Noodle Biomedical Literature Discovery MCP
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
Should I use this
Quality & Safety
A
Based on automated analysis of tool definitions and protocol compliance.
Context Cost
~7,160Tokens (tool definitions)
~10.7 KBTypical response size
Significant attention impact (5.59% of 128k context)
This is the approximate number of tokens consumed each time the server's tools are loaded into a model's context. Higher counts reduce the attention available for other tasks.
Install
One-Click Install
Add this to your `claude_desktop_config.json` file:
{
"mcpServers": {
"noodle": {
"url": "https://api.helena.bio/noodle/v1/mcp"
}
}
}Remote endpoints
https://api.helena.bio/noodle/v1/mcpstreamable-httpWhat it can do
Tool inventory
Tools (7)
🟢 Read-only🟡 Write🔴 Delete⚪ Unknown
🟢search_biomedical_literature(query, limit, sort, cursor)
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.
Input Schema
{
"type": "object",
"properties": {
"query": {
"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.",
"maxLength": 200,
"minLength": 3,
"title": "Query",
"type": "string"
},
"limit": {
"default": 20,
"description": "Maximum number of publications to return, from 1 to 25.",
"maximum": 25,
"minimum": 1,
"title": "Limit",
"type": "integer"
},
"sort": {
"default": "relevance",
"description": "Result ordering: relevance-ranked, newest publication first, or oldest publication first.",
"enum": [
"relevance",
"newest",
"oldest"
],
"title": "Sort",
"type": "string"
},
"cursor": {
"anyOf": [
{
"maxLength": 128,
"minLength": 8,
"pattern": "^[A-Za-z0-9_-]+$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.",
"title": "Cursor"
}
},
"required": [
"query"
],
"additionalProperties": false,
"title": "SearchCorpusArguments"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"query": {
"title": "Query",
"type": "string"
},
"returned_count": {
"title": "Returned Count",
"type": "integer"
},
"results": {
"items": {
"$ref": "#/$defs/PublicCorpusSearchResult"
},
"title": "Results",
"type": "array"
},
"has_more": {
"default": false,
"title": "Has More",
"type": "boolean"
},
"next_cursor": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Next Cursor"
},
"searchable_fields": {
"items": {
"type": "string"
},
"title": "Searchable Fields",
"type": "array"
},
"semantic_index_used": {
"default": false,
"title": "Semantic Index Used",
"type": "boolean"
},
"semantic_degraded_reason": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Semantic Degraded Reason"
},
"graph_used": {
"default": false,
"title": "Graph Used",
"type": "boolean"
},
"graph_version": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Version"
},
"graph_degraded_reason": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Degraded Reason"
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
}
},
"required": [
"contract_version",
"query",
"returned_count",
"results",
"searchable_fields",
"usage_boundary"
],
"$defs": {
"PublicCorpusArticleEntity": {
"additionalProperties": false,
"properties": {
"entity_type": {
"enum": [
"gene",
"variant",
"phenotype",
"pmid",
"doi",
"pmcid",
"omim"
],
"title": "Entity Type",
"type": "string"
},
"identifier": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Identifier"
},
"label": {
"title": "Label",
"type": "string"
},
"source_field": {
"enum": [
"work_identifiers.normalized_value",
"gene_mentions.gene_symbol",
"variant_mentions.normalized_variant",
"phenotype_mentions.hpo_id",
"phenotype_mentions.omim_id",
"phenotype_mentions.mesh_term",
"phenotype_mentions.phenotype_name"
],
"title": "Source Field",
"type": "string"
},
"normalization_state": {
"enum": [
"normalized",
"source_indexed"
],
"title": "Normalization State",
"type": "string"
}
},
"required": [
"entity_type",
"identifier",
"label",
"source_field",
"normalization_state"
],
"title": "PublicCorpusArticleEntity",
"type": "object"
},
"PublicCorpusSearchResult": {
"additionalProperties": false,
"properties": {
"work_id": {
"title": "Work Id",
"type": "string"
},
"pmid": {
"anyOf": [
{
"pattern": "^[0-9]{1,12}$",
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmid"
},
"title": {
"title": "Title",
"type": "string"
},
"abstract_excerpt": {
"title": "Abstract Excerpt",
"type": "string"
},
"authors": {
"items": {
"type": "string"
},
"title": "Authors",
"type": "array"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"source_url": {
