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helena-bioinformatics

Noodle Biomedical Literature Discovery MCP

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Search biomedical literature

search_biomedical_literature
Read-onlyIdempotent

Search a PubMed-derived biomedical corpus using natural-language questions or exact PMID, DOI, or PMCID identifiers to find relevant publications for professional literature discovery.

Instructions

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

TableJSON Schema
NameRequiredDescriptionDefault
sortNoResult ordering: relevance-ranked, newest publication first, or oldest publication first.relevance
limitNoMaximum number of publications to return, from 1 to 25.
queryYesNatural-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.
cursorNoOpaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
resultsYes
has_moreNo
graph_usedNo
next_cursorNo
graph_versionNo
returned_countYes
usage_boundaryYes
contract_versionYes
searchable_fieldsYes
semantic_index_usedNo
graph_degraded_reasonNo
semantic_degraded_reasonNo
Behavior3/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false, covering safety. The description adds the semantic-search behavior and the identifier-anchoring effect, which complements annotations. It does not contradict them, and the additional context is modest but useful.

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?

Two sentences, no redundant phrasing. The core purpose leads, followed by actionable identifier advice and a clear scope disclaimer. Every sentence earns its place, and the structure is ideal for quick scanning.

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?

For a search tool with a rich input schema (including cursor, sort, limit) and an output schema, the description covers the essential context: semantic nature, identifier anchoring, scope, and usage disclaimer. Nothing an agent needs to invoke it correctly is missing, given the structured annotations already carry safety information.

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 coverage is 100% with descriptive text for each parameter. The description essentially restates the query parameter's guidance about including identifiers, so it adds little beyond what the schema already provides. 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?

The description states a specific verb ('semantically search') and a specific resource ('Noodle's public PubMed-derived biomedical corpus'). This clearly distinguishes the tool from sibling detail/neighborhood tools, making its purpose unambiguous.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description advises including known identifiers for exact anchoring, which gives concrete guidance on query formulation. However, it does not explicitly state when to use this tool over siblings (e.g., when you need details for a specific publication, use get_publication_details). The disclaimer about literature discovery implies a use case but lacks explicit when-not guidance.

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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