Topic outline

  • General

    OTGA/OBIS Training Course: Marine Biogeographic Data Management
    12 - 16 February 2018, Mombasa, Kenya


    The course provides an introduction to the Ocean Biogeographic Information System (OBIS). This includes best practices in marine biogeographic data management, data publication, data access, data analysis and data visualisation. With the numerous datasets being generated through various projects and some old data yet to be captured in the database, this training provides an opportunity to manage this wealth of scientific knowledge.

    Course Aims and Objectives

    • Expand the OBIS network of collaborators
    • Improve marine biogeographic data quality
    • Increase awareness of international standards and best practices related to marine biogeographic data management
    • Increase the amount of open access data published through OBIS and its OBIS nodes
    • Increase the use of data from OBIS for research, species conservation and area-based management applications

    Learning Outcomes

    • Knowledge and understanding of OBIS structure, mission and objectives
    • Use of IPT and data publication
    • Use of Darwin Core standards for species occurrence records, taxonomy, event/sample records and additional biological and environmental parameters.
    • Data quality control tools (OBIS Quality Control: LifeWatch QC tools and Name Matching Strategy)
    • Getting data and metadata in OBIS, AfrOBIS and AfReMAS: procedures, formats, upload data and metadata via AfrOBIS IPT
    • Use of OBIS data access (web service, API/R).
    • Getting data and metadata from OBIS and WoRMS (web portal, web services, GIS)
    • Data visualisation tools (ArGIS online, …)

    Target Audience

    • Marine data managers working with marine biodiversity data
    • Staff of NODCs or ADUs/OBIS nodes working with marine biodiversity data
    • Principle Investigators of major marine biodiversity projects
    • National marine biodiversity focal points
    • Priority will be given to participants that can demonstrate to hold important data contributions to OBIS, in addition to those from gap areas in OBIS (e.g. deep sea, S-E Asia, Middle East, Africa, Arctic).

    NOTE: priority will be given to participants originating from Eastern Africa and neighbouring Small Island Developing States (SIDS). Applications from women are encouraged.

    Course Pre-requisites:

    • Candidates should be from institutions that contribute, or hold and plan to contribute, marine biogeographic data to OBIS
    • Candidates should bring marine biogeographic datasets for the hands-on exercises
    • Need to bring own laptop
    • Working knowledge of English


    Daphnis De Pooter
    Leen Vandepitte
    Nina Wambiji
    Harrison Onganda

    Check Events calendar for list of participants and more information on the event.

  • Introduction to OBIS

    • Use of Darwin Core standards for species occurrence records

      Daphnis De Pooter

      • Metadata

        Leen Vandepitte

        • Data Processing in OBIS

          Leen Vandepitte, Daphnis De Pooter

          • OBIS Data Formats

            Daphnis De Pooter

            • Data publication in OBIS

              Daphnis De Pooter, Nina Wambiji

              In this training module you will learn more about metadata standards in OBIS and how to publish metadata as well as the actual data via the Integrated Publishing Toolkit (IPT).

              First, let's learn about metadata standards. Please read the EML chapter in the OBIS manual and take the Quiz. 

              When the Quiz is completed successfully, read the IPT chapter in the OBIS manual, which explains how you can publish a dataset. When you have finished reading this chapter, you can start publishing your (test) dataset and metadata using the OBIS training IPT instance at Request a user login by emailing us at

              If you are interested to learn more about how to publish a data paper making use of EML in e.g. a Pensoft journal, you can read this article:


              • Data Access in OBIS


                • Data visualization in OBIS

                  • Useful links


                    Data access

                    Data quality control tools

                    Data products

                    More documentation

                    • OBIS Nodes Training Course 2017:

                    • OBIS youtube channel:
                      • (Afr)OBIS course 2014
                      • OBIS course 2015
                      • OBIS course 2016
                    • Processing tips and tricks

                      • Social aspects of data management

                        • Participants' presentations

                          • Course Feedback

                            Please fill in the online feedback survey here.