"title": "Source Url",
"type": "string"
},
"pubmed_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pubmed Url"
},
"match_types": {
"items": {
"enum": [
"pmid",
"doi",
"pmcid",
"title",
"abstract",
"gene",
"variant",
"phenotype",
"hpo",
"omim",
"semantic",
"graph"
],
"type": "string"
},
"title": "Match Types",
"type": "array"
},
"structured_score": {
"title": "Structured Score",
"type": "number"
},
"semantic_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"title": "Semantic Score"
},
"graph_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Score"
},
"graph_anchor_pmid": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Graph Anchor Pmid"
},
"rank_score": {
"default": 0,
"title": "Rank Score",
"type": "number"
},
"article_entities": {
"items": {
"$ref": "#/$defs/PublicCorpusArticleEntity"
},
"title": "Article Entities",
"type": "array"
}
},
"required": [
"work_id",
"pmid",
"title",
"abstract_excerpt",
"journal",
"publication_date",
"doi",
"pmc_id",
"source_url",
"pubmed_url",
"match_types",
"structured_score"
],
"title": "PublicCorpusSearchResult",
"type": "object"
}
},
"additionalProperties": false,
"title": "PublicCorpusSearchResponse"
}🟢get_publication_details(pmid)
Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.
Input Schema
{
"type": "object",
"properties": {
"pmid": {
"description": "One PubMed identifier to look up in Noodle's current public corpus, as 1 to 12 digits without a PMID prefix.",
"pattern": "^[0-9]{1,12}$",
"title": "Pmid",
"type": "string"
}
},
"required": [
"pmid"
],
"additionalProperties": false,
"title": "GetPublicationDetailsArguments"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"publication": {
"$ref": "#/$defs/PublicPublicationDetails"
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
}
},
"required": [
"contract_version",
"publication",
"usage_boundary"
],
"$defs": {
"PublicGeneMention": {
"additionalProperties": false,
"properties": {
"gene_symbol": {
"title": "Gene Symbol",
"type": "string"
},
"association_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Association Type"
},
"mention_count": {
"title": "Mention Count",
"type": "integer"
}
},
"required": [
"gene_symbol",
"association_type",
"mention_count"
],
"title": "PublicGeneMention",
"type": "object"
},
"PublicPublicationDetails": {
"additionalProperties": false,
"properties": {
"pmid": {
"pattern": "^[0-9]{1,12}$",
"title": "Pmid",
"type": "string"
},
"title": {
"title": "Title",
"type": "string"
},
"abstract": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Abstract"
},
"authors": {
"items": {
"type": "string"
},
"title": "Authors",
"type": "array"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"publication_types": {
"items": {
"type": "string"
},
"title": "Publication Types",
"type": "array"
},
"mesh_terms": {
"items": {
"type": "string"
},
"title": "Mesh Terms",
"type": "array"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"is_retracted": {
"title": "Is Retracted",
"type": "boolean"
},
"pubmed_url": {
"title": "Pubmed Url",
"type": "string"
},
"full_text_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Full Text Url"
},
"gene_mentions": {
"items": {
"$ref": "#/$defs/PublicGeneMention"
},
"title": "Gene Mentions",
"type": "array"
},
"variant_mentions": {
"items": {
"$ref": "#/$defs/PublicVariantMention"
},
"title": "Variant Mentions",
"type": "array"
}
},
"required": [
"pmid",
"title",
"abstract",
"authors",
"journal",
"publication_date",
"publication_types",
"mesh_terms",
"doi",
"pmc_id",
"is_retracted",
"pubmed_url",
"full_text_url",
"gene_mentions",
"variant_mentions"
],
"title": "PublicPublicationDetails",
"type": "object"
},
"PublicVariantMention": {
"additionalProperties": false,
"properties": {
"gene_symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene Symbol"
},
"hgvs_cdna": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs Cdna"
},
"hgvs_protein": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs Protein"
},
"normalized_variant": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Normalized Variant"
},
"clinical_significance": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Clinical Significance"
},
"evidence_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Evidence Type"
},
"sentence_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Sentence Text"
},
"confidence_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Confidence Score"
