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# Phase 11 Implementation Spec: Europe PMC Integration
> **Status**: ✅ COMPLETE
> **Implemented**: `src/tools/europepmc.py`
> **Tests**: `tests/unit/tools/test_europepmc.py`
## Overview
Europe PMC provides access to preprints and peer-reviewed literature through a single, well-designed REST API. This replaces the originally planned bioRxiv integration due to bioRxiv's API limitations (no keyword search).
## Why Europe PMC Over bioRxiv?
### bioRxiv API Limitations (Why We Abandoned It)
- bioRxiv API does NOT support keyword search
- Only supports date-range queries returning all papers
- Would require downloading entire date ranges and filtering client-side
- Inefficient and impractical for our use case
### Europe PMC Advantages
1. **Full keyword search** - Query by any term
2. **Aggregates preprints** - Includes bioRxiv, medRxiv, ChemRxiv content
3. **No authentication required** - Free, open API
4. **34+ preprint servers indexed** - Not just bioRxiv
5. **REST API with JSON** - Easy integration
## API Reference
**Base URL**: `https://www.ebi.ac.uk/europepmc/webservices/rest/search`
**Documentation**: https://europepmc.org/RestfulWebService
### Parameters
| Parameter | Value | Description |
|-----------|-------|-------------|
| `query` | string | Search keywords |
| `resultType` | `core` | Full metadata including abstracts |
| `pageSize` | 1-100 | Results per page |
| `format` | `json` | Response format |
### Example Request
```
GET https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=metformin+alzheimer&resultType=core&pageSize=10&format=json
```
## Implementation
### EuropePMCTool (`src/tools/europepmc.py`)
```python
class EuropePMCTool:
"""
Search Europe PMC for papers and preprints.
Europe PMC indexes:
- PubMed/MEDLINE articles
- PMC full-text articles
- Preprints from bioRxiv, medRxiv, ChemRxiv, etc.
- Patents and clinical guidelines
"""
BASE_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/search"
@property
def name(self) -> str:
return "europepmc"
async def search(self, query: str, max_results: int = 10) -> list[Evidence]:
"""Search Europe PMC for papers matching query."""
# Implementation with retry logic, error handling
```
### Key Features
1. **Preprint Detection**: Automatically identifies preprints via `pubTypeList`
2. **Preprint Marking**: Adds `[PREPRINT - Not peer-reviewed]` prefix to content
3. **Relevance Scoring**: Preprints get 0.75, peer-reviewed get 0.9
4. **URL Resolution**: DOI → PubMed → Europe PMC fallback chain
5. **Retry Logic**: 3 attempts with exponential backoff via tenacity
### Response Mapping
| Europe PMC Field | Evidence Field |
|------------------|----------------|
| `title` | `citation.title` |
| `abstractText` | `content` |
| `doi` | Used for URL |
| `pubYear` | `citation.date` |
| `authorList.author` | `citation.authors` |
| `pubTypeList.pubType` | Determines `citation.source` ("preprint" or "europepmc") |
## Unit Tests
### Test Coverage (`tests/unit/tools/test_europepmc.py`)
| Test | Description |
|------|-------------|
| `test_tool_name` | Verifies tool name is "europepmc" |
| `test_search_returns_evidence` | Basic search returns Evidence objects |
| `test_search_marks_preprints` | Preprints have [PREPRINT] marker and source="preprint" |
| `test_search_empty_results` | Handles empty results gracefully |
### Integration Test
```python
@pytest.mark.integration
async def test_real_api_call():
"""Test actual API returns relevant results."""
tool = EuropePMCTool()
results = await tool.search("long covid treatment", max_results=3)
assert len(results) > 0
```
## SearchHandler Integration
Europe PMC is included in `src/tools/search_handler.py` alongside PubMed and ClinicalTrials:
```python
from src.tools.europepmc import EuropePMCTool
class SearchHandler:
def __init__(self):
self.tools = [
PubMedTool(),
ClinicalTrialsTool(),
EuropePMCTool(), # Preprints + peer-reviewed
]
```
## MCP Tools Integration
Europe PMC is exposed via MCP in `src/mcp_tools.py`:
```python
async def search_europepmc(query: str, max_results: int = 10) -> str:
"""Search Europe PMC for preprints and papers."""
results = await _europepmc.search(query, max_results)
# Format and return
```
## Verification
```bash
# Run unit tests
uv run pytest tests/unit/tools/test_europepmc.py -v
# Run integration test (real API)
uv run pytest tests/unit/tools/test_europepmc.py -v -m integration
```
## Completion Checklist
- [x] `src/tools/europepmc.py` implemented
- [x] Unit tests in `tests/unit/tools/test_europepmc.py`
- [x] Integration test with real API
- [x] SearchHandler includes EuropePMCTool
- [x] MCP wrapper in `src/mcp_tools.py`
- [x] Preprint detection and marking
- [x] Retry logic with exponential backoff
## Architecture Diagram
```
┌─────────────────────────────────────────────────────────┐
│ SearchHandler │
├─────────────────────────────────────────────────────────┤
│ ┌─────────────┐ ┌──────────────┐ ┌───────────────┐ │
│ │ PubMedTool │ │ClinicalTrials│ │ EuropePMCTool │ │
│ │ │ │ Tool │ │ │ │
│ │ Peer-review │ │ Trials │ │ Preprints + │ │
│ │ articles │ │ data │ │ peer-review │ │
│ └──────┬──────┘ └──────┬───────┘ └───────┬───────┘ │
│ │ │ │ │
│ ▼ ▼ ▼ │
│ ┌─────────────────────────────────────────────┐ │
│ │ Evidence List │ │
│ │ (deduplicated, scored, with citations) │ │
│ └─────────────────────────────────────────────┘ │
└─────────────────────────────────────────────────────────┘
```
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