pubmed-stream 0.1.0__tar.gz

pubmed_stream-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pubmed-stream
+Version: 0.1.0
+Summary: Download PubMed Central full-text articles via NCBI E-utilities API. Built for biomedical research.
+Author: Haran Lab, Bucci Lab, and Microbiology & Microbiome Dynamics AI HUB
+Maintainer: University of Massachusetts
+License: MIT
+Project-URL: Repository, https://github.com/melhzy/pubmed-stream
+Project-URL: Homepage, https://github.com/melhzy/pubmed-stream
+Project-URL: Bug Tracker, https://github.com/melhzy/pubmed-stream/issues
+Keywords: pubmed,pmc,ncbi,e-utilities,literature,download,biomedical,research
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: requests>=2.25
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+
+# pubmed-stream
+
+A Python library for downloading PubMed Central (PMC) full-text articles with support for concurrent downloads, automatic rate limiting, metadata extraction, and multiple output formats.
+
+**Built on NCBI E-utilities API** for reliable, standards-compliant access to biomedical literature.
+
+## Overview
+
+`pubmed-stream` simplifies the process of downloading scientific literature from PubMed Central by leveraging the **NCBI E-utilities API** (ESearch and EFetch):
+- **Searching PMC directly** for guaranteed full-text availability
+- **Extracting structured metadata** from JATS XML (title, authors, abstract, keywords, DOI, etc.)
+- **Supporting multiple formats**: plain text, raw XML, or both in a single JSON file
+- **Handling concurrent downloads** with configurable thread pools
+- **Respecting NCBI rate limits** with automatic detection and retry logic
+- **Providing both CLI and Python API** for flexible integration
+
+Built for researchers and data scientists who need efficient, reliable access to biomedical literature.
+
+## Quick Start
+
+```bash
+# Install
+pip install .
+
+# Download articles (CLI)
+pubmed-stream download "gut microbiome" --max-results 50
+
+# Python API
+from pubmed_stream import search_and_download
+stats = search_and_download(
+    keyword="CRISPR gene editing",
+    max_results=100,
+    fmt="text"
+)
+print(f"Downloaded {stats.successful} articles in {stats.duration_seconds:.1f}s")
+```
+
+## Table of Contents
+
+- [Installation](#installation)
+- [How It Works](#how-it-works)
+- [Configuration](#configuration-optional)
+- [CLI Usage](#cli-usage)
+- [Python API](#python-api)
+- [Output Format](#output-format)
+- [Use Cases](#use-cases)
+- [Troubleshooting](#troubleshooting)
+- [Performance Tuning](#performance-tuning)
+- [Testing](#testing)
+- [Contributing](#contributing)
+- [License](#license)
+
+## Installation
+
+### From Local Clone
+
+```bash
+# Clone the repository
+git clone https://github.com/melhzy/pubmed-stream.git
+cd pubmed-stream
+
+# Install in standard mode
+pip install .
+
+# Or install in development mode (editable install)
+pip install -e ".[dev]"
+```
+
+### Requirements
+
+- Python 3.8+
+- [requests](https://pypi.org/project/requests/) (only runtime dependency)
+
+Development dependencies (optional):
+- pytest (for testing)
+- ruff (for linting)
+
+## How It Works
+
+### Architecture
+
+The library follows a modular design with three main components, all built on **NCBI E-utilities**:
+
+1. **Search Module** (`esearch_pmc`)
+   - Uses NCBI E-utilities **ESearch** to query PMC database directly
+   - Returns PMC IDs for articles with guaranteed full-text availability
+   - Handles pagination and result limiting
+
+2. **Download Module** (`efetch_pmc`)
+   - Uses NCBI E-utilities **EFetch** to retrieve full XML article data from PMC
+   - Extracts structured metadata using JATS XML parsing
+   - Converts XML to plain text (optional)
+   - Saves in requested format(s)
+
+3. **Orchestration Layer** (`search_and_download`)
+   - Combines search and download operations
+   - Manages concurrent downloads with thread pools
+   - Handles rate limiting, retries, and error recovery
+   - Tracks statistics (success/failure/skipped counts)
+
+### Search Strategy
+
+**Direct PMC Search**: Unlike some tools that search PubMed and then try to find PMC links, this library searches PMC directly. This ensures:
+- All results have full-text available
+- No broken links or paywalled content
+- Faster, more reliable downloads
+- Better results for generic queries like "microbiome" or "CRISPR"
+
+### Data Flow
+
+```
+User Query → PMC Search → PMC IDs → Concurrent Downloads → Parse XML → Extract Metadata → Save JSON
+     ↓            ↓            ↓             ↓                  ↓              ↓            ↓
+ "microbiome"  E-Search   [123, 456]    Thread Pool      JATS Parser    {title, authors}  PMC*.json
+```
+
+### Output Format Options
+
+All formats save as `.json` files with different content:
+
+**`"text"` (default)**: JSON with plain-text content
+```json
+{
+  "pmcid": "PMC12345678",
+  "metadata": {"title": "...", "authors": [...]},
+  "text": "Introduction\nThis study examines..."