}
},
"required": [
"gene_symbol",
"hgvs_cdna",
"hgvs_protein",
"normalized_variant",
"clinical_significance",
"evidence_type",
"sentence_text",
"confidence_score"
],
"title": "PublicVariantMention",
"type": "object"
}
},
"additionalProperties": false,
"title": "PublicationDetailsResponse"
}🟢get_work_details(work_id)
Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
Input Schema
{
"type": "object",
"properties": {
"work_id": {
"description": "Canonical Noodle Literature Corpus work identifier.",
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Work Id",
"type": "string"
}
},
"required": [
"work_id"
],
"additionalProperties": false,
"title": "GetWorkDetailsArguments"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"publication": {
"$ref": "#/$defs/PublicWorkDetails"
},
"usage_boundary": {
"additionalProperties": true,
"title": "Usage Boundary",
"type": "object"
}
},
"required": [
"contract_version",
"publication",
"usage_boundary"
],
"$defs": {
"PublicGeneMention": {
"additionalProperties": false,
"properties": {
"gene_symbol": {
"title": "Gene Symbol",
"type": "string"
},
"association_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Association Type"
},
"mention_count": {
"title": "Mention Count",
"type": "integer"
}
},
"required": [
"gene_symbol",
"association_type",
"mention_count"
],
"title": "PublicGeneMention",
"type": "object"
},
"PublicVariantMention": {
"additionalProperties": false,
"properties": {
"gene_symbol": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene Symbol"
},
"hgvs_cdna": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs Cdna"
},
"hgvs_protein": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Hgvs Protein"
},
"normalized_variant": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Normalized Variant"
},
"clinical_significance": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Clinical Significance"
},
"evidence_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Evidence Type"
},
"sentence_text": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Sentence Text"
},
"confidence_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Confidence Score"
}
},
"required": [
"gene_symbol",
"hgvs_cdna",
"hgvs_protein",
"normalized_variant",
"clinical_significance",
"evidence_type",
"sentence_text",
"confidence_score"
],
"title": "PublicVariantMention",
"type": "object"
},
"PublicWorkDetails": {
"additionalProperties": false,
"properties": {
"work_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Work Id",
"type": "string"
},
"pmid": {
"anyOf": [
{
"pattern": "^[0-9]{1,12}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Pmid"
},
"title": {
"title": "Title",
"type": "string"
},
"abstract": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Abstract"
},
"authors": {
"items": {
"type": "string"
},
"title": "Authors",
"type": "array"
},
"journal": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Journal"
},
"publication_date": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Publication Date"
},
"publication_types": {
"items": {
"type": "string"
},
"title": "Publication Types",
"type": "array"
},
"mesh_terms": {
"items": {
"type": "string"
},
"title": "Mesh Terms",
"type": "array"
},
"doi": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi"
},
"pmc_id": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pmc Id"
},
"is_retracted": {
"title": "Is Retracted",
"type": "boolean"
},
"pubmed_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Pubmed Url"
},
"doi_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Doi Url"
},
"full_text_url": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Full Text Url"
},
"gene_mentions": {
"items": {
"$ref": "#/$defs/PublicGeneMention"
},
"title": "Gene Mentions",
"type": "array"
},
"variant_mentions": {
"items": {
"$ref": "#/$defs/PublicVariantMention"
},
"title": "Variant Mentions",
"type": "array"
}
},
"required": [
"work_id",
"title",
"abstract",
"authors",
"journal",
"publication_date",
"publication_types",
"mesh_terms",
"doi",
"pmc_id",
"is_retracted",
"pubmed_url",
"doi_url",
"full_text_url",
"gene_mentions",
"variant_mentions"
],
"title": "PublicWorkDetails",
"type": "object"
}
},
"additionalProperties": false,
"title": "WorkDetailsResponse"
}🟢get_publication_neighborhood(pmid, from_work_id)
Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.
