Workshop overview¶
This workshop is part of the CIOOS Pacific Data Workshop (CPDW) 2026. It runs as three short presentations — each paired with hands-on Jupyter material — covering the practical mechanics of moving Darwin Core biodiversity data through the OBIS ecosystem.
The three presentations¶
| # | Presentation | Tool | What it covers |
|---|---|---|---|
| 01 | Transforming OBIS datasets for CIOOS discovery | OBIS2CIOOS |
Pulling OBIS data via REST and Parquet, resolving taxonomy via WoRMS, reshaping records for CIOOS |
| 02 | Programmatic publishing to OBIS via the IPT | pyIPT |
Automating dataset publication through the Integrated Publishing Toolkit |
| 03 | Validating Darwin Core datasets before publication | Pyobistools |
QC and Darwin Core validation prior to publishing |
The OBIS2CIOOS block runs against three notebooks (one per upstream API). The pyIPT and Pyobistools notebooks are in progress.
Format¶
| Block | Content |
|---|---|
| Talks | Three short presentations, one per tool |
| Hands-on notebooks | OBIS2CIOOS notebooks 01 → 03 (pyIPT / Pyobistools to follow) |
| Q&A | Discussion |
Audience¶
Intended for developers, data managers, and technical practitioners building reproducible workflows for biodiversity data — access, transformation, validation, and publication across ocean data systems.
The workshop assumes basic Python familiarity and some exposure to scientific data formats (CSV, Parquet, NetCDF). No prior OBIS or CIOOS experience required.
What you'll need¶
- A Google account (for Colab) or a local Python ≥ 3.11 environment
- A web browser
- Run the first setup cell of each notebook ahead of time so dependencies are cached on your Colab runtime
See setup for details on running locally.