The Ecoengine provides users with access to a wide range of data types, including data sources that have been digitized as part of multiple campus-wide efforts.
Millions of records of high quality biodiversity data from voucher specimens at four Berkeley Natural History Museum (BNHM) collections cover arthropods, amphibians, birds, reptiles, mammals, vascular plants, mosses, lichens and fungi, and including fossils. The specimen data includes core fields of geographic location, event date, taxonomic identification, etc., as well as increasingly rich and multidimensional attribute data of genomic, isotopic, ecological, and phenotypic information. These four natural history museums are active research centers with dedicated curatorial staff.
Specimen holdings across the Berkeley Natural History Museums
ca. 677,000 specimens
ca. 6,500,000 specimens
(ca. 150,000 digitized)
ca. 2,200,000 specimens
(ca. 357,000 digitized)
ca. 6,530,000 specimens
(ca. 321,000 digitized)
A technical challenge in serving these data is that, far from being static records, these museums regularly update their collection records as their many digitization efforts progress. To ensure we have the most up-to-date information, the Ecoengine refreshes the data cache on a regular basis.
Inclusion of data from the UC Field Stations and Reserves allows Ecoengine users to integrate local climate data with detailed field observations from the same areas, which will play a central role in our examination of the detailed feedbacks between the climate and biota.
The University of California Natural Reserve System encompasses 37 natural protected areas that represent many of California's most important ecosystems, and it provides living laboratories for UC researchers. So far, we have included data from four UC Berkeley reserves: Angelo Coast Range Reserve (north Coastal Range); Sagehen Creek Field Station (central Sierra Nevada); Hastings Natural History Reserve (Carmel Valley); and Blue Oak Ranch Reserve (Diablo Range), the newest UC Natural Reserve System site.
We have collected metadata on a wide range of datasets, past and present, associated with these four field stations. In our catalog you will find metadata on climate and weather station measurements, studies on species occurances, behavior, and habitat preferences, vegetation plot data, historic and current images, long-term monitoring experiments, and many more. The richness of these first-person accounts has proven especially critical to resurvey efforts that establish benchmarks from which we can measure the nature of recent global change (e.g., the NSF funded Grinnell Resurvey Project). For many of these datasets the basic metadata details are unknown (e.g., dates of sampling, experimental protocol, etc.) and the majority are not in digital form. We built an online metadata catalog to document and assess each dataset and are using this catalog to assess their value and priority for digitization.
Interested in registering your data with the Ecoengine? Find more information here.
The Ecoengine also serves fine-scale climate sensor data by accessing the Keck HydroWatch system that is deployed in the Angelo and Sagehen Creek reserves.
It allows the integration of both detailed understanding of their water cycles and microclimates. Data from almost 100 million measurements are compiled in the NRS Sensor Database, and will be dynamically linked to the Collection Database. Additional fine-scale climate data is available from the Blue Oak Ranch Reserve and includes climate records for the nearby Mt. Hamilton. In collaboration with technology partners from Silicon Valley, wireless microclimate sensor networks have been recently installed (Very Large Ecological Array, VeLEA), which will supply a data stream to the Ecoengine on climate measurements as well as water and soil parameters.
Soil biogeochemistry is intimately connected to the underlying geology, the climate, hydrological cycle, and the biota and their ecological interactions. UC Berkeley is one of the founding centers of the study of the biogeochemical forces that form soils, and we have an extensive collection of ~12,000 samples from over 3,000 sites across California from the early 20th century. The samples hold the potential for rich comparative material for recreating past vegetation and habitat, and for adding environmental indictors from the early half of the 20th century. However, prior to the Ecoengine project, less than 5% had been cataloged and georeferenced. We now have a catalog of 14,027 records - 10,311 of which are now searchable through this public portal: http://bigcb.berkeley.edu/soil/. This effort lays the groundwork for assessment of the complete collection, and will allow cross-referencing with national soil databases (e.g., STATSGO, NASIS), and for more thorough analysis of the factors that control the feedbacks between climate and the biota.
Feedbacks between climate and the biota operate over many spatial and temporal scales. To assess the impact of deeper time global change on the vegetation cover in California, and to gain a benchmark for the nature of the vegetation prior to historic times – we need data from the fossil record. We are working to integrate fossil pollen data from two sources. The first, is data collected in California by Roger Byrne's research group at UC Berkeley. His data show pronounced vegetation changes over the last 15,000 years, from conifer-dominated to more open forest conditions. The second source, is from the Clear Lake Project, which will yield data dating back to 130,000 years ago. We have worked with both projects to digitize and curate their collections within the UCMP database, which is now searchable through the Ecoengine.
A survey lead by Albert E. Weislander, a UC Berkeley forester, documented California's vegetation in the 1920s and 1930s through extensive mapped plots of vegetation types, landscape and habitat photos, detailed topoquads of vegetation types and species, and specimens. This documentation of historic vegetation is critical for assessing vegetation change over the last century, and thus for determining the effects of global change over that timeframe. Thanks in large part to the Vegetation Type Mapping Project, the mapped plots and topoquads have been digitized and are now available for researchers. Additionally, with Ecoengine support, the University and Jepson Herbaria has georeferenced the specimens, which are now directly searchable here via the Consortium of California Herbarium interface and the Ecoengine. The historic photo localities have also been georeferenced and are available to map and view through the Ecoengine user interface. Lastly, James Thorne, UC Davis, has undertaken rendering of the topoquads into GIS layers and they have been integrated into the Baselayer Database.