# PyEuropePMC (pypi · pyeuropepmc)

Search and analyse scientific literature across Europe PMC, PubMed, arXiv, and ClinicalTrials.gov

- Trust score: 45/100 (low)
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-09-20

## Components

- pypi · `pyeuropepmc`: 45/100 (this document), [markdown](https://verifymcp.io/servers/jonasheinickebio-pyeuropepmc/pyeuropepmc.md), [page](https://verifymcp.io/servers/jonasheinickebio-pyeuropepmc/pyeuropepmc)

## Channel facts

- Registry: `pypi`
- Package: `pyeuropepmc`
- Version: `3.0.0`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-09-20.

- **Supply Chain Security**: 29/100
  - Malware scan not yet available for this package.
  - CVE check failed: a known high-severity CVE affects click 8.1.8, a direct dependency. A fixed version is available.
  - Runs poetry.core.masonry.api at install time, a recognised native-build step with no shell scripting around it.
  - Dependency health was assessed across the 58 of 84 dependencies we could resolve, so this covers what we could see, not the whole tree.
- **Provenance & Transparency**: 32/100
  - Source repository is publicly reachable at the declared URL.
  - Provenance check failed: no build-provenance attestation is published.
  - License check failed: no license is declared.
  - Actively maintained (last published 3 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 75/100
  - AI-judged instruction clarity (good).
  - Tool/resource definitions use about 1610 tokens (~67/item across 24 items; 24 tools + 0 resources), lean.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 0/100
  - Stability not yet verified: not enough scan history yet (needs a 30-day window).
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
  - Structured output schemas are declared (100% of tools); any adoption earns full credit.
- **Tool Safety**: 75/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - 0 of 1 tool(s) whose name or description implies an irreversible operation declare an MCP destructiveHint annotation; "bib_merge" implies "merge" and declares readOnlyHint instead, contradicting what its own name says it does.
  - An AI judge read all 25 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

**Unverified: 1 category.** A category scored 0 because we could not verify it: a data source with nothing on this package, evidence we could not reach, or a check we could not run. We only credit what we can confirm.

## Install

### How do I install the PyEuropePMC MCP server?

PyEuropePMC runs locally as a PyPI package, launched with uvx pyeuropepmc. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add jonasheinickebio-pyeuropepmc -- uvx pyeuropepmc
```

### Cursor

```json
{
  "mcpServers": {
    "jonasheinickebio-pyeuropepmc": {
      "command": "uvx",
      "args": [
        "pyeuropepmc"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "jonasheinickebio-pyeuropepmc": {
      "command": "uvx",
      "args": [
        "pyeuropepmc"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add jonasheinickebio-pyeuropepmc -- uvx pyeuropepmc
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "jonasheinickebio-pyeuropepmc": {
      "type": "local",
      "command": [
        "uvx",
        "pyeuropepmc"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add jonasheinickebio-pyeuropepmc --command uvx --arg pyeuropepmc
```

### Hermes

```yaml
mcp_servers:
  jonasheinickebio-pyeuropepmc:
    command: "uvx"
    args: ["pyeuropepmc"]
```

### Netclaw

```json
{
  "McpServers": {
    "jonasheinickebio-pyeuropepmc": {
      "Transport": "stdio",
      "Command": "uvx",
      "Arguments": [
        "pyeuropepmc"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add jonasheinickebio-pyeuropepmc -t stdio -c uvx -a pyeuropepmc
```

### Other

```json
{
  "mcpServers": {
    "jonasheinickebio-pyeuropepmc": {
      "command": "uvx",
      "args": [
        "pyeuropepmc"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-09-17 (score 45, +30)

- [security improvement] Injection markers: unverified → pass
- [security] First check of Judged manipulation: pass
- [security] Stability: Stability not yet verified: not enough scan history yet (needs a 30-day window).
- [functional improvement] Tool coverage: unverified → 100
- [functional improvement] MCP protocol: unverified → pass
- [functional] First check of Schema quality: fail
- [functional] First check of Destructive annotations: 0
- [functional] First check of Schema quality: pass
- [functional] First check of Schema quality: good
- [functional] First check of Tool coverage: 100
- [functional] First check of Tool coverage: 100
- [functional] Package version: 2.2.1 → 3.0.0

### 2026-09-15 (score 15)

First indexed and scored.