Input Schema
{
"type": "object",
"properties": {
"pmid": {
"description": "One PubMed identifier, as 1 to 12 digits.",
"pattern": "^[0-9]{1,12}$",
"title": "Pmid",
"type": "string"
},
"from_work_id": {
"anyOf": [
{
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Optional prior work ID for a reversible graph path.",
"title": "From Work Id"
}
},
"required": [
"pmid"
],
"additionalProperties": false,
"title": "GetPublicationNeighborhoodArguments"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"enum": [
"0.1",
"0.2"
],
"title": "Contract Version",
"type": "string"
},
"anchor_work_id": {
"anyOf": [
{
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Anchor Work Id"
},
"anchor_pmid": {
"anyOf": [
{
"pattern": "^[0-9]{1,12}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Anchor Pmid"
},
"anchor_node_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Anchor Node Id",
"type": "string"
},
"graph_version": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Graph Version",
"type": "string"
},
"release_channel": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Release Channel",
"type": "string"
},
"policy_version": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Policy Version",
"type": "string"
},
"generated_at": {
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}\\.[0-9]{3}Z$",
"title": "Generated At",
"type": "string"
},
"stale_after": {
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}\\.[0-9]{3}Z$",
"title": "Stale After",
"type": "string"
},
"freshness": {
"const": "CURRENT",
"title": "Freshness",
"type": "string"
},
"nodes": {
"items": {
"$ref": "#/$defs/ArticleNeighborhoodNode"
},
"maxItems": 25,
"minItems": 9,
"title": "Nodes",
"type": "array"
},
"edges": {
"items": {
"$ref": "#/$defs/ArticleNeighborhoodEdge"
},
"maxItems": 64,
"minItems": 8,
"title": "Edges",
"type": "array"
},
"usage_boundary": {
"$ref": "#/$defs/ArticleNeighborhoodUsageBoundary"
}
},
"required": [
"contract_version",
"anchor_node_id",
"graph_version",
"release_channel",
"policy_version",
"generated_at",
"stale_after",
"freshness",
"nodes",
"edges",
"usage_boundary"
],
"$defs": {
"ArticleNeighborhoodEdge": {
"additionalProperties": false,
"properties": {
"id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Id",
"type": "string"
},
"source_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Source Id",
"type": "string"
},
"target_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Target Id",
"type": "string"
},
"reasons": {
"items": {
"$ref": "#/$defs/ArticleNeighborhoodReason"
},
"maxItems": 7,
"minItems": 1,
"title": "Reasons",
"type": "array"
}
},
"required": [
"id",
"source_id",
"target_id",
"reasons"
],
"title": "ArticleNeighborhoodEdge",
"type": "object"
},
"ArticleNeighborhoodNode": {
"additionalProperties": false,
"properties": {
"id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Id",
"type": "string"
},
"kind": {
"enum": [
"publication",
"gene",
"variant",
"phenotype",
"disease"
],
"title": "Kind",
"type": "string"
},
"label": {
"maxLength": 500,
"minLength": 1,
"title": "Label",
"type": "string"
},
"canonical_path": {
"pattern": "^/[A-Za-z0-9._~/-]{1,300}$",
"title": "Canonical Path",
"type": "string"
},
"publication_work_id": {
"anyOf": [
{
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Publication Work Id"
},
"publication_pmid": {
"anyOf": [
{
"pattern": "^[0-9]{1,12}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Publication Pmid"
},
"publication_doi": {
"anyOf": [
{
"maxLength": 255,
"minLength": 3,
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Publication Doi"
},
"publication_pmcid": {
"anyOf": [
{
