Research & Resources

Publications, presentations, datasets, and source code

Presentations

2020 SPNHC Conference Talk

iSamples Metadata Model Talk

Download slides (PDF)

Publications

1. Davies N, Deck J, Kansa EC, Kansa SW, Kunze J, Meyer C, Orrell T, Ramdeen S, Snyder R, Vieglais D, Walls RL, Lehnert K (2021) Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples. GigaScience, 10(5)https://doi.org/10.1093/gigascience/giab028

Zenodo Community

The iSamples Zenodo Community archives datasets for reproducible research, including the geoparquet files powering this site’s tutorials and Interactive Explorer.

GitHub Repositories

All iSamples source code is available at the isamplesorg GitHub org. The repositories form a tight pipeline from schema through serialization to consumers:

metadata + vocabularies      ← canonical data model & SKOS terms
          │
          ▼
        pqg                  ← property-graph parquet format + tooling
          │
          ▼
 data.isamples.org + Zenodo  ← published parquet snapshots (narrow, wide, H3, lite, facet caches)
          │
   ┌──────┴──────┐
   ▼             ▼
examples   isamplesorg.github.io
(Python)   (Web + DuckDB-WASM + Cesium)

Core repositories

Repository Role Layer
metadata Canonical data model — the 8 entity types (MaterialSampleRecord, SamplingEvent, SamplingSite, GeospatialCoordLocation, …) and their relationships schema
vocabularies SKOS vocabularies for material type, context, and specimen categories schema
pqg Property-graph Parquet format spec + conversion tooling (narrow ↔︎ wide); H3 augmentation and facet caches serialization
examples Python client and Jupyter notebooks — DuckDB + lonboard for interactive analysis. Also known as isamples-python (see below) consumer
isamplesorg.github.io This documentation site — Quarto, Observable, browser-side DuckDB-WASM, Cesium globe consumer

Domain extensions

Domain-specific vocabularies extend the core terms via skos:broader:

Legacy / infrastructure

  • isamples_inabox — the original iSamples-in-a-Box server (Solr + FastAPI). The public iSamples Central API was offline as of August 2025; the Solr schema there remains the authoritative precedent for query-dimension names (see Query Specification)