Course: Ocean Data Management for Researchers 2018

Topic outline

Introduction
Introduction
This course is aimed at researchers at the post-graduate level and provides a comprehensive introduction to a variety of marine datasets and formats and the use of software for synthesis and analysis of marine data. The importance of good research data management practices and the role of researchers will also be highlighted. Personal projects are presented by the students at the end of the course.

Aims and Objectives
- Provide an introduction to the use of software for synthesis and analysis of marine data
- Introduction to the FAIR Guiding Principles for scientific data management and stewardship
- Understand best practice for management and analysis of marine data
Learning Outcomes
- The learning outcomes of this course include:
- Knowledge and understanding of the importance of management of ocean data
- Experience in use of data analysis and visualization tools
- Recognize the importance of good research data management practice
- Awareness of European based marine research projects and data repositories
Instructors
- Greg Reed
- Lilan Krug
- Claudia Delgado
- Reiner Schlitzer
- Jonas Mortelmans
- Nathalie Tonné
- Pieter Provost
- Daphnis de Pooter
- Stefanie DeKeyzer
Venue: UNESCO/IOC Project Office for IODE, Oostende, Belgium

Dates: 3-7 December 2018

Event details on IOC Calendar and List of Participants
- Announcements Forum
- Course schedule Page
Pre Course Assignment
This topic
Pre Course Assignment
Preparation
- Participants must download the latest version of ODV (5.1.5) from https://odv.awi.de/software/download/ and install the software on their laptops. If not already done, participants must register as non-commercial users before getting access to the software.
- Participants also must download the course material package from https://drive.google.com/file/d/1SojaNEPE3uI5zUN2gib7SfPI8f319ILQ/view?usp=sharing and unzip to the desktop.
Session 1
Session 1
Introduction
Claudia Delgado

Welcome & General Introductions; Course Overview, logistics, etc.

Introduction to IOC/IODE
- OTGA PPT for courses at PO Oostende including short intro to IOC File 5MB PDF document
- OTGA PPT course Logistics at PO File 5.7MB PDF document
Session 2
Session 2
Introduction to EMODNET
Nathalie Tonné & Andree-Anne Marsan

EMODNET Wake Up Your Data
- EMODnet Secretariat INTRO-Summer school 2018.v1pptx File 14.8MB PDF document
- 20180910 EMODnetSecretariat EX+SOL v2 File 27.2MB PDF document
- EMODnet exercises Book
  These exercises are intended to make you familiar with the seven EMODnet thematic (data) portals and the data they give access to. Each Web Map Viewer allows exploring large amounts of data in a visual and interactive way. For each of these exercises, start by going to the EMODnet Central Portal www.emodnet.eu, from where you can easily access each data portal (in the main Menu, go to the tab “Data Portals”).
Session 3
Session 3
Data management for researchers
Greg Reed
- Introduction to data management for researchers File 4.3MB HTML document
  This presentation provides an introduction to data management for researchers and includes:
  
  defining data and data management
  
  understand the importance of managing data as a part of responsible research
  
  identifying the various data management tasks within the research data lifecycle
  
  understanding data in the context of the research data lifecycle
- Research data organisation File 13.5MB HTML document
  Organising your research data includes naming files and folders, deciding on which file formats to use and using standardised vocabularies will allow you to add context to your data so that you and others can understand it in the short, medium, and long-term.
- Quiz: Data management and organisation
  Test your knowledge on research data management and data organization.
- Class Activity - Vocabularies Assignment
Session 4
Session 4
Storage and processing collected data (Underway and station data)
Jonas Mortelmans
- OTGA Mortelmans ocean to interface File 71MB PDF document
Session 5 / Session 6
Session 5 / Session 6
Introduction to Saga GIS
Lilian Krug
- Introduction to SAGA Book
Session 7
Session 7
Saga GIS data conversion
Lilian Krug
- Working with shapes in SAGA Book
Session 8
Session 8
Import remote sensing data in Saga
Lilian Krug
- Working with grids in SAGA Book
Session 9 / Session 10
Session 9 / Session 10
Exploring marine data with Ocean Data View
Reiner Schlitzer

This hands-on workshop will teach ODV methods for the exploration and scientific analysis of marine data. Participants will learn how to create publication-ready maps, property-property plots and sections and how to apply simple or advanced station and sample filters. In addition, import of own data as well as visual and automatic quality control will be covered. Participants are encouraged to bring their own data.

