Table 1 Common repositories for physical and digital research items in the biosciences

From: Knowledge preservation in the era of big science and AI: strategies for sustainable scientific research

Namea

Items stored

Ref.

URL

Physical biological resources

Addgene

Plasmids and strains.

41

www.addgene.org

ATCC

Microorganisms and cell lines.

69

www.atcc.org

BioBricks Registry

Biological parts and characterisation data.

—

registry.igem.org

DSMZ

Microorganisms and cell lines.

—

www.dsmz.de

SEVA

Standardised plasmids (SEVA format).

70

seva-plasmids.com

Svalbard Seed Vault

Global long-term seed storage facility.

71

www.seedvault.no

UK Biobank

Large-scale biomedical samples resource.

72

www.ukbiobank.ac.uk

Experimental data resources

ArrayExpress

Functional genomics data.

73

www.ebi.ac.uk/arrayexpress

BioSamples

Metadata about biological samples.

74

www.ebi.ac.uk/biosamples

DDBJ

DNA and RNA sequence data.

75

www.ddbj.nig.ac.jp

EcoCyc

Genomic, metabolic, regulatory data.

76

www.ecocyc.org

EMDB

Electron microscopy data

77

www.ebi.ac.uk/emdb

ENA

Nucleic acid sequences.

78

www.ebi.ac.uk/ena

Gene Ontology

Knowledgebase for the functions of genes.

37

geneontology.org

GTEx

Tissue/cell-specific gene expression & regulation.

79

gtexportal.org

KEGG

Genomic, metabolic, and regulatory data.

80

www.genome.jp/kegg

MMDB

Molecular dynamics simulations.

27

mddbr.eu

NCBI

Wide variety of sequence and expression data including the hosting of other key repositories like GenBank, SRA and GEO.

54

www.ncbi.nlm.nih.gov

PDB

Protein structures.

81

www.rcsb.org

PDB-IHM

Integrative molecular structures

82

pdb-ihm.org

RegulonDB

Transcriptional regulation data for E. coli K-12.

83

regulondb.ccg.unam.mx

SynBioHub

Genetic parts and designs for synthetic biology.

32

synbiohub.org

UniProt

Protein sequences and annotations.

84

www.uniprot.org

Models, workflows and code

AiiDA

Automated interactive infrastructure and database for computational workflows.

43

www.aiida.net

BioModels

Models of diverse biological systems.

85

ebi.ac.uk/biomodels

Galaxy

Bioinformatics workflows.

40

galaxyproject.org

GitHub

Computer code and documentation.

—

www.github.com

Protocols, pre-prints, and other research resources

bioRxiv

Pre-print server for the biological sciences.

86

www.biorxiv.org

Dryad

General research data repository.

87

datadryad.org

Figshare

Repository for datasets, figures, and other outputs.

88

figshare.com

JoVE

Videos of experimental protocols.

—

www.jove.com

Protocols.io

Step-by-step experimental protocols.

63

protocols.io

Zenodo

Open-science repository.

89

zenodo.org

  1. a Acronyms for repositories given where commonly used. ATCC American Type Culture Collection, DSMZ: German Collection of Microorganisms and Cell Cultures, EMDB Electron Microscopy Data Bank, ENA European Nucleotide Archive, GEO Gene Expression Omnibus, GTEx Genotype-Tissue Expression, KEGG Kyoto Encyclopedia of Genes and Genomes, JoVE Journal of Visualised Experiments, MDDB Molecular Dynamics Data Bank, NCBI National Center for Biotechnology Information, PDB Protein Data Bank, PDB-IHM Protein Data Bank for Integrative and Hybrid Methods, SEVA Standard European Vector Architecture, SRA Sequence Read Archive.
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