Research Guides: Biology: Data

Data Collections

Data can be found in many places and thus it is impossible to cover every data collection. Below you will find general data collections for the life sciences, but if you need any guidance or help with finding life science data, please reach our to me via this page.

Data.gov
The Home of the U.S. Government's Open Data - Here you will find data, tools, and resources to conduct research, develop web and mobile applications, design data visualizations, and more.
Dryad
Repository of research data underlying scientific and medical publications, predominantly from peer-reviewed journal articles.
ELIXIR: The European Life-Science Infrastructure for Biological Information Resources
ELIXIR (The European Life-Science Infrastructure for Biological Information Resources) is an intergovernmental organization that provides a single integrated infrastructure for bioinformatics data, software tools, and training materials.
EMBL-EBI: European Bioinformatics Institute
A collection of freely available tools and data resources including AlphaFold (protein structures), BioModels (computational models), ChEMBL (bioactive compounds), Ensembl (genome browser), Expression Atlas (gene expression), GWAS Catalog (genome-wide association studies), Protein Data Bank (3D structures), and UniProt (protein sequences).
Figshare
General repository for research outputs, including data sets, media, papers, posters and groups of files.
NCBI Entrez
Single search portal for articles and data related to genomes, genes, proteins, chemicals and other life sciences topics. Can search a more specific data source by clicking on the name.
NIH Data Sharing Repositories
List of NIH-supported data repositories and resources that aggregate information about biomedical data. Each entry has a brief description of the repository and links to data submission and access policies.
r3data.org
Registry of Research Data Repositories - a global registry of research data repositories.
ExPASy
Portal of the SIB Swiss Institute of Bioinformatics to databases and software tools in proteomics, genomics, phylogeny, systems biology, evolution, population genetics, and transcriptomics. Formerly the Expert Protein Analysis System.
JGI: Joint Genome Institute
Tools for the analysis and functional characterization of publicly available genomes of plants, fungi, and microbes, as well as environmental metagenomes.

Avian Knowledge Network
Partnership of people, institutions and government agencies that supports the conservation of birds and their habitats by improving access to and use of data and tools. Data available on bird-monitoring, banding and citizen-based bird-surveillance.
Data Basin
Provides free access to biological, physical and socioeconomic geospatial data and maps, along with tools to create custom visualizations, drawings and analyses.
GBIF: Global Biodiversity Information Facility
GBIF facilitates free and open access to biodiversity data, enabling anyone to discover, use or publish data about all types of life on Earth.
Global Biotic Interactions (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.
KNB: Knowledge Network for Biocomplexity
International repository for ecological and environmental data. Data originate from field stations, laboratories, research sites and individual researchers around the world.
LTER: Long Term Ecological Research
The Long Term Ecological Research (LTER) Network is a collaborative of researchers and graduate students who focus on long-term ecological processes at 26 LTER sites around the United States, Antarctica, and islands in the Caribbean and Pacific.
MorphoBank
Provides collaborative tools for researchers to upload images and morphological data, and use that information to produce, edit, illustrate and annotate phylogenetic matrices. Also a repository for data associated with peer-reviewed publications.
Paleobiology Database
The Paleobiology Database is a public resource for the global scientific community. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.

BioCyc
Collection of 2988 Pathway/Genome Databases (PGDBs), each describing the genome and metabolic pathways of a single organism.
EcoCyc
A database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.
FlyBase
Database of Drosophila genes and genomes.
MaizeGDB: Maize Genetics and Genomics Database
Sequence and analysis resources on the crop plant and model organism Zea mays.
MGI: Mouse Genome Informatics
Database of laboratory mouse genetic, genomic and biologic data.
Plant Metabolic Pathway Databases
Collected by Plant Metabolic Network
Plant Model Organism Databases
Collected by Plant Metabolic Network
SGD: Saccharomyces Genome Database
Integrated biological resources for the budding yeast Saccharomyces cerevisiae along with search and analysis tools.

TAIR
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model plant Arabidopsis thaliana. Note: Certain features on this site (commenting on genes or loci, registering a new mutant gene symbol) require setting up a free user name and password. Data available from TAIR include the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. TAIR also provides extensive links to other Arabidopsis resources.

WormBase
A resource on the genetics, genomics and biology of the model organism C. elegans and related nematodes.
XenBase
Genomic, expression and functional data for the model organisms Xenopus laevis and X. tropicalis.
ZFIN: The Zebrafish Model Organism Database
Database of zebrafish genetic, genomic and developmental data.

CABI Compendium Crop Protection
A global compilation of crop protection knowledge for practical decision-making. Including information on crops, countries, pests, diseases and weeds and their natural enemies.
Note: The data is behind a paywall, but some are open access. If you have questions or need data from this resource, please contact me.
Gramene
Comparative plant genomics for crops and model organisms.
Phytozome
Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.
Plant Metabolic Pathway Databases
Provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism in plants.
Plant Model Organism Databases
Collected by Plant Metabolic Network

TAIR
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model plant Arabidopsis thaliana. Note: Certain features on this site (commenting on genes or loci, registering a new mutant gene symbol) require setting up a free user name and password. Data available from TAIR include the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. TAIR also provides extensive links to other Arabidopsis resources.