Topic outline

  • Intro Presentations

    Course Dates

    22 - 26 October 2017

    Course Venue

    Institute of Oceanography and Environment - Universiti Malaysia Terengganu (UMT)
    Mengabang Telipot
    21030 Kuala Terengganu
    Terengganu - Malaysia

    Course Instructors

  • Introduction to R (Pre-course assignment)

    In this training module you will learn some of the basics of R. This module is mandatory to enrol in the OBIS advanced training course.

    • Install R-studio
    • Install robis and obistools r packages
    • Discover robis and obistools r package functions and features
    • Reading data in R (txt, xlsx, dwc-a)
    • Inspecting data in R
    • Manipulating data in R
    • Plotting data in R
    • Mapping data in R

    Please read the Intro to R chapter in the OBIS manual. Download this R file and executive all commands.

    • Introduction to OBIS data standards and formats

      In this training module you will learn more about the data standards and data formats used in OBIS:

      • DwC terms
      • Occurrence Core
      • Occurrence Core & eMoF
      • Event Core & Occurrence & eMoF

      Please read the OBIS Manual: chapter Darwin Core and/or the slides and then proceed to the DwC Quiz. 

      When you have successfully completed the DwC Quiz, please read the OBIS manual: chapter Data Formats and/or the slides and then proceed to the Data Formats Quiz.

      • Data Access in OBIS

        • Data visualization in OBIS

          • Data Processing in OBIS (basic)

            • Data Processing in OBIS (advanced)

              • Data publication in OBIS

                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:


                • Useful links


                  Data access

                  Data quality control tools

                  Data products