Ecological Databases

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Data wikis

The Ecological Data Wiki is a source for finding ecological datasets and quickly figuring out the best ways to use them. The idea is to use the collaborative knowledge and effort of the entire ecological community to compile this information rather than relying on each scientist to contribute information for their own studies. Just think of it as the Wikipedia of ecology data.

Datasets on Github

There are many datasets that are available from the GitHub code repository site. Here's a list of datasets available on GitHub

Data repositories

Ecological archives publishes materials that are supplemental to articles that appear in the ESA journals (Ecology, Ecological Applications, Ecological Monographs, Ecosphere, Ecosystem Health and Sustainability and Bulletin of the Ecological Society of America), as well as peer-reviewed data papers with abstracts published in the printed journals. Ecological Archives is published in digital, Internet-accessible form.

Climate data layers

WorldClim is a set of global climate layers (climate grids) with a spatial resolution of about 1 square kilometer. The data can be used for mapping and spatial modeling in a GIS or with other computer programs. If you are not familiar with such programs, you can try DIVA-GIS or the R raster package.

Conservation and species threats

The IUCN Red List of Threatened Species™ provides taxonomic, conservation status and distribution information on plants, fungi and animals that have been globally evaluated using the IUCN Red List Categories and Criteria. So far almost 75000 species have been assessed.

The DOPA Explorer provides simple means to explore protected areas, identify those with most unique ecosystems and species composition and assess the pressures they are exposed to through human development. The Digital Observatory for Protected Areas (DOPA) is conceived as a set of web services (databases, modeling services, broadcasting services, ...) to provide a large variety of endusers including park managers, decision-makers and researchers with means to assess, monitor and possibly forecast the state and pressure of protected areas at the global scale.

Distribution databases

Map of Life is an ongoing project to gather many different sources for species range maps and occurrences based at Yale University. It is currently based on 55 source datasets.

Demographic databases

COMPADRE & COMADRE The COMPADRE Plant Matrix Database is scheduled for release in 2014 and will contain demographic information in the form of projection matrices for ca. 900 plant species, derived from published and personally communicated research. The database will also contain taxonomic, phylogenetic, ecological, and biogeographic covariates. Following the publication of COMPADRE, the sister database for animals, COMADRE Animal Matrix Database (>1200 species) will see the light in summer 2014. Stay tuned for an outpouring of demographic, ecological, biogeographic, taxonomic and phylogenetic information in the animal kingdom too!

Global Population Dynamics Database. This facility has been constructed by researchers at the NERC Centre for Population Biology (funded by the UK Natural Environment Research Council), in collaboration with the National Center for Ecological Analysis and Synthesis, Santa Barbara (funded by the USA National Science Foundation), and the Department of Ecology and Evolution, University of Tennessee. It is, by far, the largest collection of animal and plant population data in the world, and brings together nearly five thousand time series in one database.

Genetic databases

GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). Use search tools like BLAST to find sequences similar to a reference sequence.

Occurrence databases

Global Biodiversity Information Facility contains more than 500 million occurrences of more than 1.4 million species.

Mountain Biodiversity Portal. The Global Mountain Biodiversity Assessment (GMBA) Mountain Portal allows you to explore GBIFs biodiversity archive data for mountain regions. You can select search areas from region to globe, or mountain life zones by range of elevation or thermal belts. Mountain areas are defined by ruggedness of terrain, using SRTM30 digital elevation data.

Taxonomy and systematics databases

Encyclopedia of Life plans to have a web page for each taxon (each named organism or group of organisms). It currently contains over 1.3 million pages with associated content about the (group of) organism(s).

Tree of Life web project is an ongoing Internet project providing information about the diversity and phylogeny of life on Earth. This collaborative peer reviewed project began in 1995, and is written by biologists from around the world. Note in 2009 the project ran into funding problems from the University of Arizona. Pages and Treehouses now submitted take a considerably longer time to be approved as they're being reviewed by a small group of volunteers.

Plant trait databases

Plant Trait Database. TRY is a network of vegetation scientists headed by DIVERSITAS, IGBP, the Max Planck Institute for Biogeochemistry and an international Steering Committee.The main objectives are top provide a global archive of plant traits; promote trait-based approaches in ecology and biodiversity science; support the design of a new generation of global vegetation models. Current state of the database and network: 3 million trait records for about 69000 plant species, 591 participants from 207 scientific institutes worldwide, 256 scientific projects requesting plant trait data from TRY.

FLUXNET Database. The FLUXNET database contains information about the site location and site characteristics as well as data availability. Eddy covariance data at 30-minute frequency is maintained by the individual tower or by networks to enable standardized data processing, gap-filling, and formats.

The LEDA Traitbase. This is a database on the life history traits of the Northwest European flora. The LEDA Traitbase provides information on plant traits that describe three key features of plant dynamics: persistence, regeneration and dispersal.

Database BiolFlor. The database BiolFlor on biological and ecological traits of the flora of Germany covers almost 3660 species of vascular species including established and frequent casual alien plant species. It is the first biological-ecological database for the complete German flora with information on traits from the a broad range of topics.

BiolFlorThe database BiolFlor contains almost 3660 species and more than 60 traits. This data results from several projects conducted in the Department of Community Ecology (UFZ - Centre for Environmental Research) over the last 10 years.

CLO-PLA CLO-PLA is a database of plant traits concerning clonal growth and vegetative regeneration of Central European flora.

TraitNet TraitNet is a dedicated network to the advancement and integration of trait-based evolutionary and ecological research. The website interlinks other trait-databases around the web.

GLOPNET GLOPNET is a multi-investigator group studying and accumulating global data on plant traits. The point of GLOPNET is to pull together data from many investigators and biomes to make new syntheses and encourage the collection and compilation of data.

BROT database This is a comprehensive database for Mediterranean basin species.

The Palnts The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories.

EFCal The Ecological Flora of California (EFCal) is a new component of the Jepson Flora Project that will provide ecological information on the California flora. EFCal will serve as a comprehensive database of ecological characteristics including life history, phenology, morphology and other traits for the California flora.

New York Flora Atlas The New York Flora Atlas is a source of information for the distribution of plants within the state, as well as information on plant habitats, associated ecological communities, and taxonomy. In addition, users can learn about the location of vouchered specimens and see images to get a better visual for each plant.

Ecological Traits of New Zealand Flora This database holds a list of all native and all naturalised higher plant species. Most effort to date has been on entering data on the naturalised flora and this information is updated from time to time.