Research Guides: Cell Biology & Molecular Genetics: Data

Introduction to CB&MG Data

For general life sciences data, including zoological, evolutionary, and ecological data, please see the Biology LibGuide.

Below you will find selected databases for cell biology & molecular genetics. For a more exhaustive and expansive list of cell biology & molecular genetics databases, please see the NAR Database Summary Paper Category List.

If you need help finding data for your project, please contact your librarian.

Data Collections

American Type Culture Collection (ATCC)
ATCC is the premier global biological materials resource and standards organization whose mission focuses on the acquisition, authentication, production, preservation, development, and distribution of standard reference microorganisms, cell lines, and other materials.
European Collection of Authenticated Cell Cultures
Scientists across the world use PHE Culture Collection materials to determine the effects of drugs, cosmetics, radiation, viruses, chemical and biological weapons, pesticides and household chemicals on human cells.
Reactome
Reactome is an open access biological pathway map that allows for searching and visual, click-based browsing of biomolecules within their networks of interaction.
Tabula Sapiens Data Portal
Tabula Sapiens is a first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects. It is a transcriptome map that creates a detailed portrait of cell types as well as their distribution and variation in gene expression across tissues and within the endothelial, epithelial, stromal and immune compartments.

chEMBL
ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.
Harvard Chemistry Dataverse
Harvard Dataverse chemistry topic contains datasets on a wide variety of chemistry publications and topics.
NMRShiftdb
nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. The nmrshiftdb2 software is open source, the data is published under an open content license. The core of nmrshiftdb2 are fully assigned spectra with raw data and peak lists (we have pure peak lists as well). Those datasets are peer reviewed by a board of reviewers. The project is supported by a scientific advisory board. nmrshiftdb2 is part of the NFDI4Chem initiative and will provide a component for a curated repository there. Please consult the documentation for more detailed information.

PubChem
PubChem is a database with information on the chemical properties and biological activities of small molecules. It is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. Links from PubChem's chemical structure records to other Entrez databases provide information on biological properties. These include links to PubMed scientific literature and NCBI's protein 3D structure resource. Links to PubChem's bioassay database present the results of biological screening. Links to depositor web sites provide further information.
Reaxys
Reaxys is a web-based platform based on three chemical information databases: (Former) CrossFire Beilstein, (Former) CrossFire Gmelin and the Patent Chemistry Database (PCD). In addition, Reaxys is an extensive repository of experimentally validated data, including structures, reactions (including multi-step reactions) and physical properties. It also contains pharmacological, eco-toxicological and toxicological data, specific bioassay results, logPs, toxicity values, and other valuable data. Reaxys allows searching for substances by chemical name or by structure, as well as for single and multi-step reactions. Searches can also be performed for citations, which are indexed from the primary organic, inorganic and organometallic chemistry journal literature going back to 1772, as well as from the patent literature.

BioCyc
Collection of 2988 Pathway/Genome Databases (PGDBs), each describing the genome and metabolic pathways of a single organism.
DNA Data Bank of Japan
A public database of nucleotide sequences established at the Bioinformation and DDBJ Center of the National Institute of Genetics (NIG).
Entrez
Entrez is the search box on the NCBI platform that allows you to search across over 30 NCBI databases. When you run a search, you will see a list of the NCBI databases and the number of matches found in each database.
European Nucleotide Archive
A repository providing free and unrestricted access to annotated DNA and RNA sequences.
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.
KEGG
The Kyoto Encyclopedia of Genes and Genomes is a free database of information on biological systems, genomes, chemicals, and health and disease developed by Kanehisa Laboratories. It has a wealth of linked biological data and bioinformatics tools, including pathway maps and hierarchical classifications of biomolecules.
National Center for Biotechnology Information (NCBI)
NCBI provides public access to biomedical and genomic information through its multiple databases and tools.
Nucleic Acid Knowledgebase (NAKB)
The Nucleic Acid Knowledgebase (NAKB) is a portal for 3D structural information about Nucleic Acids, and a successor to the Nucleic Acid Database (NDB).
RCSB Protein Data Bank (RCSB PDB)
Worldwide repository for information about 3D structures of biological macromolecules. Provides tools for structure visualization.
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.

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 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.

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.

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.