+}
+```
+
+**`"xml"`**: JSON with raw JATS XML string
+```json
+{
+  "pmcid": "PMC12345678",
+  "metadata": {"title": "...", "authors": [...]},
+  "xml": "<article>...</article>"
+}
+```
+
+**`"both"`**: JSON with both XML and text
+```json
+{
+  "pmcid": "PMC12345678",
+  "metadata": {"title": "...", "authors": [...]},
+  "xml": "<article>...</article>",
+  "text": "Introduction\nThis study examines..."
+}
+```
+
+**Why unified JSON?**
+- Consistent file handling (always `.json`)
+- Metadata always included
+- Easy to query and filter
+- Smaller storage (text-only is ~50% smaller than XML)
+- Backward compatible with existing pipelines
+
+## Configuration (optional)
+
+Set these environment variables for best results:
+
+```bash
+# PowerShell
+$env:NCBI_API_KEY = "YOUR_KEY"   # raises rate limit from 3→10 req/s
+$env:NCBI_EMAIL   = "you@example.com"
+
+# Bash / Zsh
+export NCBI_API_KEY="YOUR_KEY"
+export NCBI_EMAIL="you@example.com"
+```
+
+You can also pass `--api-key` / `--email` on the command line.
+
+### Rate Limits
+
+NCBI enforces rate limits on API requests:
+
+- **Without API key**: 3 requests/second
+- **With API key**: 10 requests/second
+
+The library **automatically detects** whether you have an API key and adjusts the rate limit accordingly:
+- With API key: 0.1s between requests (10 req/s)
+- Without API key: 0.34s between requests (3 req/s)
+
+You can override this with `--rate-limit` if needed, but the auto-detection works well for most cases.
+
+**Recommendation**: Get a free API key to download ~3x faster. Without a key, the library still works but is slower.
+
+## CLI usage
+
+After installation the `pubmed-stream` command is available:
+
+```bash
+# Download up to 50 articles as JSON (default, concurrent)
+pubmed-stream download "frailty cytokines" --max-results 50
+
+# Sequential mode for unstable networks
+pubmed-stream download "gut microbiome" --sequential
+
+# Custom output directory
+pubmed-stream download "Alzheimer microbiome" -o ./my_papers
+
+# Verbose logging
+pubmed-stream download "frailty" -v --max-results 5
+
+# Show version
+pubmed-stream --version
+```
+
+The same interface is available via `python -m pubmed_stream`:
+
+```bash
+python -m pubmed_stream download "frailty cytokines" --max-results 50
+```
+
+### CLI options
+
+| Flag | Description | Default |
+|------|-------------|---------|
+| `keyword` | PubMed search query (positional) | required |
+| `--max-results` | Maximum articles to download | 100 |
+| `--format` | Output format: `text`, `xml`, `both` (all save as `.json`) | `text` |
+| `--output-dir`, `-o` | Base output directory | `./publications` |
+| `--api-key` | NCBI API key | `NCBI_API_KEY` env var |
+| `--email` | Contact email for NCBI | `NCBI_EMAIL` env var |
+| `--sequential` | Disable concurrent downloads | concurrent |
+| `--workers` | Concurrent thread count | 5 |
+| `--exclude-text` | Omit `text` field in JSON (~30% smaller) | included |
+| `--rate-limit` | Min seconds between requests | auto: 0.1 with key, 0.34 without |
+| `--user-agent` | Custom HTTP `User-Agent` | `pubmed-stream/<ver>` |
+| `--verbose`, `-v` | DEBUG-level logging | INFO |
+
+### Exit codes
+
+| Code | Meaning |
+|------|---------|
+| 0 | At least one article downloaded (or all already cached) |
+| 1 | No results found for the query |
+| 2 | All download attempts failed |
+
+## Python API
+
+### Basic Usage
+
+```python
+from pubmed_stream import search_and_download
+
+# Download articles with default settings
