MINDEX - Mycosoft Fungal Observation Database

Version: 2.0.0
Last Updated: 2026-01-15T14:30:00Z
Port: 8001

Overview

MINDEX (Mycosoft Index) is the central database for fungal observations, species data, and environmental measurements. It serves as the authoritative source for:

• Fungal species observations with GPS coordinates
• Environmental sensor data from MycoBrain devices
• Geocoded location data
• Audit trail for all data events

🚀 Quick Start

# Install dependencies
pip install -r requirements.txt

# Run migrations
python -m mindex_api.db migrate

# Start API server
uvicorn mindex_api.main:app --host 0.0.0.0 --port 8001

🐳 Docker

docker-compose up -d

📡 API Endpoints

Endpoint	Method	Description
/api/v1/observations	GET	List observations
/api/v1/observations	POST	Create observation
/api/v1/observations/{id}	GET	Get observation
/api/v1/observations/{id}	PATCH	Update observation
/api/v1/species	GET	List species
/api/v1/events	POST	Log event
/api/v1/events/batch	POST	Batch log events
/health	GET	Health check

📊 Database Schema

-- Observations
CREATE TABLE observations (
    id UUID PRIMARY KEY,
    species_id UUID REFERENCES species(id),
    latitude REAL,
    longitude REAL,
    location_name TEXT,
    location_source TEXT,
    observed_at TIMESTAMP,
    created_at TIMESTAMP DEFAULT NOW()
);

-- Species
CREATE TABLE species (
    id UUID PRIMARY KEY,
    scientific_name TEXT NOT NULL,
    common_name TEXT,
    family TEXT,
    genus TEXT
);

-- Events (Audit Trail)
CREATE TABLE events (
    id UUID PRIMARY KEY,
    event_type TEXT NOT NULL,
    entity_id TEXT,
    collector TEXT,
    timestamp TIMESTAMP,
    data JSONB,
    created_at TIMESTAMP DEFAULT NOW()
);

🔗 Integrations

Website Integration

The Mycosoft Website consumes MINDEX data via:

• REST API for observations and species
• Redis pub/sub for real-time event logging

Geocoding Pipeline

Observations without GPS coordinates are enriched by the geocoding service:

1. Service queries MINDEX for observations with has_gps=false
2. Uses Nominatim/Photon to geocode location names
3. Updates observations with lat/lon via PATCH

MycoBrain Integration

MycoBrain devices send environmental data that gets logged as events:

• Temperature, humidity, air quality
• Volatile compound analysis
• Location tracking

CREP Dashboard Integration

MINDEX fungal observations are visualized on the CREP (Common Relevant Environmental Picture) dashboard:

• Real-time fungal markers on global map
• Species distribution heatmaps
• Observation clustering by density
• Pop-up details with species info and images

See the Website Repository for CREP dashboard details.

📚 Documentation

• ETL Sync Guide
• NatureOS Integration
• MycoBrain Integration

⚙️ Configuration

DATABASE_URL=postgresql://mindex:YOUR_PASSWORD@localhost:5432/mindex
REDIS_URL=redis://localhost:6379

📝 Changelog

2026-01-15

• Added batch event logging endpoint
• Implemented geocoding pipeline integration
• Added Redis pub/sub for real-time events
• Integrated with CREP dashboard for real-time fungal visualization
• Added 1.2M+ fungal observations to MINDEX database
• Enhanced species taxonomy with GBIF synchronization

📜 License

Copyright © 2026 Mycosoft. All rights reserved.