The Ocean Biodiversity Information System (OBIS) is the most comprehensive gateway to the world’s ocean biodiversity and biogeographic data and information. OBIS provides open access to this quality-controlled data that adheres to biodiversity standards (Darwin Core, EML). This course is a continuation of the Contributing and publishing datasets to OBIS (self-paced), which remained open only for staff and collaborators of OBIS Nodes (under invitation of OBIS Secretariat).

The aim of this course is to teach the step-by-step basics for how to format and publish datasets according to these standards to contribute to OBIS, and adopt best practices in the management of marine life data. This training course is self-guided and designed to teach learners how to structure datasets to contribute to OBIS. The course will guide users step-by-step through the OBIS data life cycle, including: identifying an appropriate data structure, applying Darwin Core Archive formatting, conducting quality control steps, publishing data, and accessing data from OBIS. 

This course is an updated version.

Learning goals

• Describe the OBIS data life cycle
• Restructure a flat dataset into a Darwin Core-Archive format, following OBIS best practices
• Identify appropriate Biodiversity Information Standards (TDWG) vocabulary for your dataset
• Interpret and resolve quality control flags
• Publish data and metadata on an IPT
• Obtain OBIS data from the Mapper tool, R, API

Target audience 

Participation in this course is restricted to staff and collaborators in OBIS Nodes, invited by OBIS Secretariat, open initially from 15 December 2025 to 15 December 2026.

Course content

The course is divided into the following Modules:

Module 1. Introduction to data publishing and Darwin Core

Module 2. Introduction to data formatting

Module 3. Formatting data tables

Module 4. DNA Derived Data

Module 5. Controlled Vocabulary

Module 6. Conducting Quality Control

Module 7. Publishing your Data

Module 8. Accessing Data from OBIS

These modules will cover: 

• Darwin Core standards (Relational databases, Core and Extension tables)
• Formatting data to publish in OBIS (Creating Event, Occurrence, and ExtendedMeasurementOrFact tables; Mapping standardized vocabulary; Using World Register of Marine Species (WoRMS) Taxon Match tool; Understand how to compile genetic, acoustic, habitat, imaging, and/or tracking data for OBIS)
• Conducting quality control (Dealing with uncertain data fields e.g. temporal, spatial, taxonomic; Troubleshooting difficult data types or missing data)
• Publishing data (Filling metadata; Using, publishing, and updating datasets on IPT)
• Accessing and downloading data from OBIS (Full data exports, R, API; Using Mapper tool to subset data) 

Duration

This is a 32-hour self-paced online course (asynchronously), open continuously from 15 December 2025 to 31 December 2026.

Lead Instructor

• Dr. Elizabeth Lawrence (OBIS training officer)

Other course contributors

• Carolina Peralta Brichtova
• Ruben Perez Perez
• Pieter Provoost
• Saara Suominen
• Leen Vandepitte
• Marcos Zárate