// SCAN REPORT

Pubmed Search

63 tools. 10 can modify or destroy data without limits.

1 destructive tool with no built-in limits. Policy required.

Last updated: 11 Jun 2026

10 can modify or destroy data

53 read-only

63 tools total

Community server · catalogue entry verified 11/06/2026

How to control Pubmed Search ↓

TOOL MAP

What Pubmed Search exposes to your agents

Read (53) Write / Execute (9) Destructive / Financial (1)

Running more than one server? Check your whole stack →

MOST DANGEROUS TOOLS

Critical Risk

The most dangerous Pubmed Search tools

Destructive · High delete_pipeline The delete_pipeline tool permanently removes stored pipeline configurations and their execution history without apparent recovery mechanism. Execute · Medium schedule_pipeline The name 'schedule_pipeline' implies triggering or scheduling an automated workflow or pipeline execution, which falls under Execute. Write · Medium configure_institutional_access The tool appears to set or modify institutional access parameters, which is a Write operation (creates/modifies configuration data reversibly). Write · Low export_citations Exporting citations is a reversible write operation—it creates formatted output (BibTeX, RIS, JSON, etc.) without destructively altering the original database records or executing arbitrary code.

10 of Pubmed Search's 63 tools can modify, destroy, or commit something on every call — and an agent calls them with no built-in limits.

POLICY

How to control Pubmed Search

PolicyLayer is an MCP gateway — it sits between your AI agents and Pubmed Search, and nothing reaches the server without passing your rules. These are the rules we recommend:

Deny destructive operations

{
  "delete_pipeline": {
    "deny_if": [
      {
        "conditions": [],
        "on_deny": "Blocked by default. Requires approval."
      }
    ]
  }
}

Destructive tools should never be available to autonomous agents without human approval.

Rate limit write operations

{
  "configure_institutional_access": {
    "limits": [
      {
        "counter": "configure_institutional_access_per_hour",
        "window": "hour",
        "max": 30,
        "scope": "grant"
      }
    ]
  }
}

Prevents bulk unintended modifications from agents caught in loops.

Cap read operations

{
  "build_citation_tree": {
    "limits": [
      {
        "counter": "build_citation_tree_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

Create a free account and register Pubmed Search — nothing to install.
Add these rules — paste them, or build them visually. Tune the limits to your setup.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

ENFORCE POLICY ON PUBMED SEARCH →

Free to start. No card required.

FULL CATALOGUE

All 63 Pubmed Search tools

DESTRUCTIVE 1 tools

Destructive delete_pipeline Delete a saved pipeline configuration and its execution history.

EXECUTE 1 tools

Execute schedule_pipeline schedule_pipeline

WRITE 8 tools

Write configure_institutional_access configure_institutional_access Write export_citations Export citations in various formats. Write generate_search_queries generate_search_queries Write manage_pipeline manage_pipeline Write merge_search_results merge_search_results Write prepare_export prepare_export Write save_literature_notes save_literature_notes Write save_pipeline save_pipeline

READ 53 tools

Read build_citation_tree build_citation_tree Read build_research_timeline build_research_timeline Read parse_pico parse_pico Read analyze_clinical_question Return an agent-guided PICO schema for a clinical question. Read analyze_fulltext_access analyze_fulltext_access Read analyze_search_query analyze_search_query Read analyze_timeline_milestones analyze_timeline_milestones Read compare_timelines compare_timelines Read diagnose_institutional_access diagnose_institutional_access Read expand_search_queries expand_search_queries Read expand_search_terms Expand a search topic with MeSH terms and synonyms. Read fetch_article_details fetch_article_details Read find_citations Find articles that cite a given article. Read find_citing_articles find_citing_articles Read find_in_core find_in_core Read find_related Find articles related to a given article. Read find_related_articles find_related_articles Read get_article Get detailed information about a specific article by PMID. Read get_article_figures get_article_figures Read get_article_fulltext_links get_article_fulltext_links Read get_article_references get_article_references Read get_cached_article 從 session 快取取得文章詳情。 Read get_citation_metrics get_citation_metrics Read get_compound_details Get detailed information about a compound by PubChem CID. Read get_compound_literature Get PubMed articles linked to a compound. Read get_core_fulltext get_core_fulltext Read get_core_paper Get detailed information about a CORE paper. Read get_fulltext Get full text of an article from Europe PMC. Read get_gene_details Get detailed information about a gene by NCBI Gene ID. Read get_gene_literature get_gene_literature Read get_institutional_link get_institutional_link Read get_performance_metrics [DEV] Get MCP tool execution performance metrics. Read get_pipeline_history get_pipeline_history Read get_references Get the reference list of an article. Read get_session_log get_session_log Read get_session_pmids get_session_pmids Read get_session_summary get_session_summary Read get_text_mined_terms get_text_mined_terms Read list_pipelines list_pipelines Read list_resolver_presets list_resolver_presets Read load_pipeline load_pipeline Read read_session read_session Read search_biomedical_images search_biomedical_images Read search_clinvar search_clinvar Read search_compound Search PubChem for chemical compounds. Read search_core search_core Read search_core_fulltext search_core_fulltext Read search_gene Search NCBI Gene database. Read search_literature search_literature Read search_pubmed search_pubmed Read test_institutional_access test_institutional_access Read verify_reference_list verify_reference_list Read convert_icd_mesh convert_icd_mesh

EXPLORE

Related servers

Other MCP servers with similar tools — same risk classification, starter policies for each.

FAQ

Questions about Pubmed Search

Can an AI agent delete data through the Pubmed Search MCP server? +

Yes. The Pubmed Search server exposes 1 destructive tools including delete_pipeline. These permanently remove resources with no undo. PolicyLayer blocks destructive tools by default so they never reach the upstream server.

How do I prevent bulk modifications through Pubmed Search? +

The Pubmed Search server has 8 write tools including configure_institutional_access, export_citations, generate_search_queries. Set a rate limit in your policy -- for example, 10 calls per hour prevents an agent from making more than 10 modifications per hour. PolicyLayer enforces this at the gateway, before calls reach Pubmed Search.

How many tools does the Pubmed Search MCP server expose? +

63 tools across 4 categories: Destructive, Execute, Read, Write. 53 are read-only. 10 can modify, create, or delete data.

How do I enforce a policy on Pubmed Search? +

Register the Pubmed Search MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every Pubmed Search tool call.

Deterministic rules across all 63 Pubmed Search tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON PUBMED SEARCH →

Free to start. No card required.

63 Pubmed Search tools catalogued and risk-classified — across an index of 43,000+ MCP servers.