biosample-enricher 0.1.0rc1

Infer AI-friendly metadata about biosamples from multiple sources

Biosample Enricher

Infer AI-friendly environmental and geographic metadata about biosamples from multiple sources.

Overview

Biosample Enricher provides 8 specialized services for enriching biosample metadata with environmental and geographic information from authoritative data sources. Each service focuses on a specific domain (elevation, weather, soil, marine, land cover, geocoding, geographic features) and returns structured, type-safe data ready for analysis or AI applications.

Features

• 8 Specialized Services: Elevation, soil, weather, marine, land cover, forward/reverse geocoding, geographic features
• Service-Based Architecture: Independent services with focused responsibilities
• Type Safety: Full type hints with Pydantic validation and mypy checking
• Smart Caching: HTTP caching with coordinate canonicalization for efficiency
• Multiple Providers: Automatic fallback between data providers (USGS, Google, OSM, etc.)
• Click-Based CLIs: User-friendly command-line tools for each service
• Flexible Installation: Core services only, or add optional mongodb/metrics/schema extras

Installation

Prerequisites

• Python 3.11 or higher
• UV package manager (recommended)

Add to Your Project (Recommended)

# Basic installation - all 8 enrichment services
uv add biosample-enricher

# With optional dependencies
uv add biosample-enricher --extra metrics   # Metrics and visualization
uv add biosample-enricher --extra mongodb   # MongoDB support for NMDC/GOLD
uv add biosample-enricher --extra schema    # Schema analysis tools
uv add biosample-enricher --extra all       # All optional features

From Source (Development)

# Clone and install
git clone https://github.com/contextualizer-ai/biosample-enricher.git
cd biosample-enricher
uv sync

# With optional extras
uv sync --extra mongodb    # MongoDB support
uv sync --extra metrics    # Metrics and visualization
uv sync --extra schema     # Schema analysis tools
uv sync --extra all        # Everything

Quick Start

Python API

The package exports 8 services from the top level:

from biosample_enricher import (
    ElevationService,
    ElevationRequest,
    SoilService,
    WeatherService,
    MarineService,
    LandService,
    ReverseGeocodingService,
    ForwardGeocodingService,
    OSMFeaturesService,
)
from datetime import date

# Get elevation for a location
elevation_service = ElevationService()
request = ElevationRequest(latitude=40.7128, longitude=-74.0060)
observations = elevation_service.get_elevation(request)

for obs in observations:
    if obs.value_numeric is not None:
        print(f"{obs.provider.name}: {obs.value_numeric}m")
# Output:
# usgs_3dep: 13.15m
# google_elevation: 13.26m
# open_topo_data: 25.0m
# osm_elevation: 51.0m

# Get weather data for a location and date
weather_service = WeatherService()
weather_result = weather_service.get_daily_weather(
    lat=37.7749,
    lon=-122.4194,
    target_date=date(2024, 1, 15)
)
print(f"Temperature: {weather_result.temperature.value}°C")
print(f"Precipitation: {weather_result.precipitation.value}mm")

# Get soil properties
soil_service = SoilService()
soil_result = soil_service.enrich_location(
    latitude=40.7128,
    longitude=-74.0060,
    depth_cm="0-5cm"
)
print(f"Provider: {soil_result.provider}")
print(f"Quality score: {soil_result.quality_score}")

# Get marine data (SST, bathymetry, chlorophyll)
marine_service = MarineService()
marine_result = marine_service.get_comprehensive_marine_data(
    latitude=36.6,
    longitude=-121.9,
    target_date=date(2024, 1, 15)
)
if marine_result.sea_surface_temperature:
    print(f"Sea surface temp: {marine_result.sea_surface_temperature.value}°C")
if marine_result.bathymetry:
    print(f"Water depth: {marine_result.bathymetry.value}m")

# Reverse geocoding (coordinates -> place names)
geocoding_service = ReverseGeocodingService()
result = geocoding_service.reverse_geocode(lat=40.7128, lon=-74.0060)
if result:
    print(f"Location: {result.get_formatted_address()}")

# Get nearby geographic features
osm_service = OSMFeaturesService()
features = osm_service.get_features_for_location(
    latitude=37.7749,
    longitude=-122.4194,
    radius_m=1000
)
if features and features.named_features:
    for feature in features.named_features[:5]:
        print(f"{feature.name} ({feature.category}): {feature.distance_km:.2f}km")

CLI Usage

Each service has its own CLI command:

# Elevation lookup
uv run elevation-lookup lookup --lat 40.7128 --lon -74.0060

# Soil data
uv run soil-enricher lookup --lat 40.7128 --lon -74.0060 --depth 10

# Weather data
uv run weather-enricher lookup --lat 37.7749 --lon -122.4194 --date 2024-01-15

# Marine data
uv run marine-enricher lookup --lat 36.6 --lon -121.9 --date 2024-01-15

# Land cover
uv run land-enricher lookup --lat 40.7128 --lon -74.0060

# Batch processing from CSV
uv run elevation-lookup batch --input samples.csv --lat-col latitude --lon-col longitude

# Version info
uv run biosample-version

Services

1. Elevation Service

Get elevation data from multiple providers (USGS, Google, Open Topo Data).

Providers: USGS (US only, free), Google (global, requires API key), Open Topo Data (global, free)

Python:

from biosample_enricher import ElevationService, ElevationRequest

service = ElevationService()
request = ElevationRequest(latitude=40.7128, longitude=-74.0060)
observations = service.get_elevation(request)

CLI:

uv run elevation-lookup lookup --lat 40.7128 --lon -74.0060

2. Soil Service

Get soil properties (texture, pH, organic carbon, etc.).

