CPDW 2026 — OBIS Developer Workshop¶
From Observations to Ocean Data Systems¶
Developer Workflows for OBIS Access, Validation, and Publishing
A developer-focused working session at the CIOOS Pacific Data Workshop 2026 — three short presentations, each paired with a hands-on Jupyter notebook, covering the practical mechanics of moving Darwin Core biodiversity data through the OBIS ecosystem.
About the session¶
Darwin Core provides a shared vocabulary for biodiversity records, enabling interoperable data exchange across biodiversity and ocean data systems. The Ocean Biodiversity Information System (OBIS) relies on Darwin Core–aligned datasets to support the integration, discovery, and reuse of marine biodiversity observations.
This working session presents a developer-focused walkthrough of practical workflows for accessing, transforming, validating, and publishing biodiversity data within the OBIS ecosystem and related ocean data infrastructures.
Intended for developers, data managers, and technical practitioners interested in building reproducible workflows for biodiversity data transformation, validation, and publication across ocean data systems.
The three presentations¶
| # | Presentation | Tool | Notebook |
|---|---|---|---|
| 01 | Transforming OBIS datasets for CIOOS discovery | OBIS2CIOOS |
see notebooks ↓ |
| 02 | Programmatic publishing to OBIS via the IPT | pyIPT |
(coming soon) |
| 03 | Validating Darwin Core datasets before publication | Pyobistools |
Validate biodiversity data |
01 — OBIS2CIOOS¶
A set of translation tools that transform OBIS datasets into formats suitable for discovery through the Canadian Integrated Ocean Observing System (CIOOS). The hands-on portion is split across three notebooks, one per API the OBIS2CIOOS pipeline depends on:
Download the slides (OBIS2CIOOS.pptx) →
- 01 — OBIS REST API —
/v3/dataset,/v3/occurrence,/v3/facet; cursor pagination; thecountry=/geometry=quirks. - 02 — Parquet + DuckDB — the
iobis/obis-open-dataS3 exports queried directly with DuckDB. - 03 — WoRMS + pyworms — resolving
scientificNamestrings to authoritative AphiaIDs and full classifications via the World Register of Marine Species.
02 — pyIPT¶
A Python module that enables programmatic dataset publishing to OBIS via the Integrated Publishing Toolkit (IPT) using standard web requests.
03 — Pyobistools¶
A Python toolkit supporting validation and quality control of Darwin Core datasets prior to publication.
Download the slides (CPDW_Pyobistools_CIOOS.pptx) →
- Validate biodiversity data —
check_fields,check_occurrence_core_and_extension,check_eventids,check_measurementids,check_scientificname_and_ids, andcheck_onlandapplied to synthetic Darwin Core datasets with intentional errors.
Hosts¶
- TBD — Ocean Tracking Network
- TBD — St. Lawrence Global Observatory
- Simon Beauvillier and Richard Kelly — CIOOS Coordination Office
Get started¶
- New to the workshop? Read the overview.
- Want to run the notebooks locally? See setup.
- Curious about the demo dataset? See demo dataset.