"pattern": "^PMC[0-9]+$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Publication Pmcid"
}
},
"required": [
"id",
"kind",
"label",
"canonical_path"
],
"title": "ArticleNeighborhoodNode",
"type": "object"
},
"ArticleNeighborhoodProvenance": {
"additionalProperties": false,
"properties": {
"source": {
"maxLength": 160,
"minLength": 1,
"title": "Source",
"type": "string"
},
"record_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Record Id",
"type": "string"
},
"canonical_url": {
"anyOf": [
{
"maxLength": 2048,
"type": "string"
},
{
"type": "null"
}
],
"title": "Canonical Url"
},
"retrieved_at": {
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}\\.[0-9]{3}Z$",
"title": "Retrieved At",
"type": "string"
}
},
"required": [
"source",
"record_id",
"canonical_url",
"retrieved_at"
],
"title": "ArticleNeighborhoodProvenance",
"type": "object"
},
"ArticleNeighborhoodReason": {
"additionalProperties": false,
"properties": {
"kind": {
"enum": [
"shared_gene",
"shared_variant",
"shared_phenotype",
"shared_disease",
"cites",
"cited_by",
"semantic_relatedness"
],
"title": "Kind",
"type": "string"
},
"label": {
"maxLength": 500,
"minLength": 1,
"title": "Label",
"type": "string"
},
"score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Score"
},
"model_version": {
"anyOf": [
{
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"type": "string"
},
{
"type": "null"
}
],
"title": "Model Version"
},
"provenance": {
"$ref": "#/$defs/ArticleNeighborhoodProvenance"
}
},
"required": [
"kind",
"label",
"score",
"model_version",
"provenance"
],
"title": "ArticleNeighborhoodReason",
"type": "object"
},
"ArticleNeighborhoodUsageBoundary": {
"additionalProperties": false,
"properties": {
"review_required": {
"const": true,
"title": "Review Required",
"type": "boolean"
},
"patient_context_evaluated": {
"const": false,
"title": "Patient Context Evaluated",
"type": "boolean"
},
"semantic_similarity_is_evidence": {
"const": false,
"title": "Semantic Similarity Is Evidence",
"type": "boolean"
}
},
"required": [
"review_required",
"patient_context_evaluated",
"semantic_similarity_is_evidence"
],
"title": "ArticleNeighborhoodUsageBoundary",
"type": "object"
}
},
"additionalProperties": false,
"title": "ArticleNeighborhoodResponse"
}🟢get_work_neighborhood(work_id, from_work_id)
Retrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
Input Schema
{
"type": "object",
"properties": {
"work_id": {
"description": "Canonical work identifier to place at the graph center.",
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Work Id",
"type": "string"
},
"from_work_id": {
"anyOf": [
{
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Optional prior work ID for a reversible graph path.",
"title": "From Work Id"
}
},
"required": [
"work_id"
],
"additionalProperties": false,
"title": "GetWorkNeighborhoodArguments"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"enum": [
"0.1",
"0.2"
],
"title": "Contract Version",
"type": "string"
},
"anchor_work_id": {
"anyOf": [
{
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Anchor Work Id"
},
"anchor_pmid": {
"anyOf": [
{
"pattern": "^[0-9]{1,12}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Anchor Pmid"
},
"anchor_node_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Anchor Node Id",
"type": "string"
},
"graph_version": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Graph Version",
"type": "string"
},
"release_channel": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Release Channel",
"type": "string"
},
"policy_version": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"title": "Policy Version",
