pubs.qmd

---
title: "Research & Resources"
subtitle: Publications, presentations, datasets, and source code
bibliography: isamples-outcomes.bib
csl: cite-full-inline.csl
nocite: |
  @*
number-sections: false
---

## Presentations {.unnumbered}

### 2020 SPNHC Conference Talk {.unnumbered}

{{< video https://youtu.be/eRUw5NMksFo?t=105 >}}

### iSamples Metadata Model Talk {.unnumbered}

<embed src="assets/2022-11_iSamplesMetadata.pdf" type="application/pdf" width="100%" height="600px">

[Download slides (PDF)](assets/2022-11_iSamplesMetadata.pdf)

## Publications {.unnumbered}

::: {#refs}
:::

## Zenodo Community {.unnumbered}

The [iSamples Zenodo Community](https://zenodo.org/communities/isamples) archives datasets for reproducible research, including the geoparquet files powering this site's tutorials and Interactive Explorer.

- [iSamples Combined Dataset](https://zenodo.org/communities/isamples) — 6.7M samples from SESAR, OpenContext, GEOME, and Smithsonian
- All data files are also served from [`data.isamples.org`](https://data.isamples.org) with HTTP range request support

## GitHub Repositories {.unnumbered}

All iSamples source code is available at the [isamplesorg GitHub org](https://github.com/isamplesorg/). 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 {.unnumbered}

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

### Domain extensions {.unnumbered}

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

- [metadata_profile_earth_science](https://github.com/isamplesorg/metadata_profile_earth_science) — mineral groups, rock/sediment types, sampled-feature roles
- [metadata_profile_biology](https://github.com/isamplesorg/metadata_profile_biology) — sampled-feature extensions for biological specimens
- [metadata_profile_archaeology](https://github.com/isamplesorg/metadata_profile_archaeology) — OpenContext-style material and object-type extensions

### Legacy / infrastructure {.unnumbered}

- [isamples_inabox](https://github.com/isamplesorg/isamples_inabox) — the original iSamples-in-a-Box server (Solr + FastAPI). The public [iSamples Central](https://central.isample.xyz/isamples_central/) API was offline as of August 2025; the Solr schema there remains the authoritative precedent for query-dimension names (see [Query Specification](query-spec.qmd))

### Related documents {.unnumbered}

- [Query Specification](query-spec.qmd) — substrate-neutral query contract (v0.1)
- [Serialization catalog](SERIALIZATIONS.md) — every published parquet file with role, size, upstream, and consumer

::: {.callout-note}
### Naming note: `examples` vs `isamples-python`

The Python client repo is called `examples` on GitHub but is referred to as `isamples-python` in its own README, the Zenodo deposition metadata, and most prose documentation. This mismatch is known and slated for reconciliation — likely a GitHub repo rename with automatic redirects handling prior links.
:::