- Intro Presentations
- 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 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
- 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 used in OBIS:
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 Access in OBIS
- Data visualization in OBIS
Data visualization in OBIS
- Data Processing in OBIS (basic)
Data Processing in OBIS (basic)
- Data Processing in OBIS (advanced)
Data Processing in OBIS (advanced)
- 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.
- Useful links
OBIS manual: http://iobis.org/manual
DwC terms by Core and Extensions: http://rs.gbif.org
BODC NERC Vocabulary search interface: https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search
OBIS website: http://www.iobis.org
OBIS mapper: http://iobis.org/mapper
OBIS download toolbox: http://download.iobis.org
OBIS R package: http://github.com/iobis/robis
OBIS API: http://api.iobis.org
OBIS GeoServer (WMS/WFS): http://iobis.org/geoserver
OBIS hosted IPTs: http://ipt.iobis.org
Data quality control tools
OBIS QC tools (R package): https://github.com/iobis/obistools
OBIS geocoding tool: http://iobis.github.io/map
OBIS plotter: http://iobis.github.io/plotter
OBIS coordinates conversion tool: https://obis.shinyapps.io/coordinates/
WoRMS taxon match tool: http://marinespecies.org/aphia.php?p=match
OBIS statistics and indicators: http://iobis.org/indicators