"type": "string"
},
"generated_at": {
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}\\.[0-9]{3}Z$",
"title": "Generated At",
"type": "string"
},
"stale_after": {
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}\\.[0-9]{3}Z$",
"title": "Stale After",
"type": "string"
},
"freshness": {
"const": "CURRENT",
"title": "Freshness",
"type": "string"
},
"nodes": {
"items": {
"$ref": "#/$defs/ArticleNeighborhoodNode"
},
"maxItems": 25,
"minItems": 9,
"title": "Nodes",
"type": "array"
},
"edges": {
"items": {
"$ref": "#/$defs/ArticleNeighborhoodEdge"
},
"maxItems": 64,
"minItems": 8,
"title": "Edges",
"type": "array"
},
"usage_boundary": {
"$ref": "#/$defs/ArticleNeighborhoodUsageBoundary"
}
},
"required": [
"contract_version",
"anchor_node_id",
"graph_version",
"release_channel",
"policy_version",
"generated_at",
"stale_after",
"freshness",
"nodes",
"edges",
"usage_boundary"
],
"$defs": {
"ArticleNeighborhoodEdge": {
"additionalProperties": false,
"properties": {
"id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Id",
"type": "string"
},
"source_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Source Id",
"type": "string"
},
"target_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Target Id",
"type": "string"
},
"reasons": {
"items": {
"$ref": "#/$defs/ArticleNeighborhoodReason"
},
"maxItems": 7,
"minItems": 1,
"title": "Reasons",
"type": "array"
}
},
"required": [
"id",
"source_id",
"target_id",
"reasons"
],
"title": "ArticleNeighborhoodEdge",
"type": "object"
},
"ArticleNeighborhoodNode": {
"additionalProperties": false,
"properties": {
"id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Id",
"type": "string"
},
"kind": {
"enum": [
"publication",
"gene",
"variant",
"phenotype",
"disease"
],
"title": "Kind",
"type": "string"
},
"label": {
"maxLength": 500,
"minLength": 1,
"title": "Label",
"type": "string"
},
"canonical_path": {
"pattern": "^/[A-Za-z0-9._~/-]{1,300}$",
"title": "Canonical Path",
"type": "string"
},
"publication_work_id": {
"anyOf": [
{
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Publication Work Id"
},
"publication_pmid": {
"anyOf": [
{
"pattern": "^[0-9]{1,12}$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Publication Pmid"
},
"publication_doi": {
"anyOf": [
{
"maxLength": 255,
"minLength": 3,
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Publication Doi"
},
"publication_pmcid": {
"anyOf": [
{
"pattern": "^PMC[0-9]+$",
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Publication Pmcid"
}
},
"required": [
"id",
"kind",
"label",
"canonical_path"
],
"title": "ArticleNeighborhoodNode",
"type": "object"
},
"ArticleNeighborhoodProvenance": {
"additionalProperties": false,
"properties": {
"source": {
"maxLength": 160,
"minLength": 1,
"title": "Source",
"type": "string"
},
"record_id": {
"pattern": "^[A-Za-z0-9][A-Za-z0-9:._/-]{0,159}$",
"title": "Record Id",
"type": "string"
},
"canonical_url": {
"anyOf": [
{
"maxLength": 2048,
"type": "string"
},
{
"type": "null"
}
],
"title": "Canonical Url"
},
"retrieved_at": {
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}:[0-9]{2}\\.[0-9]{3}Z$",
"title": "Retrieved At",
"type": "string"
}
},
"required": [
"source",
"record_id",
"canonical_url",
"retrieved_at"
],
"title": "ArticleNeighborhoodProvenance",
"type": "object"
},
"ArticleNeighborhoodReason": {
"additionalProperties": false,
"properties": {
"kind": {
"enum": [
"shared_gene",
"shared_variant",
"shared_phenotype",
"shared_disease",
"cites",
"cited_by",
"semantic_relatedness"
],
"title": "Kind",
"type": "string"
},
"label": {
"maxLength": 500,
"minLength": 1,
"title": "Label",
