Holos: Berkeley Ecoinformatics Engine is a biodiversity informatics distributed data portal and toolkit for accessing and visualizing integrated boiological and environmental datasets to address questions of global change biology.
Holos aims to be model for informatics that promotes open science and platform agnostic toolkits. We create web-based building blocks to access data from established repositories while promoting best practices to uncover ‘dark’ datasets from orphaned or remote labs. Our architecture is structured to promote use of the biodiversity and environmental datasets in data-driven, transparent platforms. We welcome developers and researchers of all disciplines to use the Ecoengine tools and hopefully be inspired to create their own with Ecoengine-based applications.
On our main page holos.berkeley.edu, we have two interactive tools which require no programming:
You can also access Ecoengine data via R Statistical programming language with rOpenSci's Ecoengine R package.
Developers are directed to the documentation on how to use our Ecoengine API.
Holos taps a wide range of biodiversity and environmental datasets. The full information about each provider can be found on the Data Sources and Participating Instutions Pages. Here is a summary list of the data sources.
For biodiversity data, such as specimens, fossils, herbaria sheets and other species occurrences, we follow the guidelines and best practices developed and refined by Canadsys and VertNet. For publication and distribution, each data source used should be cited with the data set name, publisher or affiliated institution, a link to the resource and the data accesssed.
All of the data in the Ecoengine are listed on the Data Sources Page: https://holos.berkeley.edu/resources/datasources/
Proper citation of a record should include:
Yes! Built on the Django REST framework, Ecoengine is a self-documenting API that will return data in JSON, GeoJSON, CSV and other data formats. Developers can see the full documentation and tips on our how to get the most out of our Ecoengine API at this link: https://ecoengine.berkeley.edu/docs/.
Yes! The Compare tool will visualize any sample data stored in a GeoJSON format. These can be stored in third-party GIS hosting sites like CartoDB, then copy and paste in the URL for your GeoJSON data into Compare tool's Add button to see your data set with Ecoengine's.