Databases & Subject Guides: Ecology: Data Resources

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Search Engines

DataONE
From the Data Observation Network for Earth (DataONE), use this search engine to find datasets from several of the repositories below as well as others.
GLoBI
Global Biotic Interactions (GloBI) provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, pathogen-host, parasite-host) by combining existing open datasets using open source software.

Ecological Data Repositories

Columbia Environmental Research Center (CERC)
From the United States Geological Survey (USGS), the Columbia Environmental Research Center focuses on environmental contaminants and the effects of habitat alterations on aquatic and terrestrial ecosystems.
Dryad Digital Repository
The Dryad Digital Repository is a curated resource that makes the data underlying scientific publications discoverable, freely reusable, and citable. Dryad provides a general-purpose home for a wide diversity of datatypes.
ESA Data Registry
This is a publicly accessible registry describing scientific data sets on ecology and the environment. The data sets registered here are associated with articles published in the journals of the Ecological Society of America.
Knowledge Network for Biocomplexity (knb)
The Knowledge Network for Biocomplexity (KNB) is an international repository intended to facilitate ecological and environmental research.
Long Term Ecological Research (LTER) Network
The US. long-term ecological research network consists of 28 sites with a rich history of ecological inquiry, collaboration across a wide range of research topics, and engagement with students, educators, and community members.
National Ecological Observatory Network (NEON)
The National Ecological Observatory Network (NEON) provides open data to understand changing ecosystems. NEON is a project sponsored by the US National Science Foundation (NSF).
NatureServe Explorer
NatureServe is the definitive source for information on rare and endangered species and ecosystems in the Americas. This field guide of life provides information on the 100,000 species and ecosystems that we track.
TERN AEKOS
A gateway to Australian ecology data: 98,000 sites of vegetation plot data; 250 ecology attributes; Australian-wide coverage.

Sampling of Data Books

Handbook of Meta-Analysis in Ecology and Evolution by Julia Koricheva (Editor); Jessica Gurevitch (Editor); Kerrie Mengersen (Editor) Meta-analysis is a powerful statistical methodology for synthesizing research evidence across independent studies. This is the first comprehensive handbook of meta-analysis written specifically for ecologists and evolutionary biologists, and it provides an invaluable introduction for beginners as well as an up-to-date guide for experienced meta-analysts. The chapters, written by renowned experts, walk readers through every step of meta-analysis, from problem formulation to the presentation of the results. The handbook identifies both the advantages of using meta-analysis for research synthesis and the potential pitfalls and limitations of meta-analysis (including when it should not be used). Different approaches to carrying out a meta-analysis are described, and include moment and least-square, maximum likelihood, and Bayesian approaches, all illustrated using worked examples based on real biological datasets. This one-of-a-kind resource is uniquely tailored to the biological sciences, and will provide an invaluable text for practitioners from graduate students and senior scientists to policymakers in conservation and environmental management. Walks you through every step of carrying out a meta-analysis in ecology and evolutionary biology, from problem formulation to result presentation Brings together experts from a broad range of fields Shows how to avoid, minimize, or resolve pitfalls such as missing data, publication bias, varying data quality, nonindependence of observations, and phylogenetic dependencies among species Helps you choose the right software Draws on numerous examples based on real biological datasets
ISBN: 9780691137292
Publication Date: 2013-04-21
Eco-Stats: Data Analysis in Ecology by David Warton This book introduces ecologists to the wonderful world of modern tools for data analysis, especially multivariate analysis. For biologists with relatively little prior knowledge of statistics, it introduces a modern, advanced approach to data analysis in an intuitive and accessible way. The book begins by reviewing some core principles in statistics, and relates common methods to the linear model, a general framework for modeling data where the response is continuous. This is then extended to discrete data using generalized linear models, to designs with multiple sampling levels via mixed models, and to situations where there are multiple response variables via model-based approaches to multivariate analysis. Along the way there is an introduction to: important principles in model selection; adaptations of the model to handle non-linearity and cyclical variables; dependence due to structured correlation in time, space or phylogeny; and design-based techniques for inference that can relax some of the modelling assumptions. It concludes with a range of advanced topics in model-based multivariate analysis relevant to the modern ecologist, including fourth corner, latent variable and copula models. Examples span a variety of applications including environmental monitoring, species distribution modeling, global-scale surveys of plant traits, and small field experiments on biological controls. Math Boxes throughout the book explain some of the core ideas mathematically for readers who want to delve deeper, and R code is used throughout. Accompanying code, data, and solutions to exercises can be found in the ecostats R package on CRAN.
ISBN: 9783030884420
Publication Date: 2022-08-12
Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and Stan by Jérôme Guélat; Bettina Almasi; Pius Korner-Nievergelt; Franzi Korner-Nievergelt; Tobias Roth; Stefanie von Felten Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN examines the Bayesian and frequentist methods of conducting data analyses. The book provides the theoretical background in an easy-to-understand approach, encouraging readers to examine the processes that generated their data. Including discussions of model selection, model checking, and multi-model inference, the book also uses effect plots that allow a natural interpretation of data. Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN introduces Bayesian software, using R for the simple modes, and flexible Bayesian software (BUGS and Stan) for the more complicated ones. Guiding the ready from easy toward more complex (real) data analyses ina step-by-step manner, the book presents problems and solutions--including all R codes--that are most often applicable to other data and questions, making it an invaluable resource for analyzing a variety of data types.
ISBN: 9780128013700
Publication Date: 2015-04-13
Data Analysis in Vegetation Ecology by Otto Wildi Evolving from years of teaching experience by one of the top experts in vegetation ecology, Data Analysis in Vegetation Ecology aims to explain the background and basics of mathematical (mainly multivariate) analysis of vegetation data. The book lays out the basic operations involved in the analysis, the underlying hypotheses, aims and points of views. It conveys the message that each step in the calculations has a specific, straightforward meaning and that patterns and processes known by ecologists often find their counterpart in mathematical operations and functions. The first chapters introduce the elementary concepts and operations and relate them to real-world phenomena and problems. Later chapters concentrate on combinations of methods to reveal surprising features in data sets. Showing how to find patterns in time series, how to generate simple dynamic models, how to reveal spatial patterns and related occurrence probability maps.
ISBN: 9780470664971
Publication Date: 2010-07-14
Spatial Data Analysis in Ecology and Agriculture Using R by Richard Plant Assuming no prior knowledge of R, Spatial Data Analysis in Ecology and Agriculture Using R provides practical instruction on the use of the R programming language to analyze spatial data arising from research in ecology and agriculture. Written in terms of four data sets easily accessible online, this book guides the reader through the analysis of each data set, including setting research objectives, designing the sampling plan, data quality control, exploratory and confirmatory data analysis, and drawing scientific conclusions. Based on the author s spatial data analysis course at the University of California, Davis, the book is intended for classroom use or self-study by graduate students and researchers in ecology, geography, and agricultural science with an interest in the analysis of spatial data. "
ISBN: 1280121726
Publication Date: 2012-12-10

