Topic outline

  • General

    OTGA/OBIS Training Course: OBIS Nodes Train the Trainers
    27 November - 1 December 2017, Oostende, Belgium

    Training the OBIS nodes and the trainers (at the OBIS nodes and OceanTeacher regional training centres) was considered a top priority at the 6th SG-OBIS meeting (Japan, 2017). This training will include o.a.:

    • The application of ratified Darwin Core terms
    • OBIS-ENV-DATA standard (combining sampling events, occurrences, abiotic+ biotic measurements and sampling facts).
    • QC tools (including the OBIS tools R package: https://github.com/iobis/obistools)
    • Data publication (IPT), including metadata management
    • Data access and visualization (including the OBIS R package: https://github.com/iobis/robis)
    • There will be time for discussions and tackling specific use cases including output.

    Check Events calendar for documents and list of participants.

  • 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 RStudio
    • 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 try to execute all commands.

    • Introduction to OBIS data standards and formats

      In this training module you will learn more about the data standards and data formats according to Darwin Core practices, used to publish your data in OBIS. We will go into more depth in the application of the Darwin Core terms, how to standardize your data according to specific formats (for example, formats for date and time, geographic coordinates, etc). You will learn how to apply identifiers and use controlled vocabularies.

      Please read the DwC lessons and then proceed to each Quiz. For more information on this topic please also check the OBIS Manual: chapter Darwin Core and Data format.

      • 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 http://ipt.iobis.org/training/. Request a user login by emailing us at info@iobis.org.

            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: https://riojournal.com/articles.php?id=13088&instance_id=3548166.

             

            • Data Access in OBIS

              • Data visualization in OBIS

                • Useful links

                  General

                  Data access

                  Data quality control tools

                  Data products

                  • Participants' presentations

                    • Course Feedback

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