Research Guides: Biology (New York/Shanghai/Abu Dhabi): Biological Data & Nomenclature

Overview

There's a lot of data available out there and this page can't include it all. Are you looking for sample electrocardiogram data? Do you wish you could easily compare the lifespans of different species in one database? Contact us and we'll see what we can find.

General Life Science Data

Data.gov
Open Federal, state and local data from the United States government.
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.
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
Taxonomic information on plants, animals, fungi, and microbes of North America and the world. Use taxonomic serial number. For example, bactrian camel: ITIS taxonomic Serial No.: 625026
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.
TreeBASE
Repository of phylogenetic information, specifically user-submitted trees and the data used to generate them. Data in TreeBASE are available to the public if they have been used in a peer-reviewed publication.

Neuroscience Data

Collaborative Research in Computational Neuroscience (CRCNS)
The CRCNS data sharing website hosts high-quality experimental data sets that are valuable for testing computational models of the brain and new analysis methods. Data include physiological recordings from sensory and memory systems, as well as eye movement data.
Human Connectome Projects
Comprehensively mapping human brain circuitry in 1200 healthy adults using cutting-edge methods of noninvasive neuroimaging. Imaging, behavioral data, and genomic data are all made freely available to the research community as the data is collected. In addition, other laboratories using similar data collection techniques are releasing their data via this web site.
LONI Image Data Archive
Environment for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. To access data from "Open Use" studies all you need is an account. For other studies, you must request access by submitting a data use application.
Neuroimaging Informatics Tools & Resources Clearinghouse (NITRC)
Facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses—including popular tools as well as those that once might have been hidden in another researcher's laboratory or some obscure corner of cyberspace.
NeuroMorpho
Inventory of digitally reconstructed neurons associated with peer-reviewed publications.
Neuroscience Information Framework (NIF) Data Federation
Simultaneously queries multiple individual databases and data sets through a single search interface. Results categorized by data type and nervous system level.
OpenfMRI
Project dedicated to free and open sharing of functional magnetic resonance imaging (fMRI) data sets, including raw data.

Brain Atlases

Allen Brain Atlas
From the Allen Institute for Brain Science, interactive atlases that integrate genomic and neuroanatomical data.
Prenatal Mouse Brain Atlas
Color images and annotated diagrams of: Gestational Days 12, 14, 16 and 18 Sagittal, coronal and horizontal section (2)
Brain Biodiversity Bank Atlases
Michigan State University Brain Biodiversity Bank provides brain atlases for multiple species, including human, sheep, dolphin and axolotl. Images available for public use, with permission.
BrainMaps.org
Interactive atlas that allows you to search for and retrieve data about brain structure and function. Complete data sets available for several vertebrate species.

You can also search for brain atlases (many are available as ebooks) in the catalog.

Netter's Atlas of Neuroscience E-Book

Molecular Biology & Biochemistry

Collections

National Center for Biotechnology Information (NCBI)
NCBI provides public access to biomedical and genomic information through its multiple databases and tools.
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.
European Bioinformatics Institute
Part of the European Molecular Biology Laboratory (EMBL), the EBI provides a wide range of databases, software tools, and resources.

BioCyc This link opens in a new window
BioCyc is a collection of 13075 Pathway/Genome Databases (PGDBs), plus software tools for exploring them [Karp17].

Nucleic Acids Research Annual Database Issue: 2020

Sequences

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.

Genes & Expression

BioProject
Collection of genomics, functional genomics, and genetic studies with links to their datasets. [NCBI database]
Gene
Database of genes from a wide range of species, with a focus on genomes that have been completely sequenced. [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]

Structure

PDB: Protein Data Bank
Worldwide repository for information about 3D structures of biological macromolecules. Provides tools for structure visualization.
Nucleic Acid Database
Archive of structural information about nucleic acids.

Organism Names & Taxonomy

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.
NCBI Taxonomy
National Center for Biotechnology Information (NCBI) database of names and classification for all organisms represented in NCBI sequence databases.
Integrated Taxonomic Information System
Taxonomic information on plants, animals, fungi, and microbes of North America and the world. Use taxonomic serial number. For example, bactrian camel: ITIS taxonomic Serial No.: 625026

Model Organisms

Plant Model Organism Databases
Collected by Plant Metabolic Network

BioCyc This link opens in a new window
BioCyc is a collection of 13075 Pathway/Genome Databases (PGDBs), plus software tools for exploring them [Karp17].

FlyBase
Database of Drosophila genes and genomes.
MGI: Mouse Genome Informatics
Database of laboratory mouse genetic, genomic and biologic data.
ZFIN: The Zebrafish Model Organism Database
Database of zebrafish genetic, genomic and developmental data.

Names (& Naming) of Genes & Variants

You'll often see that genes have multiple names, symbols, and IDs associated with them. This can cause confusion when reporting on genes or sequences and also when searching for them. Gene nomenclature committees and molecular sequence databases provide standardized names and identifiers as well as known synonyms.

Approved gene symbol: There are species-specific rules about naming genes. Nomenclature committees that assign gene names and symbols exist for a variety of organisms (see below).
Accession IDs: Molecular sequence databases assign unique accession numbers to each submitted sequence. The International Nucleotide Sequence Database Collaboration (DDBJ/EMBL-EBI/NCBI) assigns accessions in a specific format.
Gene variants: HGVS is the standard for reporting human gene variants. Organism-specific nomenclature committees provide species-specific rules for unambiguously naming variants. See below for links to more specific resources and information.

Converting Identifiers

bioDBnet: Database to Database Conversions
Allows for conversions of identifiers from one database to other database identifiers or annotations.

Humans

HGNC GeneNames
Human. Curated online repository of HGNC-approved gene names, gene families and associated resources. Currently, over 39,000 gene symbols are included
HGVS Guidelines
Human Genome Variation Society guidelines for naming sequence variants.
Mutalyzer
Suite of tools to help create and check sequence variant names in HGVS format.

Other Organisms

Vertebrate Gene Nomenclature Committee
VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. The VGNC also coordinates with other vertebrate nomenclature committees to ensure genes are named in line with their human homologs.
Mouse Nomenclature
Rat Nomenclature
Xenopus Nomenclature
Chicken Nomenclature
Zebrafish Nomenclature
Fly Nomenclature
Nematode Nomenclature