## MCP tools (24)

### `unified_search` (~107 tokens)

Search across multiple literature sources (PubMed, arXiv, Semantic Scholar, OpenAlex,
ClinicalTrials.gov) in parallel, with automatic cross-source deduplication.

Input parameters:

- `limit` (integer): Max results per source
- `query` (string, required): Search query
- `sources`: Sources to query, e.g. ['europepmc', 'arxiv', 'semantic_scholar', 'openalex', 'clinicaltrials']. Defaults to the server's configured source set.

### `search_papers` (~81 tokens)

Search Europe PMC for papers (single source — prefer `unified_search` for
multi-source coverage).

Input parameters:

- `limit` (integer): Number of results
- `query` (string, required): Search query
- `result_type` (string): Europe PMC result type
- `sort` (string): Sort order, e.g. 'cited' or 'date'

Output parameters:

- `result` (array)

### `get_paper_details` (~55 tokens)

Get detailed paper information by PMID, PMCID, or DOI (Europe PMC).

Input parameters:

- `doi` (string): DOI
- `pmcid` (string): PMCID
- `pmid` (string): PubMed ID

### `search_authors` (~37 tokens)

Search for authors in Europe PMC.

Input parameters:

- `limit` (integer): Number of results
- `query` (string, required): Author name or affiliation

Output parameters:

- `result` (array)

### `get_paper_citations` (~45 tokens)

Get papers that cite a given paper (Europe PMC).

Input parameters:

- `limit` (integer): Max citing papers to return
- `pmid` (string, required): PubMed ID

Output parameters:

- `result` (array)

### `citation_snowball` (~111 tokens)

Walk the citation graph forward (cited-by), backward (references), or both, with
configurable depth and a minimum-citation-count filter.

Input parameters:

- `identifier` (string, required): Paper ID (PMID, DOI, or Semantic Scholar ID)
- `max_depth` (integer): Recursion depth (0 = no limit)
- `max_papers` (integer): Max papers per level
- `min_citations` (integer): Minimum citation count filter
- `strategy` (string): Snowball direction

### `clinical_trial_search` (~83 tokens)

Search ClinicalTrials.gov for studies by condition, intervention, or free-text query.

Input parameters:

- `condition`: Medical condition filter
- `intervention`: Intervention/treatment filter
- `limit` (integer): Max results
- `query` (string): Free-text search query
- `status`: Recruitment status filter, e.g. ACTIVE, COMPLETED, RECRUITING

### `fulltext_index_query` (~103 tokens)

Search the local SQLite FTS5 full-text index for papers whose full text matches
a query.

A fresh index handle is opened per call rather than cached: SQLite connections are
only safe to use from the thread that created them, and each call may run on a
different worker thread.

Input parameters:

- `index_path`: Path to the SQLite index file (optional)
- `limit` (integer): Max results
- `query` (string, required): Full-text search query

### `paper_figures` (~132 tokens)

Extract figures, tables and supplementary files from a PMC Open Access article.

Each item carries its label, caption and the Europe PMC URL its file can be
downloaded from. A figure supplement also names the figure it belongs to.

Input parameters:

- `doi` (string): DOI (alternative to pmcid)
- `include_supplements` (boolean): Include supplementary material
- `include_tables` (boolean): Include <table-wrap> elements
- `pmcid` (string): PMC ID of the article, e.g. PMC1234567
- `pmid` (string): PubMed ID (alternative to pmcid)

### `analyze_citations` (~57 tokens)

Analyze citation context for a paper using an LLM (requires an LLM provider).

Input parameters:

- `context` (string): Citation context description
- `pmid` (string, required): PubMed ID
- `task` (string): Analysis task description

### `compare_citations` (~65 tokens)

Compare citations between two papers using an LLM (requires an LLM provider).

Input parameters:

- `pmid1` (string, required): PubMed ID of first paper
- `pmid2` (string, required): PubMed ID of second paper
- `task` (string): Comparison task description

### `summarize_citations` (~50 tokens)

Summarize citation activity for a paper using an LLM (requires an LLM provider).

Input parameters:

- `citation_count` (integer): Number of citations
- `pmid` (string, required): PubMed ID

### `paper_screening` (~74 tokens)

Automated paper screening with PRISMA-compliant criteria, using an LLM (requires
an LLM provider).

Input parameters:

- `exclusion_criteria` (array, required): Exclusion criteria
- `inclusion_criteria` (array, required): Inclusion criteria
- `limit` (integer): Papers to screen
- `query` (string, required): Search query

### `research_question_analysis` (~49 tokens)

Expand and analyze a research question using an LLM (requires an LLM provider).

