-
licenseNot graded
qualityNot graded
maintenanceAn MCP server implementation that enables searching and retrieving research articles from PubMed with specific focus on open access content filtering and full-text link retrieval.
8 npm
3
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mcp-simple-pubmed
by andybrandt
MCP Simple PubMed
Un servidor MCP que proporciona acceso a artículos de PubMed a través de la API de Entrez.
Características
Buscar en la base de datos PubMed usando palabras clave
Acceder a los resúmenes de los artículos
Descargue el texto completo cuando esté disponible (para artículos de acceso abierto disponibles directamente en PubMed)
Tenga en cuenta que la herramienta devuelve una versión XML del texto completo. Sin embargo, es más útil para las IA que un texto legible para humanos, ya que les proporciona información adicional sobre la estructura del documento. Al menos, esto es lo que Claude 3.5 Sonnet dijo preferir.
Tenga en cuenta también que la incapacidad de esta herramienta, y posiblemente otras, para mostrar el texto completo de un artículo podría no deberse a su falta de disponibilidad. Al probar esta herramienta, encontré un artículo que no tenía el texto completo en PubMed y, cuando Claude accedió a la URL de la publicación (que obtuvimos a través del DOI) mediante la función de búsqueda, recibió un error de "prohibido". Sin embargo, pude acceder a la misma página con un navegador normal.
En otras palabras, si su asistente de inteligencia artificial no puede obtener el texto completo de un artículo usando esta herramienta, vale la pena intentarlo manualmente con un navegador web normal.
Por último, esta herramienta, por supuesto, no te da acceso a artículos de pago. Puedes consultarlos a través del acceso a tu biblioteca o, como último recurso, a través de algún sitio web que se esfuerce por facilitar el acceso gratuito a investigaciones financiadas con fondos públicos.
Related MCP server: mcp-pubmed
Instalación
Instalación mediante herrería
Para instalar Simple PubMed para Claude Desktop automáticamente a través de Smithery :
npx -y @smithery/cli install mcp-simple-pubmed --client claudeInstalación manual
pip install mcp-simple-pubmedConfiguración
El servidor requiere las siguientes variables de entorno:
PUBMED_EMAIL: Su dirección de correo electrónico (requerida por NCBI)PUBMED_API_KEY: Clave API opcional para límites de velocidad más altos
El límite de velocidad estándar es de 3 solicitudes por segundo. No se implementó ninguna limitación de velocidad, ya que es muy improbable que, en un escenario de uso típico, su IA genere más tráfico. Si la necesita, puede registrarse para obtener una clave API que le proporcionará 10 solicitudes por segundo. Lea más sobre esto en las páginas del NCBI .
Uso con Claude Desktop
Agregue a su configuración de Claude Desktop ( claude_desktop_config.json ):
(Mac OS)
{
"mcpServers": {
"simple-pubmed": {
"command": "python",
"args": ["-m", "mcp_simple_pubmed"],
"env": {
"PUBMED_EMAIL": "your-email@example.com",
"PUBMED_API_KEY": "your-api-key"
}
}
}
}(Ventanas)
{
"mcpServers": {
"simple-pubmed": {
"command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe",
"args": [
"-m",
"mcp_simple_pubmed"
],
"env": {
"PUBMED_EMAIL": "your-email@example.com",
"PUBMED_API_KEY": "your-api-key"
}
}
}
}Licencia
Licencia MIT
Available Tools
2 toolsget_paper_fulltextGet a paper's full textARead-only
Get full text of a PubMed article using its ID.
This tool attempts to retrieve the complete text of the paper if available through PubMed Central. If the paper is not available in PMC, it will return a message explaining why and provide information about where the text might be available (e.g., through DOI).
Example usage: get_paper_fulltext(pmid="39661433")
Returns:
If successful: The complete text of the paper
If not available: A clear message explaining why (e.g., "not in PMC", "requires journal access")
ParametersJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pmid | Yes |
Output Schema
ParametersJSON Schema
| Name | Required | Description |
|---|---|---|
| result | Yes |
TDQS
A4.3/5.0
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already indicate readOnlyHint=true and openWorldHint=true, but the description adds valuable behavioral context: it explains that retrieval depends on availability in PubMed Central, describes fallback behavior (returning messages with explanations), and mentions alternative sources like DOI. This enhances transparency beyond the annotations.
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?
The description is well-structured and front-loaded with the core purpose, followed by behavioral details and example usage. Every sentence adds value without redundancy, making it efficient and easy to parse.
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 tool's complexity (fetching full text with fallbacks), the description is complete: it covers purpose, usage, behavior, and output scenarios. With an output schema present, it appropriately omits detailed return value explanations, focusing on high-level outcomes like success/failure messages.