+stats = search_and_download(
+    keyword="gut microbiome inflammation",
+    max_results=50,
+    fmt="text",  # or "xml", "both"
+    output_dir="publications",
+)
+
+print(f"Downloaded: {stats.successful}")
+print(f"Skipped (already exist): {stats.skipped}")
+print(f"Failed: {stats.failed}")
+print(f"Success rate: {stats.success_rate:.1f}%")
+print(f"Duration: {stats.duration_seconds:.1f}s")
+```
+
+### Advanced Usage
+
+```python
+from pubmed_stream import search_and_download
+from pathlib import Path
+
+# Full control over all parameters
+stats = search_and_download(
+    keyword="CRISPR gene editing",
+    max_results=100,
+    fmt="both",              # Save both XML and text
+    api_key="your_api_key",  # Or use NCBI_API_KEY env var
+    use_concurrent=True,     # Enable parallel downloads
+    max_workers=10,          # Use 10 threads
+    include_text=True,       # Include plain-text field
+    output_dir=Path("./research/crispr"),
+    user_agent="MyResearchBot/1.0",
+    email="researcher@university.edu",
+    rate_limit=0.15,         # Custom rate limit
+)
+
+# Access detailed statistics
+print(f"Total found in PMC: {stats.total_found}")
+print(f"Requested: {stats.requested}")
+print(f"Output: {stats.output_dir}")
+```
+
+### Low-Level API
+
+For more control, use the underlying functions:
+
+```python
+from pubmed_stream import esearch_pmc, efetch_pmc, create_session, RateLimiter
+from pathlib import Path
+
+# Create session and rate limiter
+session = create_session("MyApp/1.0")
+rate_limiter = RateLimiter(0.1)  # 10 req/s
+
+# Search for PMC IDs
+pmcids, total_found = esearch_pmc(
+    term="microbiome AND aging",
+    max_results=20,
+    api_key="your_key",
+    session=session,
+    rate_limiter=rate_limiter
+)
+
+print(f"Found {len(pmcids)} PMC IDs (total: {total_found})")
+
+# Download individual articles
+for pmcid in pmcids:
+    success, status = efetch_pmc(
+        pmcid=pmcid,
+        out_dir=Path("downloads"),
+        fmt="text",
+        api_key="your_key",
+        session=session,
+        rate_limiter=rate_limiter,
+        include_text=True
+    )
+    
+    if success:
+        print(f"✓ Downloaded PMC{pmcid}")
+    else:
+        print(f"✗ Failed PMC{pmcid}: {status}")
+
+session.close()
+```
+
+### Metadata Extraction
+
+The library automatically extracts metadata from JATS XML:
+
+```python
+from pubmed_stream import extract_metadata_from_pmc_xml
+
+xml_content = """<article>...</article>"""  # Your PMC XML
+
+metadata = extract_metadata_from_pmc_xml(xml_content)
+
+# Available metadata fields
+print(metadata.get("title"))          # Article title
+print(metadata.get("journal"))        # Journal name
+print(metadata.get("doi"))            # DOI
+print(metadata.get("pmid"))           # PubMed ID
+print(metadata.get("pmcid"))          # PMC ID
+print(metadata.get("authors"))        # List of authors
+print(metadata.get("abstract"))       # Abstract text
+print(metadata.get("keywords"))       # Keywords list
+print(metadata.get("year"))           # Publication year
+print(metadata.get("pub_date"))       # Full publication date
+```
+
+## Output Format
+
+### Directory Structure
+
+Articles are organized by search query:
+
+```
+publications/
+  gut_microbiome_inflammation/
+    PMC12345678.json
+    PMC12345679.json
+    PMC12345680.json
+  alzheimer_disease/
+    PMC11111111.json
+    PMC22222222.json
+```
+
+Query strings are slugified (spaces→underscores, special characters removed) for clean directory names.
