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GBIF occurrence data access and download

October 15, 2012

These are some notes for a student training course on species distribution modelling (BIO4115 and BIO9115) from October to December 2012 at the Natural History Museum, University of Oslo (NHM-UiO).

What is the Global Biodiversity Information Facility?

GBIF enables free and open access to biodiversity data online. We’re an international government-initiated and funded initiative focused on making biodiversity data available to all and anyone, for scientific research, conservation and sustainable development.

Darwin Core: What? Where? When?

Using the GBIF data portal:

Using Artskart, Artsdatabanken:

Using the REST web-service:

Examples for beet:

Examples for dragon head:

You may also want to use an R package to download GBIF presence data:

DISMO:

library(dismo)
# get GBIF data with function:
betavulgaris <- gbif("Beta", "vulgaris", geo = T)
dragonhead <- gbif("Dracocephalum", "ruyschiana", geo = T)
sugarkelp <- gbif("Saccharina", "latissima", geo = T)

You may want to use R to plot a map with a preview of the point data:

# plot occurrences:
library(maptools)
data(wrld_simpl)
plot(wrld_simpl, col = "light yellow", axes = T)
points(betavulgaris$lon, betavulgaris$lat, col = "red", cex = 0.5)
text(-140, -50, "Beet")
# -- alternative for Dragonhead:
points(dragonhead$lon, dragonhead$lat, col = "red", cex = 0.5)
text(-140, -50, "Dragonhead")

RGBIF:

OpenModeller
You may also use the OpenModeller software to access and download GBIF occurrence data. OpenModeller provides a common platform for a number of prediction modelling algorithms – including Maxent.
Lat-long to UTM 33
The environment predictor variables we will use in this course will be in UTM grid 33. So we need to convert the occurrence point data from the lat-long format to UTM 33. The following web page can do this.
See also:
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