What is Holos: Berkeley Ecoinformatics Engine?

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.

How can I use Holos?

On our main page holos.berkeley.edu, we have two interactive tools which require no programming:

  1. The EXPLORE tool allows users to query specimens, observations, photos and more. Searches can also be refined by date or by using our faceted filters, which include geographic and taxonomic categories, georeferenced or not, and observation type. Lastly, the mapping interface and toolbox on the right provides users with geospatial layers to build upon and overlay as well as geographic boundaries to hone searches. 
  2. The COMPARE tool enables users to examine multiple species from a range of different data sources. The same boundaries, environmental layers and basemaps available in the EXPLORE are also available here.

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.

What types of data are accessible via Holos?

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.

  • Berkeley Sensor Database, University of California Natural Reserve System
  • Berkeley Soil Collection, Department of Environmental Science Policy and Management, University of California Berkeley (coming soon)
  • California Academy of Sciences Botany
  • California Academy of Sciences Entomology
  • California Academy of Sciences Herpetology
  • California Academy of Sciences Ichthyology
  • California Academy of Sciences Ornithology
  • Calphotos, Berkeley Natural History Museums, UC Berkeley
  • Consortium of California Herbaria, The University and Jepson Herbaria, UC Berkeley
  • Essig Museum of Entomology, UC Berkeley
  • LACM Vertebrate Collection, Natural History Museum of Los Angeles County
  • Museum of Vertebrate Zoology (MVZ) Bird Collection, UC Berkeley
  • MVZ Bird Observations, UC Berkeley
  • MVZ Egg and Nest Collection, UC Berkeley
  • MVZ Herpetological Collection UC Berkeley
  • MVZ Herpetological Observations UC Berkeley
  • MVZ Hildebrand Collection UC Berkeley
  • MVZ Mammal Collection UC Berkeley
  • MVZ Mammal Observations UC Berkeley
  • UC NRS Field Station Checklist Berkeley Initiative in Global Change Biology, UC Berkeley
  • UC Museum of Paleontology
  • Wieslander Vegetation Type Mapping Project, Department of Environmental Science Policy and Management, UC Berkeley
Under the Boundaries option on Explore, there are raster layers available for the Jepson Regions, US Ecoregions III, University of California Natural Reserve System (UCNRS), and Global Administrative Areas (GADM). Soon, we hope to add NASA NEX future climate layers and Paleo model layers.

What are the policies for using data in Holos?

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:

  • [dataset name] . [affiliate Institution] . [link to dataset] (accessed on [date])


Can I create my own application using Holos data?

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/.

Can I see my own data with Holos?

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.

For further questions, email us at: ecoengine[at]berkeley.edu