About

Calphotos http://joycegross.com/various/retakes/2013june/index.html

Cook Peak near Isabella (1927) superimposed with Lake Isabella (2013), Kernville, California. Mashup by H. Constable.

Holos: Mobilizing Data for Understanding Global Change

Overview

Predicting biodiversity responses to global environmental change is a multi-faceted challenge, which requires a holistic understanding of the complex interactions and feedback among organisms, climate, and their physical and biotic environments across space and time.

Holos aims to digitize and aggregate many diverse biological and environmental collections into the Berkeley Ecoinformatics Engine ('Ecoengine'), a web service that can be searched and visualized via graphical tools: Explore, Compare, and other Applications. The data in the Ecoengine is global in scope, and since much of the data is sourced from the University of California museums, reserves and partners, the data coverage for California is very good.

We aim to be a model for informatics that promotes open science and agnostic toolkits. Our architecture is structured to promote use of integrated biodiversity and environmental datasets in data-driven, transparent platforms. 

We intentionally separate the data collection from the application interfaces to allow easy, customizable, extensions of how and what data are served. This allows new data to be continually added to and curated by participating museum collections. We achieve this through the Ecoengine's API, or web services, which is incorporated into online web tools, portals and desktop applications allowing access and dynamic visualization.

We welcome developers and researchers of all skills to use the Ecoengine tools and hopefully be inspired to create their own useful tools with Ecoengine's application.

Origins

The Ecoengine was imagined by UC researchers in need of a tool to access and explore integrated biological and environmental data over space and time. Such a tool would pull from a diversity of online data repositories and display them in an easy-to-use, map-based interface to satisfy the growing demand for a holistic understanding of global change science.

Thanks to the Berkeley Initiative in Global Change Biology and to generous funding by the William M Keck Foundation in 2012, our team built a data-driven platform using an Application Programming Interface (API) that taps an array of data streams, some of which were digitized exclusively for the Ecoengine.

These inaugural datasets are diverse spanning taxonomic groups and time spans, from fish and amphibians to lichens and redwoods, from modern to Pleistocene. We describe these UC Berkeley resources mobilized in the first project in Data Discovery, however, the architecture of the Ecoengine is not specific to these collections and our extent is global.

We have benefited greatly from existing biodiversity digitization and aggregation projects including GBIFiDigBioVertnetCalBugConsortium of California Herbaria, among others as well as innovative, geospatial visualization projects like Cal-Adapt and NASA Earth Exchange. The Ecoengine presents a unique combination of features, making it an invaluable tool for biodiversity and global change research:

  • Biological data from disparate sources and collecting methods are integrated using a common set of core fields;
  • Environmental and biolotical data are combined within the same mapping interface;
  • Spatial and temporal data attributes are emphasized, facilitating the exploration and analysis of spatio-temporal trends in both biodiversity and the environment.

Please contact us if you have questions or comments!