LibGuides: Biology: Data Collections

General Life Sciences Data

This page serves as a small jumping-off-point into the vast world of open data. If there is something specific you'd like to find, please don't hesitate to contact us.

Dryad
Repository of research data underlying scientific and medical publications, predominantly from peer-reviewed journal articles.
Figshare
General repository for research outputs, including data sets, media, papers, posters and groups of files.
National Library of Medicine (NLM) Dataset Catalog
The Dataset Catalog is a catalog of biomedical datasets from various repositories for users to search, discover, retrieve, and connect with datasets to accelerate scientific research. This beta version aims to collect user feedback to inform future product development.
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.
re3data.org
Global registry of research data repositories.

Ecology & Evolutionary Biology Data

Avian Knowledge Network (AKN)
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.
Catalog of Life
Single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.6 million species.
Data Basin
Provides free access to biological, physical and socioeconomic geospatial data and maps, along with tools to create custom visualizations, drawings and analyses.
Global Biodiversity Information Facility (GBIF)
GBIF facilitates free and open access to biodiversity data, enabling anyone to discover, use or publish data about all types of life on Earth.
Integrated Taxonomic Information System (ITIS)
Authoritative taxonomic information on plants, animals, fungi and microbes of North America and the world. Full database or specific taxonomic group data available for download.
Knowledge Network for Biocomplexity (KNB)
International repository for ecological and environmental data. Data originate from field stations, laboratories, research sites and individual researchers around the world.
Long Term Ecological Research (LTER) Data Portal
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. The LTER Data Portal contains ecological data packages contributed by past and present LTER sites.
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.
NCBI Taxonomy
National Center for Biotechnology Information (NCBI) database of names and classification for all organisms represented in NCBI sequence databases.

Molecular Biology, Cell Biology & Biochemistry Data

Collections

European Bioinformatics Institute
Part of the European Molecular Biology Laboratory (EMBL), the EBI provides a wide range of databases, software tools, and resources.
ExPASy
ExPASY, the SIB Swiss Institute of Bioinformatics Resource Portal, provides access to databases and software tools in different areas of the life sciences, including proteomics, genomics and phylogeny.
National Center for Biotechnology Information (NCBI)
NCBI provides public access to biomedical and genomic information through its multiple databases and tools.
Nucleic Acids Research Annual Database Issue 2019

Sequence Data

Nucleotide
Collection of sequences from multiple sources, including GenBank, RefSeq, and Protein Data Bank (PDB). Searching Nucleotide will yield results from each of its component databases, which can also be searched separately. [NCBI database]
SRA: Sequence Read Archive
Repository for raw sequencing data from next-generation sequencing technologies. [NCBI database]
UniProt
Universal Protein Resource (UniProt), a collaboration between the European Bioinformatics Institute, the SIB Swiss Institute of Bioinformatics and Protein Information Resource, provides high-quality, freely accessible protein sequence and functional information.

Gene & Expression Data

BioProject
Collection of genomics, functional genomics, and genetic studies with links to their datasets. [NCBI database]
dbGAP: Database of Genotypes and Phenotypes
Archive and distribution center for results of studies that investigate the interaction of genotype and phenotype, including GWAS and molecular diagnostic assays. [NCBI database]
Gene
Database of genes from a wide range of species, with a focus on genomes that have been completely sequenced. [NCBI database]

Structure

Cambridge Structural Database (WebCSD) This link opens in a new window
Provides bibliographic, chemical, and crystallographic records for organic molecules and metal-organic compounds, current
Current; the Cambridge Structural Database (WebCSD) consists of the bibliographic, chemical, and crystallographic (single crystal and powder diffraction) records for organic molecules and metal-organic compounds whose 3-D structures have been determined using x-diffraction and/or neutron diffraction. Almost all records have the three-dimensional coordinate data for at least non-hydrogen atoms. The crystal structure data comes from the open literature or direct deposits by researchers. Search by substructure, reduced cell, similarity, or text/numeric.

AlphaFold Protein Structure Database
"AlphaFold is an AI system developed by Google DeepMind that predicts a protein’s 3D structure from its amino acid sequence."
Nucleic Acid Database
Archive of structural information about nucleic acids.
PDB: Protein Data Bank
Worldwide repository for information about 3D structures of biological macromolecules. Provides tools for structure visualization.

Model Organisms

FlyBase
Database of Drosophila genes and genomes.
MGI: Mouse Genome Informatics
Database of laboratory mouse genetic, genomic and biologic data.
Plant Model Organism Databases
Collected by Plant Metabolic Network
WormBase
"WormBase is an international consortium of biologists and computer scientists providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes."
ZFIN: The Zebrafish Model Organism Database
Database of zebrafish genetic, genomic and developmental data.

TAIR: The Arabidopsis Information Resource This link opens in a new window
- This link opens in a new window
A database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes 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 linkouts from our data pages to other Arabidopsis resources.

Plant Data & Other Resources

Grameme
Comparative grass genomics (rice, maize, sorghum, barley, oats, wheat, rye)
Phytozome
Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute. Families of related genes representing the modern descendants of ancestral genes are constructed at key phylogenetic nodes. These families allow easy access to clade-specific orthology/paralogy relationships as well as insights into clade-specific novelties and expansions. As of release v11, Phytozome provides access to sixty-five sequenced and annotated green plant genomes.
Plant Metabolic Network
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
International Plant Names Index (IPNI)
IPNI provides nomenclatural data (spelling, author, types and first place/date of publication) for the scientific names of vascular plants from family to infraspecific ranks.
re3data - Plant Sciences
Research Data Repositories tagged with "Plant Sciences"