Data Sources

Data.gov
Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets.
EPA Open Data
This site is a single place to find a vast selection of EPA data sources, organized into topics such as air and water that are in easily downloadable formats.
ESA Data Registery
The data sets registered here are associated with articles published in the journals of the Ecological Society of America. See individual registry entries for citation information as well as usage rights.
Ecological Data Wiki
The site is as a source for identifying ecological datasets and quickly figuring out the best ways to use them. Just think of it as the Wikipedia of ecology data.
Global Biodiversity Information Facility - Data-holding institutions around the world share information about where and when species have been recorded. The GBIF network draws all these sources together through the use of data standards. Publishers provide open access to their datasets using machine-readable Creative Commons licence designations, allowing scientists, researchers and others to apply the data in hundreds of peer-reviewed publications and policy papers each year.
Global Invasive Species Database - The Global Invasive Species Database is a free, online searchable source of information about alien and invasive species that negatively impact biodiversity. The GISD aims to increase public awareness about invasive species and to facilitate effective prevention and management activities by disseminating specialist’s knowledge and experience to a broad global audience.
National Ecological Observatory Network - The National Ecological Observatory Network (NEON) provides open data to understand changing ecosystems. NEON is a project sponsored by the US National Science Foundation (NSF).
National Phenology Network Data
Phenology data available for download, explore through visualizations, and search for other phenology data sets.
NOAA OneStop Designed for Data Discovery - The portal gives access to nearly 35,000 collections and millions of individual records spanning geophysical, ocean, coastal, weather, and climate data. OneStop also features multimedia previews and direct data downloads, when available. It establishes an additional online access point to expand usage of NOAA’s data.
Plants of the World - An international collaborative programme that makes available digitized data of the world’s flora gathered from the past 250 years of botanical exploration and research. It delivers information on the taxonomy, identification, images, distribution, traits, threat status, molecular phylogenies and uses of vascular plants worldwide.
TreeBASE
TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa.
VertNet
VertNet takes four classic vertebrate networks (FishNet, MaNIS, HerpNET, ORNIS), to combine them into a single integrated data portal.

Social Explorer
Social Explorer provides access to current and historical census data and demographic information and lets users create maps and reports to illustrate, analyze, and understand demography and social change. Among other documents Social Explorer includes the entire US Census from 1790 to 2010, annual updates from the American Community Survey, the Religious Congregations and Membership Study (RCMS) from 1980 to 2010 and Carbon Emissions Data for 2002 from the Vulcan Project.

Life Science Repositories

FAIRsharing Databases
A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them; partly compiled with the support of Oxford University Press (NAR Database Issue and DATABASE Journal).
Biological Sciences Data Repositories
From Nature, recommended data repositories for biological sciences, as well as links to repositories for other research areas.
Life Sciences Research Data Repositories
A registry of over 900 data repositories in the life sciences from re3data.org
NIH Data Sharing Repositories
Lists of biomedical repositories from the US National Institutes of Health.

STEM Team

Stephanie Blair

Grey Literature

Gray literature is literature that is scholarly, but not peer-reviewed nor published in a "traditional" scholarly format such as a university press book or a scientific journal.

Examples of gray literature are:

Posters
Conference Proceedings
Gray literature can help inform our search strategy. We can also learn from gray literature what science is currently being done on the bench, in the lab, or in the field, as many scientists don't publish all of their work in a scientific paper until their findings are complete. We also need to recognize that not all scientists work in academia; many of them work in the corporate, nonprofit, or government sectors. By reading and understanding how research is being currently done in the field, we can get a fuller picture of our research topic(s).
Government Reports/Webpages/Statistics
Reputable Nonprofit Organization Reports/Webpages/Statistics
Interactive Maps
Datasets or Databases
Preprints (articles that are posted to a preprint server before they are submitted to a journal and PRIOR to being peer reviewed)

Sources:

Ecology: Data Resources