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 0%, but the description compensates by explaining that the 'pmid' parameter is used to identify the PubMed article. However, it does not provide additional details like format constraints or examples beyond the basic usage. With one parameter and no schema descriptions, the baseline is met but not exceeded.
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 clearly states the specific action ('retrieve the complete text') and resource ('PubMed article using its ID'), distinguishing it from the sibling tool 'search_pubmed' which likely searches rather than fetches full text. It explicitly mentions PubMed Central as the source, adding specificity.
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 provides clear context on when to use this tool (to get full text of a PubMed article by ID) and implies when not to use it (if you need to search, use 'search_pubmed'). However, it does not explicitly name the alternative or detail exclusions, such as handling non-PubMed IDs.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
search_pubmedSearch articles about medical and life sciences research available on PubMed.ARead-only
Search PubMed for medical and life sciences research articles.
You can use these search features:
Simple keyword search: "covid vaccine"
Field-specific search:
Title search: [Title]
Author search: [Author]
MeSH terms: [MeSH Terms]
Journal: [Journal]
Date ranges: Add year or date range like "2020:2024[Date - Publication]"
Combine terms with AND, OR, NOT
Use quotation marks for exact phrases
Examples:
"covid vaccine" - basic search
"breast cancer"[Title] AND "2023"[Date - Publication]
"Smith J"[Author] AND "diabetes"
"RNA"[MeSH Terms] AND "therapy"
The search will return:
Paper titles
Authors
Publication details
Abstract preview (when available)
Links to full text (when available)
DOI when available
Keywords and MeSH terms
Note: Use quotes around multi-word terms for best results.
ParametersJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | ||
| max_results | No |
Output Schema
ParametersJSON Schema
| Name | Required | Description |
|---|---|---|
| result | Yes |
TDQS
A4.7/5.0
Behavior4/5
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations indicate readOnlyHint=true and openWorldHint=true, which the description aligns with by describing a search operation. The description adds valuable behavioral context beyond annotations, such as available search features, return format details (e.g., paper titles, authors, abstract preview), and performance tips, though it doesn't mention rate limits or authentication needs.
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?
The description is well-structured and front-loaded with the core purpose, followed by bullet points and examples that efficiently convey usage without unnecessary details. Every sentence adds value, making it concise and easy to scan.
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 tool's complexity (search with multiple features), low schema coverage (0%), and presence of an output schema, the description is complete enough. It thoroughly explains search capabilities, return values, and usage, compensating for the lack of schema descriptions and leveraging the output schema for return format details.
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?
With schema description coverage at 0%, the description compensates well by explaining the 'query' parameter through search features and examples, and it implies the 'max_results' parameter by mentioning return details. However, it doesn't explicitly define 'max_results' or its default value, leaving some gap.
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 clearly states the tool's purpose: 'Search PubMed for medical and life sciences research articles.' This specifies the verb ('Search'), resource ('PubMed'), and domain ('medical and life sciences research articles'), distinguishing it from the sibling tool 'get_paper_fulltext' which presumably retrieves full text rather than searching.
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?
The description provides explicit guidance on when to use this tool by detailing search features and examples, and it implicitly distinguishes from the sibling tool 'get_paper_fulltext' by focusing on search functionality rather than full-text retrieval. It also includes a note on best practices ('Use quotes around multi-word terms for best results').
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Tool Schema Changelog
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
2 tool updates
v1.0.0- First observed
get_paper_fulltext - First observed
search_pubmed
TDQS
A4.2/5.0
Scored across 2 tools
Disambiguation5/5
The two tools have clearly distinct purposes: get_paper_fulltext retrieves the full text of a specific article by ID, while search_pubmed performs keyword-based searches across the PubMed database. There is no overlap or ambiguity between these functions.
Naming Consistency5/5
Both tools follow a consistent verb_noun naming pattern: get_paper_fulltext and search_pubmed. The naming is clear and predictable, with no deviations in style or convention.
Tool Count3/5
With only two tools, the server feels thin for a PubMed interface, as it lacks operations like fetching paper metadata, filtering search results, or managing citations. While the tools cover basic retrieval and search, more comprehensive coverage would typically require additional tools.
Completeness2/5
The tool set is significantly incomplete for a PubMed domain. It lacks essential operations such as get_paper_metadata (for details like authors, journal, abstract without full text), filter_search_results, or citation-related tools. This will likely cause agent failures when trying to perform common PubMed tasks beyond simple search and full-text retrieval.
Maintenance
ActivityInactive
ResponsivenessUnresponsive
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