A web application to unlock primary biodiversity data from published literature


GitHub release

GitHub issues

CC-0 license

Biodiversity Observations Miner

A web application to unlock primary biodiversity data from published literature

Running the application

To run locally on your computer:

1.- Fork or download the repository to a directory on your computer

2.- Open the R Project container file

3.- Make sure you have all R packages installed and updated to run the app (see below)

4.- Run the app with RStudio.

Alternatively, you can run the shiny::runGitHub() function. Function arguments: repo= "BiodiversityObservationsMiner", username= "fgabriel1891".

Important! Before using Biodiversity Observations Miner locally we recommend to have R and Rstudio installed and up to date.

For comments, suggestions and bugs please open an issue


The idea to develop this web application is set in the context of increasing the digital mobility and interoperability of biodiversity data wordwide. I developed Biodiversity Observations Miner with guidance and input from W. Daniel Kissling and Emiel van Loon of the Institute of Biodiversity and Ecosystems Dynamics (IBED) from the University of Amsterdam (UvA).

R packages required


Biodiversity Observations Miner uses tools from the GlobalNamesArchitecture (GNA) implemented in the taxize package. Thanks to Scott Chamberlain for modifications to taxize that improved the functionality of this application. Credits to the developers of the individual packages that Biodiversity Observations Miner is dependent on. Terms composing the pollination biodiversity dictionary were selected in collaboration with Joan Casanelles