Hello, novice question here. I have looked in FAQs but not found my answer.
Is it possible to download data using the Occurrence tab for a subset of taxa? Initially I am looking for occurence data for mammalia in the Mekong Basin region. I am assuming that I should not have to download everything and then filter afterwards.
(Background to query. We are building a predictive model for disease outbreaks and don’t want to predict diseases in species that do not exist in the area!)
Many thanks in advance for any advice
You can filter your query by country or smaller administrative units, such as states, county, municipal, etc. You can also use polygons to narrow it down. Here’s a query using a simplified polygon for the Mekong Basin based on shape files found in this repository.
In addition to Daniel’s answer (thanks Daniel!) you might find our Data Use Club recorded webinar useful.
In particular this session introducing the GBIF interface and how to filter records and perhaps this session introducing to the GBIF API (if you need more advanced queries).
You certainly can, there are filters on the occurrence tab which include taxonomy and place information. If you set these filters you can then download just a subset of all occurrence data. You can set it to a higher taxonomy and get all the children, and you can even provide your own polygons to limit the spatial scope. I’ve added some filters as an example in the screenshot below:
You might also be interested in using the API to do this (but are limited to 100.000 occurrences per query, no way around it), there are handy wrappers like GitHub - gbif/pygbif: GBIF Python client and Interface to the Global Biodiversity Information Facility API • rgbif
The download service isn’t limited to 100.000 records like the API is, and even provides a DOI for use in publications! If you use it in a publication, the dataset will be retained. If you don’t, it’s removed after a while, but you can of course archive it yourself somewhere like Zenodo.