+
+### JSON Schema
+
+Each JSON file contains:
+
+```json
+{
+  "pmcid": "PMC12345678",
+  "source": "PMC",
+  "download_date": "2026-02-17T12:30:45.123456",
+  "metadata": {
+    "title": "The Role of Gut Microbiome in Inflammation",
+    "journal": "Nature Medicine",
+    "journal_title": "Nature Medicine",
+    "journal_nlm_ta": "Nat Med",
+    "journal_iso_abbrev": "Nat. Med.",
+    "doi": "10.1038/s41591-024-12345-6",
+    "pmid": "38123456",
+    "pmcid": "PMC12345678",
+    "year": "2024",
+    "month": "11",
+    "day": "15",
+    "pub_date": {
+      "year": "2024",
+      "month": "11",
+      "day": "15"
+    },
+    "authors": [
+      "Smith, John A.",
+      "Johnson, Mary B.",
+      "Williams, Robert C."
+    ],
+    "abstract": "Background: The gut microbiome plays a crucial role...",
+    "keywords": [
+      "microbiome",
+      "inflammation",
+      "gut health"
+    ]
+  },
+  "text": "Introduction\nThe human gut microbiome comprises...",
+  "xml": "<article>...</article>"
+}
+```
+
+**Field descriptions:**
+- `pmcid`: PubMed Central identifier
+- `source`: Always "PMC"
+- `download_date`: ISO 8601 timestamp
+- `metadata`: Structured article information
+- `text`: Plain-text content (if `fmt="text"` or `fmt="both"`)
+- `xml`: Raw JATS XML string (if `fmt="xml"` or `fmt="both"`)
+
+### Format Comparison
+
+| Format | File Type | Contains | Use Case | Size |
+|--------|-----------|----------|----------|------|
+| `text` | `.json` | metadata + text | Vector DBs, search, NLP | Smallest (~50% of XML) |
+| `xml` | `.json` | metadata + xml | Section parsing, structure analysis | Medium |
+| `both` | `.json` | metadata + xml + text | Comprehensive analysis | Largest |
+
+## Use Cases
+
+### 1. Literature Review & Meta-Analysis
+
+```python
+# Download recent papers on a specific topic
+stats = search_and_download(
+    keyword="COVID-19 vaccine efficacy",
+    max_results=200,
+    fmt="text",
+    output_dir="covid19_review"
+)
+
+# Process downloaded articles
+import json
+from pathlib import Path
+
+for json_file in Path("covid19_review/covid_19_vaccine_efficacy").glob("*.json"):
+    with open(json_file) as f:
+        article = json.load(f)
+    
+    print(f"Title: {article['metadata']['title']}")
+    print(f"Year: {article['metadata']['year']}")
+    print(f"Abstract: {article['metadata']['abstract'][:200]}...")
+```
+
+### 2. Vector Database Embedding
+
+```python
+# Download for embedding into vector database
+stats = search_and_download(
+    keyword="machine learning healthcare",
+    max_results=1000,
+    fmt="text",  # Plain text is ideal for embeddings
+    include_text=True
+)
+
+# Example: Embed into ChromaDB
+import chromadb
+from pathlib import Path
+import json
+
+client = chromadb.Client()
+collection = client.create_collection("medical_papers")
+
+for json_file in Path("publications/machine_learning_healthcare").glob("*.json"):
+    with open(json_file) as f:
+        article = json.load(f)
+    
+    collection.add(
+        documents=[article["text"]],
+        metadatas=[{
+            "title": article["metadata"]["title"],
+            "year": article["metadata"]["year"],
+            "doi": article["metadata"].get("doi", ""),
+        }],
+        ids=[article["pmcid"]]
+    )
+```
+
+### 3. Section-Level Analysis
+
+```python
+# Download with XML for detailed structure parsing
+stats = search_and_download(
+    keyword="CRISPR therapy clinical trials",
+    max_results=50,
+    fmt="xml"  # Get raw XML for section extraction
+)
+