"type": "string"
},
"score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Score"
},
"model_version": {
"anyOf": [
{
"pattern": "^[A-Za-z0-9][A-Za-z0-9._:-]{0,127}$",
"type": "string"
},
{
"type": "null"
}
],
"title": "Model Version"
},
"provenance": {
"$ref": "#/$defs/ArticleNeighborhoodProvenance"
}
},
"required": [
"kind",
"label",
"score",
"model_version",
"provenance"
],
"title": "ArticleNeighborhoodReason",
"type": "object"
},
"ArticleNeighborhoodUsageBoundary": {
"additionalProperties": false,
"properties": {
"review_required": {
"const": true,
"title": "Review Required",
"type": "boolean"
},
"patient_context_evaluated": {
"const": false,
"title": "Patient Context Evaluated",
"type": "boolean"
},
"semantic_similarity_is_evidence": {
"const": false,
"title": "Semantic Similarity Is Evidence",
"type": "boolean"
}
},
"required": [
"review_required",
"patient_context_evaluated",
"semantic_similarity_is_evidence"
],
"title": "ArticleNeighborhoodUsageBoundary",
"type": "object"
}
},
"additionalProperties": false,
"title": "ArticleNeighborhoodResponse"
}🟢get_corpus_summary
Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.
Input Schema
{
"type": "object",
"properties": {},
"additionalProperties": false,
"title": "GetCorpusSummaryArguments"
}Output Schema
{
"type": "object",
"properties": {
"contract_version": {
"const": "1.0",
"title": "Contract Version",
"type": "string"
},
"generated_at": {
"title": "Generated At",
"type": "string"
},
"counts": {
"$ref": "#/$defs/PublicCorpusCounts"
},
"sources": {
"items": {
"$ref": "#/$defs/PublicCorpusSource"
},
"title": "Sources",
"type": "array"
},
"deduplication_keys": {
"items": {
"type": "string"
},
"title": "Deduplication Keys",
"type": "array"
},
"scope": {
"title": "Scope",
"type": "string"
}
},
"required": [
"contract_version",
"generated_at",
"counts",
"sources",
"deduplication_keys",
"scope"
],
"$defs": {
"PublicCorpusCounts": {
"additionalProperties": false,
"properties": {
"source_records": {
"title": "Source Records",
"type": "integer"
},
"unique_works": {
"title": "Unique Works",
"type": "integer"
},
"gene_mentions": {
"title": "Gene Mentions",
"type": "integer"
},
"variant_mentions": {
"title": "Variant Mentions",
"type": "integer"
},
"phenotype_mentions": {
"title": "Phenotype Mentions",
"type": "integer"
},
"evidence_links": {
"title": "Evidence Links",
"type": "integer"
}
},
"required": [
"source_records",
"unique_works",
"gene_mentions",
"variant_mentions",
"phenotype_mentions",
"evidence_links"
],
"title": "PublicCorpusCounts",
"type": "object"
},
"PublicCorpusSource": {
"additionalProperties": false,
"properties": {
"source_id": {
"title": "Source Id",
"type": "string"
},
"display_name": {
"title": "Display Name",
"type": "string"
},
"source_type": {
"title": "Source Type",
"type": "string"
},
"source_records": {
"title": "Source Records",
"type": "integer"
},
"unique_works": {
"title": "Unique Works",
"type": "integer"
},
"evidence_links": {
"title": "Evidence Links",
"type": "integer"
}
},
"required": [
"source_id",
"display_name",
"source_type",
"source_records",
"unique_works",
"evidence_links"
],
"title": "PublicCorpusSource",
"type": "object"
}
},
"additionalProperties": false,
"title": "PublicCorpusSummaryResponse"
}🟢support_helena
Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.
Input Schema
{
"type": "object",
"properties": {},
"additionalProperties": false
}Output Schema
{
"type": "object",
"additionalProperties": true
}Community
Evidence
Recent observations
verifiedversion not recorded7 tools
verifiedversion not recorded7 tools
verifiedversion not recorded7 tools