Manual

Data visualization using online GIS tools

CartoDB

Example: displaying occurrences

In this section I will show how to visualize occurrence data downloaded from the OBIS mapper. In this case, I used all occurrences of Pterois volitans. This dataset is available at https://github.com/iobis/training/tree/master/manual/cartodb.

Adding the data

In CartoDB, go to Your datasets > New dataset, drag or upload the CSV file, and click Connect dataset. The go to Your maps > New map, select the dataset you just uploaded, and click Create map.

Getting the occurrence year

The data downloaded from the mapper contains a date, but CartoDB doesn’t allow using date fields for visualization. However, we can extract the year from the date using SQL:

Visualizing the occurrence year

To color the occurrences according to year, use the choropleth visualization and select the year column.

The result:

Example: exploring quality flags

In this section I will explain how to visualize the experimental data quality flags in OBIS. For more information on these quality flags, see Fishing for data and sorting the catch: assessing the data quality, completeness and fitness for use of data in marine biogeographic databases by Leen Vandepitte et al. An explanation on how to do this in R can be found here.

The code and data for this section are available at https://github.com/iobis/training/tree/master/manual/qc.

Extract data from OBIS

The quality flags are not available in the standard data downloads from the OBIS portal. To get the flags, we will access the database directly.

Convert the qc field to quality flags

All quality flags are contained in the qc field. We can use SQL to extract the individual flags.

Visualizing the flags

Use the category visualization and select the quality flag of interest.

The result should look like this:

Example: displaying OBIS summaries

In this example we’ll create a map using the OBIS:summaries layer. This layer contains statistics per grid cell such as number of records and number of species, as well as some biodiversity indices. To download the shapefile for this layer, use this URL:

http://www.iobis.org/geoserver/OBIS/ows?service=WFS&version=1.0.0&request=GetFeature&typeName=OBIS:summaries&viewparams=table:map1deg_with_geom&outputformat=shape-zip

This downloads the summaries layer with a 1 degree grid. Coarser or finer grids can be retrieved by changing the table view parameter. The shapefile is also available here.

Displaying different summaries

To display the number of records per grid cell, go to the Map layer wizard, select Choropleth and change Column to n. You may also want to change the color ramp and the color ramp transparency, and remove the polygon stroke.

Other interesting summaries are s (number of species), simpson (Simpson diversity index), shannon, (Shannon diversity index) and es (ES50).