+# Parse sections from XML
+import xml.etree.ElementTree as ET
+import json
+from pathlib import Path
+
+for json_file in Path("publications/crispr_therapy_clinical_trials").glob("*.json"):
+    with open(json_file) as f:
+        article = json.load(f)
+    
+    # Parse XML to extract sections
+    root = ET.fromstring(article["xml"])
+    
+    # Find all sections with sec-type attribute
+    for sec in root.findall(".//sec[@sec-type]"):
+        sec_type = sec.get("sec-type")
+        title = sec.find("title")
+        
+        if title is not None:
+            print(f"Section: {sec_type} - {title.text}")
+```
+
+### 4. Batch Processing with Keywords
+
+```python
+# Process multiple queries from CSV
+import pandas as pd
+
+keywords_df = pd.read_csv("research_keywords.csv")
+
+for _, row in keywords_df.iterrows():
+    print(f"Processing: {row['keyword']}")
+    
+    stats = search_and_download(
+        keyword=row['keyword'],
+        max_results=row['max_articles'],
+        fmt="both",  # Get both formats for flexibility
+        output_dir="batch_download"
+    )
+    
+    print(f"  Downloaded: {stats.successful}, Success rate: {stats.success_rate:.1f}%")
+```
+
+## Troubleshooting
+
+### Common Issues
+
+**1. "0 downloads" but high PMC result count**
+- **Cause**: Files already downloaded (skipped)
+- **Solution**: Check `stats.skipped` - this is actually success! Delete folder to re-download.
+
+**2. Rate limiting (HTTP 429)**
+- **Cause**: Exceeding NCBI rate limits
+- **Solution**: 
+  - Get a free API key (increases limit from 3→10 req/s)
+  - Use `--rate-limit` to slow down: `--rate-limit 0.5`
+  - The library automatically retries with backoff
+
+**3. "Unavailable" articles**
+- **Cause**: Article not in PMC or embargoed
+- **Solution**: Normal - not all PubMed articles have PMC full-text. The library only returns available articles.
+
+**4. Network timeouts**
+- **Cause**: Unstable internet connection
+- **Solution**: Use `--sequential` mode: `pubmed-stream download "query" --sequential`
+
+**5. Memory issues with large downloads**
+- **Cause**: Processing too many articles concurrently
+- **Solution**: Reduce workers: `--workers 2` or use `--sequential`
+
+### Debugging
+
+Enable verbose logging to see detailed information:
+
+```bash
+pubmed-stream download "microbiome" -v --max-results 10
+```
+
+```python
+import logging
+logging.basicConfig(level=logging.DEBUG)
+
+from pubmed_stream import search_and_download
+stats = search_and_download(keyword="test", max_results=5)
+```
+
+## Performance Tuning
+
+### Concurrent vs Sequential
+
+**Concurrent (default)**: Faster for stable networks
+```bash
+pubmed-stream download "query" --workers 10  # 10 parallel downloads
+```
+
+**Sequential**: More reliable for unstable networks
+```bash
+pubmed-stream download "query" --sequential
+```
+
+### Optimal Settings by Network
+
+| Network Quality | Mode | Workers | Rate Limit |
+|----------------|------|---------|------------|
+| Excellent | Concurrent | 10 | 0.1 (with API key) |
+| Good | Concurrent | 5 | 0.1 |
+| Fair | Concurrent | 2-3 | 0.2 |
+| Poor | Sequential | 1 | 0.34 |
+
+### Performance Benchmarks
+
+Typical download speeds (with API key, 5 workers):
+- **Small articles** (~50KB): 2-5 articles/second
+- **Medium articles** (~200KB): 1-3 articles/second
+- **Large articles** (~1MB): 0.5-1 articles/second
+
+Example: 100 medium-sized articles ≈ 45-60 seconds
+
+Note: The raw XML is not included in JSON format to save storage. Use `--format xml` if you need the raw XML.