Providers: SoilGrids (global coverage), USDA NRCS (US only)

Python:

from biosample_enricher import SoilService

service = SoilService()
soil_result = service.enrich_location(
    latitude=40.7128,
    longitude=-74.0060,
    depth_cm="0-5cm"
)

CLI:

uv run soil-enricher lookup --lat 40.7128 --lon -74.0060 --depth 10

3. Weather Service

Get historical weather data (temperature, precipitation, humidity, etc.).

Providers: Open-Meteo (free, global), Meteostat (free, global)

Python:

from biosample_enricher import WeatherService
from datetime import date

service = WeatherService()
weather_result = service.get_daily_weather(
    lat=37.7749,
    lon=-122.4194,
    target_date=date(2024, 1, 15)
)

CLI:

uv run weather-enricher lookup --lat 37.7749 --lon -122.4194 --date 2024-01-15

4. Marine Service

Get marine data (sea surface temperature, bathymetry, chlorophyll).

Providers: NOAA OISST (SST), GEBCO (bathymetry), ESA CCI (chlorophyll)

Python:

from biosample_enricher import MarineService
from datetime import date

service = MarineService()
marine_result = service.get_comprehensive_marine_data(
    latitude=36.6,
    longitude=-121.9,
    target_date=date(2024, 1, 15)
)

CLI:

uv run marine-enricher lookup --lat 36.6 --lon -121.9 --date 2024-01-15

5. Land Service

Get land cover classification.

Providers: ESA WorldCover, MODIS, NLCD (US only)

Python:

from biosample_enricher import LandService

service = LandService()
land_result = service.enrich_location(
    latitude=40.7128,
    longitude=-74.0060
)

CLI:

uv run land-enricher lookup --lat 40.7128 --lon -74.0060

6. Reverse Geocoding Service

Convert coordinates to human-readable addresses.

Providers: OSM Nominatim (free), Google Geocoding (requires API key)

Python:

from biosample_enricher import ReverseGeocodingService

service = ReverseGeocodingService()
result = service.reverse_geocode(lat=40.7128, lon=-74.0060)
if result:
    print(result.get_formatted_address())

7. Forward Geocoding Service

Convert addresses/place names to coordinates.

Providers: OSM Nominatim (free), Google Geocoding (requires API key)

Python:

from biosample_enricher import ForwardGeocodingService

service = ForwardGeocodingService()
result = service.geocode("New York City")
if result and result.locations:
    for location in result.locations[:3]:
        print(f"{location.formatted_address}: {location.latitude}, {location.longitude}")

8. OSM Features Service

Get nearby geographic features (parks, water bodies, landmarks).

Providers: OpenStreetMap Overpass API (free), Google Places (requires API key)

Python:

from biosample_enricher import OSMFeaturesService

service = OSMFeaturesService()
features = service.get_features_for_location(
    latitude=37.7749,
    longitude=-122.4194,
    radius_m=1000
)
if features and features.named_features:
    for feature in features.named_features[:5]:
        print(f"{feature.name} ({feature.category})")

API Keys

Only required for Google services (optional - OSM alternatives available for everything):

# Single API key for all Google services
export GOOGLE_MAIN_API_KEY="your-key-here"

All other services are free and require no authentication.

Development

Setup

# Clone repository
git clone https://github.com/contextualizer-ai/biosample-enricher.git
cd biosample-enricher

# Complete development setup
make dev-setup

Testing

# Run fast tests (excludes network/slow tests)
make test-fast

# Run all tests with coverage
make test-cov

# Run specific test categories
make test-unit          # Unit tests only
make test-integration   # Integration tests

Code Quality

# Format, lint, type-check, test
make dev-check

# Full CI validation
make check-ci

# Individual checks
make format       # Format with ruff
make lint         # Lint with ruff
make type-check   # Type check with mypy
make dep-check    # Check dependencies with deptry

Project Structure

biosample-enricher/
├── biosample_enricher/
│   ├── __init__.py           # Public API exports
│   ├── elevation/            # Elevation service
│   ├── soil/                 # Soil service
│   ├── weather/              # Weather service
│   ├── marine/               # Marine service
│   ├── land/                 # Land cover service
│   ├── reverse_geocoding/    # Reverse geocoding
│   ├── forward_geocoding/    # Forward geocoding
│   ├── osm_features/         # Geographic features
│   ├── models.py             # Core data models
│   ├── http_cache.py         # HTTP caching
│   └── cli*.py               # CLI commands
├── tests/                    # Test suite
├── pyproject.toml           # Project configuration
└── Makefile                 # Development automation

Dependencies

Core Dependencies

• Always installed: pandas, rasterio, meteostat (required for weather aggregation and global soil coverage)
• CLI and data validation: click, pydantic, requests, rich, pyyaml

Optional Dependencies

• mongodb: pymongo for fetching from NMDC/GOLD databases (evaluation/demo only)
• metrics: matplotlib, seaborn for visualization
• schema: genson for schema analysis

Install with: uv sync --extra mongodb or uv sync --extra all

Contributing

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Make your changes
4. Run checks (make dev-check)
5. Commit (git commit -m 'Add amazing feature')
6. Push (git push origin feature/amazing-feature)
7. Open a Pull Request

See CLAUDE.md for detailed development guidelines.

License

MIT License - see LICENSE file for details.

Acknowledgments

• Built with UV for fast package management
• CLI powered by Click
• Data validation with Pydantic
• Console output with Rich
• Caching with requests-cache

Support

• Issues: GitHub Issues
• Email: [e-mail]