        },
        {
          "type": "null"
        }
      ],
      "title": "From Work Id",
      "default": null,
      "description": "Optional prior work ID for a reversible graph path."
    }
  },
  "additionalProperties": false
}

get_work_details

Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.

read-only

Argument	Type	Description
work_id*	string	Canonical Noodle Literature Corpus work identifier.

Input schema (JSON)

{
  "type": "object",
  "title": "GetWorkDetailsArguments",
  "required": [
    "work_id"
  ],
  "properties": {
    "work_id": {
      "type": "string",
      "title": "Work Id",
      "pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
      "description": "Canonical Noodle Literature Corpus work identifier."
    }
  },
  "additionalProperties": false
}

get_work_neighborhood

Retrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.

read-only

Argument	Type	Description
work_id*	string	Canonical work identifier to place at the graph center.
from_work_id	any	Optional prior work ID for a reversible graph path.

Input schema (JSON)

{
  "type": "object",
  "title": "GetWorkNeighborhoodArguments",
  "required": [
    "work_id"
  ],
  "properties": {
    "work_id": {
      "type": "string",
      "title": "Work Id",
      "pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
      "description": "Canonical work identifier to place at the graph center."
    },
    "from_work_id": {
      "anyOf": [
        {
          "type": "string",
          "pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$"
        },
        {
          "type": "null"
        }
      ],
      "title": "From Work Id",
      "default": null,
      "description": "Optional prior work ID for a reversible graph path."
    }
  },
  "additionalProperties": false
}

search_biomedical_literature

Semantically search Noodle's public PubMed-derived biomedical corpus. Include known PMID, DOI, or PMCID identifiers in the query so they can act as exact anchors. Results are for literature discovery and professional review, not diagnosis or treatment.

read-only

Argument	Type	Description
sort	string	Result ordering: relevance-ranked, newest publication first, or oldest publication first.
limit	integer	Maximum number of publications to return, from 1 to 25.
query*	string	Natural-language literature question or exact PMID, DOI, PMCID, gene, variant, phenotype, HPO, or OMIM query. Include every known publication identifier when comparing or finding related papers.
cursor	any	Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.

Input schema (JSON)

{
  "type": "object",
  "title": "SearchCorpusArguments",
  "required": [
    "query"
  ],
  "properties": {
    "sort": {
      "enum": [
        "relevance",
        "newest",
        "oldest"
      ],
      "type": "string",
      "title": "Sort",
      "default": "relevance",
      "description": "Result ordering: relevance-ranked, newest publication first, or oldest publication first."
    },
    "limit": {
      "type": "integer",
      "title": "Limit",
      "default": 20,
      "maximum": 25,
      "minimum": 1,
      "description": "Maximum number of publications to return, from 1 to 25."
    },
    "query": {
      "type": "string",
      "title": "Query",
      "maxLength": 200,
      "minLength": 3,
      "description": "Natural-language literature question or exact PMID, DOI, PMCID, gene, variant, phenotype, HPO, or OMIM query. Include every known publication identifier when comparing or finding related papers."
    },
    "cursor": {
      "anyOf": [
        {
          "type": "string",
          "pattern": "^[A-Za-z0-9_-]+$",
          "maxLength": 128,
          "minLength": 8
        },
        {
          "type": "null"
        }
      ],
      "title": "Cursor",
      "default": null,
      "description": "Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page."
    }
  },
  "additionalProperties": false
}

support_helena

Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.

read-only

No arguments.

Input schema (JSON)

{
  "type": "object",
  "properties": {},
  "additionalProperties": false
}