Python examples for exploring 6.7 million material samples from scientific collections worldwide using high-performance geoparquet analysis and visualization.
# Install dependencies
poetry install --with examples
# Activate environment
poetry shell
# Launch Jupyter for examples
jupyter lab examples/basic/This repository provides Jupyter notebooks for analyzing material sample data from the iSamples project. The iSamples metadata model is domain-agnostic, supporting samples from geology, biology, archaeology, environmental science, and other fields.
Data Sources:
- SESAR: 4.6M geological samples
- OpenContext: 1M archaeological samples
- GEOME: 605K genomic samples
- Smithsonian: 322K museum specimens
All data accessed via geoparquet files on Cloudflare R2 - no API required.
| Notebook | Description |
|---|---|
isamples_explorer.ipynb ⭐ | Interactive explorer with faceted search, map/table views |
geoparquet.ipynb ⭐ | Advanced lonboard visualization with zoom-layered rendering |
pqg_demo.ipynb | Property graph queries with DuckDB |
schema_comparison.ipynb | Narrow vs wide format comparison |
isample-archive.ipynb | Remote parquet analysis via DuckDB |
See examples/README.md for detailed descriptions.
- Queries: DuckDB on remote parquet via HTTP range requests
- Visualization: Lonboard (WebGL), Matplotlib, Folium
- Data Processing: Pandas, GeoPandas, Polars
- Jupyter: IPyWidgets, IPyDatagrid, Sidecar
All examples use parquet files served from Cloudflare R2:
importduckdb# Wide format (~280 MB, 20M rows)WIDE_URL="https://pub-a18234d962364c22a50c787b7ca09fa5.r2.dev/isamples_202601_wide.parquet"# Query directly - DuckDB fetches only needed datacon=duckdb.connect()
df=con.sql(f"SELECT * FROM '{WIDE_URL}' WHERE n = 'OPENCONTEXT' LIMIT 1000").df()# Install with examples dependencies
poetry install --with examples
# Run tests
poetry run pytest tests/
# Docker Jupyter environment
./run_docker.sh [port] # default port 8890The original API client (src/isamples_client/) targeted https://central.isample.xyz/isamples_central/ which is no longer operational. This code has been moved to archive/defunct-api-client/ for historical reference.
Planning documents from the API-to-parquet transition are in archive/planning/.
| Repo | Purpose | Start Here |
|---|---|---|
| isamplesorg-metadata | Schema definition (8 types, 14 predicates) | src/schemas/isamples_core.yaml |
| isamplesorg.github.io | Browser tutorials (DuckDB-WASM + Cesium) | tutorials/isamples_explorer.qmd |
| vocabularies | SKOS vocabulary terms | Material types, context categories |
- Lonboard - Fast geospatial visualization
- DuckDB - High-performance analytical database
- iSamples Project - Internet of Samples initiative