Input parameters:

- `research_question` (string, required): Research question
- `time_frame` (string): Time frame for literature search

### `preprint_analysis` (~59 tokens)

Preprint-specific quality assessment using an LLM (requires an LLM provider).

Input parameters:

- `pmid` (string, required): PubMed ID
- `preprint_server` (string): Preprint server, e.g. bioRxiv, medRxiv

### `literature_review` (~70 tokens)

Generate a comprehensive literature review using an LLM (requires an LLM
provider).

Input parameters:

- `excluded_topics`: Topics to exclude from the review
- `key_concepts` (array, required): Key concepts to cover
- `research_topic` (string, required): Research topic
- `time_frame` (string): Time frame

### `knowledge_graph` (~51 tokens)

Build a knowledge graph from research literature using an LLM (requires an LLM
provider).

Input parameters:

- `entities`: Key entities
- `relationships`: Known relationships
- `research_domain` (string, required): Research domain

### `bib_parse_string` (~32 tokens)

Parse a BibTeX string into structured entries.

Input parameters:

- `content` (string, required): BibTeX-formatted string

### `bib_validate` (~31 tokens)

Validate BibTeX entries for completeness and correctness.

Input parameters:

- `content` (string, required): BibTeX string to validate

### `bib_to_ris` (~32 tokens)

Convert BibTeX entries to RIS format.

Input parameters:

- `content` (string, required): BibTeX-formatted string

Output parameters:

- `result` (string)

### `bib_to_csl` (~34 tokens)

Convert BibTeX entries to CSL-JSON format.

Input parameters:

- `content` (string, required): BibTeX-formatted string

Output parameters:

- `result` (array)

### `ref_resolve_doi` (~29 tokens)

Resolve a DOI to bibliographic metadata.

Input parameters:

- `doi` (string, required): DOI to resolve

### `ref_resolve_pmid` (~32 tokens)

Resolve a PubMed ID to bibliographic metadata.

Input parameters:

- `pmid` (string, required): PubMed ID

### `bib_merge` (~36 tokens)

Merge multiple BibTeX libraries, deduplicating by DOI.

Input parameters:

- `libraries` (array, required): BibTeX-formatted strings to merge

## Diagnostics

Captured diagnostic sections: Provenance, Install scripts, Vulnerabilities, Dependencies. The full working is on the page: https://verifymcp.io/servers/jonasheinickebio-pyeuropepmc/pyeuropepmc#diagnostics

## Score history

- 2026-09-20: 45
- 2026-09-19: 45
- 2026-09-18: 45
- 2026-09-17: 45
- 2026-09-16: 15
- 2026-09-15: 15

## Common questions

### What is the PyEuropePMC MCP server?

PyEuropePMC is an MCP server listed in the public MCP registry as io.github.JonasHeinickeBio/pyeuropepmc. Search and analyse scientific literature across Europe PMC, PubMed, arXiv, and ClinicalTrials.gov. This page covers its PyPI package (pyeuropepmc).

### Is the PyEuropePMC MCP server safe to use?

PyEuropePMC scores 45 out of 100 on VerifyMCP. We recorded 3 known advisories against it as of 20 September 2026. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the PyEuropePMC MCP server expose?

PyEuropePMC exposes 24 tools: unified_search, search_papers, get_paper_details, search_authors, get_paper_citations, and 19 more. Their descriptions and schemas cost roughly 1,455 tokens of context every time the server is loaded.

### Is the PyEuropePMC MCP server still maintained?

PyEuropePMC is still listed as active in the MCP registry. We last reached this channel on 20 September 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

## Links

- PyPI project: https://pypi.org/project/pyeuropepmc/
- Socket report: https://socket.dev/pypi/package/pyeuropepmc
- Repository: https://github.com/JonasHeinickeBio/pyEuropePMC
- Website: https://jonasheinickebio.github.io/pyEuropePMC/
- Changelog RSS feed: https://verifymcp.io/servers/jonasheinickebio-pyeuropepmc/pyeuropepmc.xml
- Changelog JSON feed: https://verifymcp.io/servers/jonasheinickebio-pyeuropepmc/pyeuropepmc.json
- HTML version of this page: https://verifymcp.io/servers/jonasheinickebio-pyeuropepmc/pyeuropepmc