Preparation
- Participants must download the latest version of ODV (5.1.5) from https://odv.awi.de/software/download/ and install the software on their laptops. If not already done, participants must register as non-commercial users before getting access to the software.
- Participants also must download the course material package from https://drive.google.com/file/d/1SojaNEPE3uI5zUN2gib7SfPI8f319ILQ/view?usp=sharing and unzip to the desktop.
- ODV Course Agenda Page
Session 11
Session 11
Ocean Data View: import table and convert it to point shape
Lilian Krug
- World Ocean Database - from ODV to SAGA Book
- osd_all_liberia_wod.gz File 2MB Archive (GZ)
- osd_jas_0m_10m_liberia_wod_odv.txt File 2.2MB Text file
- osd_jfm_0m_10m_liberia_wod_odv.txt File 1.1MB Text file
- osd_jas_3500m_4500m_liberia_wod_odv.txt File 200.2KB Text file
- osd_jfm_3500m_4500m_liberia_wod_odv.txt File 215.8KB Text file
Session 12
Session 12
Introduction to marine biological data management
by Daphnis de Pooter

Course content
- Taxonomy and data management
- World Register of Marine Species (WoRMS)
- Assignment matching taxon names with WoRMS
- Marine Biological Data (introduction)
- Marine Biodiversity Data Landscape in Europe
- Assignment using the LifeWatch Belgium VRE
- Assignment using the EMODnet download portal
- Introduction to Marine Biological Data Management File 7.9MB Powerpoint 2007 presentation
- Assignment taxonmatch
- Assignment taxonmatch - solution Page
  Restricted Not available unless: The activity Assignment taxonmatch is marked complete
- Assignment Lifewatch Belgium Virtual Research Environment Page
- Assignment Lifewatch Belgium Virtual Research Environment - solution URL
Session 13
Session 13
Introduction to OBIS
Pieter Provoost

Outline:
- What is OBIS?
- The OBIS data system
- Data standards
- Publishing data to OBIS
- Quality control
- Data access
This session includes a hands-on part on OBIS data access using R. To prepare for this session, please install the latest versions of R and RStudio, which can be downloaded here:
- R: https://cloud.r-project.org
- RStudio: https://www.rstudio.com/products/rstudio/download/#download
The example code is available here: https://github.com/iobis/training/blob/master/odmr/script.R
- Presentation File 91.1MB Powerpoint 2007 presentation
Session 14
Session 14
Good Data Management (including the FAIR data principles and the Marine Data Archive)
Stefanie DeKeyzer
- OTGA FAIR DM and MDA-2 File 57.7MB PDF document
Session 15
Session 15
Assignment

To demonstrate how the skills learned in this course can be applied to any selected area, prepare selected data products for an area of interest (AOI). For the individual projects select an area no smaller than about 10-deg by 10-deg. The area should include about 1/3 coastal, 1/3 continental shelf, 1/3 deep blue sea. Prepare a collection of images and analysis products from the previous exercises for the selected AOI. Then prepare a powerpoint presentation of the results to present on the final day.
- Upload your presentations Assignment
Session 16
Session 16
Visit to the Marine Station Oostende (MSO)

The Marine Station Oostende (MSO) is a coastal satellite laboratory available for all Flemish marine scientists. The MSO comprises multifunctional laboratories, provides storage capacity for scientific equipment and has space for public activities. (http://www.vliz.be/en/marine-station-ostend)
Course Conclusion and Feedback
Course Conclusion and Feedback
Please complete the feedback survey on your opinions on the course. The survey seeks to find out about your views of the course and will provide feedback to OTGA on how to improve the learning process, administration, facilities and logistic arrangements. Your views are important for continuous improvement. The survey is anonymous. Please fill in the online feedback survey here.
Course photos
Course photos
- Pictures Gallery Lightbox Gallery