+
+## Testing
+
+The repository includes a comprehensive Jupyter notebook for testing all features:
+
+```bash
+# Install Jupyter
+pip install jupyter
+
+# Launch test notebook
+jupyter notebook test_download.ipynb
+```
+
+The notebook demonstrates:
+- Basic and advanced download scenarios
+- All format options (text, xml, both)
+- Concurrent vs sequential modes
+- Error handling and edge cases
+- Performance comparisons
+- Low-level API usage
+
+### Running Tests
+
+```bash
+# Install development dependencies
+pip install -e ".[dev]"
+
+# Run tests (if available)
+pytest tests/
+```
+
+## Contributing
+
+Contributions are welcome! Please:
+
+1. Fork the repository
+2. Create a feature branch: `git checkout -b feature-name`
+3. Make your changes with clear commit messages
+4. Add tests if applicable
+5. Ensure code passes linting: `ruff check .`
+6. Submit a pull request
+
+### Code Style
+
+- Follow PEP 8
+- Use type hints where appropriate
+- Add docstrings for public functions
+- Keep functions focused and modular
+
+## Development Roadmap
+
+Future enhancements being considered:
+- [ ] Support for PubMed (non-PMC) abstracts
+- [ ] Advanced search query builder
+- [ ] Automatic deduplication
+- [ ] Progress bars for CLI
+- [ ] Export to BibTeX/RIS formats
+- [ ] Integration with citation managers
+- [ ] Parallel processing for metadata extraction
+
+## FAQ
+
+**Q: Why JSON instead of separate XML/TXT files?**  
+A: Unified JSON format provides consistent structure, always includes metadata, and simplifies file operations. You can still get raw XML (as a string field) if needed.
+
+**Q: Can I use this for commercial purposes?**  
+A: Yes, under the MIT license. However, respect NCBI's usage policies and rate limits.
+
+**Q: How do I get an NCBI API key?**  
+A: Register at https://www.ncbi.nlm.nih.gov/account/ and generate an API key in your account settings. It's free.
+
+**Q: Does this violate NCBI terms of service?**  
+A: No - this library is built on official NCBI E-utilities APIs (ESearch and EFetch), respects rate limits, and includes proper user-agent headers in compliance with NCBI usage policies.
+
+**Q: Can I resume interrupted downloads?**  
+A: Yes - already-downloaded files are automatically skipped (shown in `stats.skipped`).
+
+**Q: What's the difference between PMC and PubMed?**  
+A: PubMed contains citation abstracts for millions of papers. PMC (PubMed Central) is a subset with full-text articles. This library accesses PMC for complete article text.
+
+## Project Structure
+
+```
+pubmed-stream/
+├── pubmed_stream/              # Main package
+│   ├── __init__.py            # Public API exports
+│   ├── __main__.py            # python -m pubmed_stream entry point
+│   ├── cli.py                 # Command-line interface
+│   ├── downloader.py          # Core download logic
+│   └── py.typed               # Type hint marker
+├── examples/
+│   ├── keywords/              # Sample keyword CSV files
+│   │   ├── pmc_literature_keywords.csv
+│   │   └── ...
+│   └── utils/                 # Helper scripts
+│       ├── manage_text_field.py
+│       └── test_pmc_availability.py
+├── test_download.ipynb        # Comprehensive test notebook
+├── pyproject.toml            # Project metadata and dependencies
+├── README.md                 # This file
+└── .gitignore               # Git ignore rules
+```
+
+## Acknowledgments
+
+This library was developed to support biomedical research at the **University of Massachusetts** by:
+- **Haran Lab**
+- **Bucci Lab**
+- **Microbiology & Microbiome Dynamics AI HUB**
+
+Special thanks to:
+- **NCBI** for providing the E-utilities API and open access to PubMed Central
+- The open-source community for Python ecosystem tools
+
+## Citation
+
+If you use this library in your research, please cite:
+
+```bibtex
+@software{pubmed_stream_2026,
+  title = {pubmed-stream: Python Library for PMC Article Downloads via NCBI E-utilities},
+  author = {Haran Lab and Bucci Lab and Microbiology \& Microbiome Dynamics AI HUB},
+  organization = {University of Massachusetts},
+  year = {2026},
+  url = {https://github.com/melhzy/pubmed-stream},
+  note = {Built on NCBI E-utilities API}
+}
+```
+
+## License
+
+MIT License
+
+Copyright (c) 2026 University of Massachusetts  
+Haran Lab, Bucci Lab, and Microbiology & Microbiome Dynamics AI HUB
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+---
+
+**Contact**: For questions or support, please open an issue on GitHub.
+
+**Repository**: https://github.com/melhzy/pubmed-stream