BioAnalyzer

A scientific paper analysis tool focused on microbiome research and BugSigDB curation readiness.

Features

• Browse Papers: Search papers by PMID and analyze them for BugSigDB curation readiness
• Chat Assistant: Interactive AI-powered assistance for analysis questions

Key BugSigDB Curation Fields

The system analyzes papers for the following 6 essential fields that determine curation readiness:

1. Host Species: Primary organism being studied
2. Body Site: Microbiome sample collection location
3. Condition: Disease/treatment/exposure being studied
4. Sequencing Type: Molecular method used (16S, metagenomics, etc.)
5. Taxa Level: Taxonomic level analyzed (phylum, genus, species, etc.)
6. Sample Size: Number of samples analyzed

Curation Readiness: A paper is considered ready for curation when all 6 fields are present and well-documented.

Architecture

• FastAPI Backend: Python-based API server with AI-powered analysis
• AI Models: Integration with Google Gemini for intelligent paper analysis
• Frontend: Modern web interface built with Bootstrap and vanilla JavaScript
• Core Functionality: Automated extraction and assessment of curation fields from scientific papers

Prerequisites

• Docker and Docker Compose
• Python 3.11+ (for local development)
• API Keys:
  • NCBI API key for PubMed access
  • Google Gemini API key for AI analysis

Installation

1. Clone the repository:

git clone <repository-url>
cd BioAnalyzer

2. Create environment file:

cp .env.example .env
# Edit .env with your API keys

3. Start the development environment:

./dev.sh start-build

Development

The development environment includes hot reloading:

# Start with build (first time)
./dev.sh start-build

# Start without build (daily development)
./dev.sh start-no-build

# Stop services
./dev.sh stop

# View logs
./dev.sh logs

# Check status
./dev.sh status

API Usage

Enhanced Analysis

Single Paper Analysis

POST /enhanced_analysis/{pmid}

Analyze a single paper for BugSigDB curation readiness.

Batch Analysis

POST /enhanced_analysis_batch

Analyze multiple papers for BugSigDB curation readiness.

Curation Statistics

GET /curation/statistics

Get statistics about how well the 6 essential curation fields are being identified across all analyzed papers.

License

Artistic-2.0