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Foundations

This module includes instruction to ensure all participants are at the same level before delving into the data mobilization topics. You will receive an introduction on how to access GBIF mediated data, your responsibilities as a user, and other data sources and tools that you will be putting into use during the rest of the course. Lastly, you will be asked to install the Wallace software as part of this module. Paragraph1, sentence1. Sentence 2. Sentence 3.

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Terminology

API

Data Access

User Profile

Search capability

Data downloads

There is technically only one way to generate a GBIF download, and that is through the downloads API (https://www.gbif.org/developer/occurrence). Here I list 3 interfaces to the downloads API. All of these send a JSON request with filters to the GBIF servers where it is interpreted and a download is generated. I strongly recommend using rgbif::occ_download() except if you have a very simple request.

Here is an example using curl. I do not really recommend editing JSON directly for generating downloads. I just present this here for completeness and for better understanding how the downloads API actually works. You can see here that even a very simple download is verbose. For building complex reproducible downloads from GBIF, there is no better tool than rgbif::occ_download() for generating occurrence downloads. Especially if you are using R for the rest of your analysis, this will allow you to produce end-to-end scripts of your research. reference for domain specific language:

Data can be downloaded in three formats

  • Simple: Tab delimited CSV. Only contains the data after GBIF interpretation. No multimedia included. More information about CSV

  • Darwin Core Archive: The Darwin Core Archive (DwC-A) contains both the original data as publisher provided it and the GBIF interpretation. Links (but not files) to multimedia included. More information about DwC-A

  • Species list: Tab delimited CSV with the distinct list of names in the search result.

Citation

Note
 In this video (12:26), you will review …​ used in this course. If you are unable to watch the embeded Vimeo video, you can download it locally. (MP4 - 44.5 MB)
Note
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