Marine Biogeographic Data processing using OBIS
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.
Dates: 23 - 26 September 2018
Venue: INIOAS, Terhan, Iran
Check Events calendar for the list of participants.
- Introduction to R (pre-course assignment)
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 and INIOAS as PEGO-OBIS node
Introduction to OBIS and INIOAS as PEGO-OBIS node
- Introduction to Deep Sea node & WoRMS
Introduction to Deep Sea node & WoRMS
- State of the art on marine biodiversity knowledge of the Persian Gulf and the Gulf of Oman
State of the art on marine biodiversity knowledge of the Persian Gulf and the Gulf of Oman
- Introduction to Black Sea node
Introduction to Black Sea node
(Oleksandr Neprokin (Sasha))
- Introduction to OBIS data standards and formats
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 (basic)
- Data publication in OBIS
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 email@example.com.
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
Data visualization in OBIS
- Introduction to R
- Biodiversity data visualisation tools Introduction to ArcGIS & QGIS
Biodiversity data visualisation tools Introduction to ArcGIS & QGIS
(Keyvan Kabiri & Abdolvahab Maghsoudlou)
- Useful links
Data quality control tools
- Participants' presentations
- Course 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, OBIS and INIOAS on ways to improve the learning process, administration, facilities and logistic arrangements. Your views are important for continual improvement. The survey is anonymous. Please fill in the online feedback survey here.