AKDatUM: Arctos, iNat, GBIF

Posted by Cam on 2022-01-20 for AKDatUM workshop

Short URL to here: is.gd/akdcam

Data

Evidence of the occurrence of an organism at a place and time:

• Physical collections (specimens)
• Observations (without or with photographs)

Key data:

• Where? (long/lat)
• When?
• What species?
• Recorded by who?

Data stores

Specimen information is stored in a museum collections database. At UAF, for Alaska, we use Arctos: arctos.database.museum

The largest open repository of human observation data is iNaturalist: inaturalist.org

The largest global biodiversity occurrence data store, which contains the data in Arctos and iNaturalist and many other sources, is GBIF, the Global Biodiversity Information Facility: gbif.org

Obtaining the data

Each of these sites allows:

• Queries via their web pages and downloads of queried data, via a browser
• More comprehensive access to their data via an API (Application Programming Interface)

Arctos

To download data from Arctos:

• Make a user account and log in
• Query the database using the search boxes at arctos.database.museum
• On the results page, find the drop-down named “Tools: Map, Customize or Download” and select Download

The Arctos API endpoint can be seen here; the results are in JSON. Information about the Arctos API can be found here.

An efficient way to get large data downloads from Arctos is via the IPT dumps (from Vertnet) prepared for importing the data into GBIF.

iNaturalist

• Make a user account and log in
• Go to ‘Explore’ and enter a taxon and a place
• Click the ‘Filters’ box and the advanced search options will appear. At the bottom left is a link for Download.
• Adjust your search details and the fields you want returned and go to ‘4. Export’

Information about the API is here

GBIF

• Make a user account and log in
• Type a species name into the search bar
• Select the taxonomic name alternative you want
• A general page for that taxon will appear, with many kinds of data (images, map, etc.)
• Click on the green ‘OCCURRENCES’ box on the right, near the top
• Now click on DOWNLOAD
• Select the kind of data package you want (‘Simple’ should be fine)

Information about the API is here

Data integration

The freedom of the data in Arctos and iNat permits data integration in third party applications. A simple demonstration using data extracted via the APIs can be seen here.