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Data Repositories

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A data repository is a location where digital objects are stored and documented, and which enable the separate publication and archiving of these objects. Data access can be either open or restricted to a group of users.

Benefits of publishing data in a repository

Criteria to select a trusted repository

Below are listed criteria you might want to consider when selecting a repository where to publish your data:

Order of preference for selecting a repository

  1. A certified resposity (CoreTrustSeal, nestor/DIN 31644, ISO 16363)
  2. A well-established repository in your discipline that offers a specific scope (e. g. supporting a specific metadata schema).
  3. One of the repositories recommended by your funding organization or the funding program.
  4. Your institution’s repository (if available).
  5. A cost-free interdisciplinary repository (e.g. Figshare, Zenodo).
  6. Another repository that you can search for using the above-mentioned criteria in a repository finder.

Well-established repositories for data deposition in microbiology

Below are listed well-established repositories in microbiology. For each repository, the FAIRsharing and re3data pages are linked. On the FAIRsharing page, you will find information such as which journals endorse the repository (under “Collections & Recommendations” and then “In Policies”). On the re3data page, you will find information such as the above-mentioned criteria to select a trusted repoository.

Data type Data repository FAIRsharing re3data
All research output Zenodo FAIRsharing re3data
Crystallographic data Cambridge Structural Database (CSD) FAIRsharing re3data
Geospatial data Malaria Atlas Project (MAP) / re3data
Image data BioImage Archive FAIRsharing re3data
  Cell Image Library FAIRsharing re3data
Linked genotype and phenotype data European Genome-phenome Archive (EGA) FAIRsharing re3data
Macromolecular structures Worldwide Protein Data Bank (wwPDB) FAIRsharing re3data
  RCSB Protein Data Bank (RCSB PDB) FAIRsharing re3data
  Protein Data Bank of Japan (PDBj) FAIRsharing re3data
  Protein Data Bank of Europe (PDBe) FAIRsharing re3data
  Biological Magnetic Resonance Data Bank (BMRB) FAIRsharing re3data
Electron microscopy data Electron Microscopy Data Bank (EMDB) FAIRsharing re3data
  Electron Microscopy Public Image Archive (EMPIAR) FAIRsharing re3data
Microbiome data MGnify FAIRsharing re3data
Nucleic acid sequences GenBank FAIRsharing re3data
  DNA Data Bank of Japan (DDBJ) FAIRsharing re3data
  European Nucleotide Archive (ENA) FAIRsharing re3data
  Sequence Read Archive (SRA) FAIRsharing re3data
  Genome Sequence Archive (GSA) FAIRsharing re3data
Genetic polymorphism European Variation Archive (EVA) FAIRsharing re3data
Functional genomics Gene Expression Omnibus (GEO) FAIRsharing re3data
  ArrayExpress FAIRsharing re3data
  GenomeRNAi / re3data
  European Genome-phenome Archive (EGA) FAIRsharing re3data
  Database of Interacting Proteins (DIP) FAIRsharing re3data
  IntAct FAIRsharing re3data
  Japanese Genotype-phenotype Archive (JGA) FAIRsharing re3data
  PubChem FAIRsharing re3data
  Genomic Expression Archive (GEA) FAIRsharing re3data
  Genome-Wide Association Studies (GWAS) Catalog FAIRsharing /
Protein sequences UniProt FAIRsharing re3data
Proteomes PRoteomics IDEntifications (PRIDE) Archive database FAIRsharing re3data
Quantitative and predictive food microbiology ComBase / re3data
Scientific texts and data PUBLISSO – Repository for Life Sciences FAIRsharing re3data
Species interaction data Global Biotic Interactions (GloBI) / /
Standardized bacterial information Bacterial Diversity Metadatabase (BacDive) FAIRsharing re3data
Vertebrate-virus network VIRION / /

Data publishing in the PUBLISSO – Repository for Life Sciences (FRL)

Repository details

  • Data types: scientific texts and research data from the fields of medicine, health, nutritional, environmental and agricultural sciences
  • Open Access: yes
  • Terms of use & License: yes
  • PID system: yes (DOI)
  • Certification or repository standard: no
  • Policy: yes ( see “Data Policy”, only in German)
  • Archiving: yes
  • Costs: free of charge
  • Data curation & quality control: no
  • Data guarantee: availability for at least 10 years and transfer to a long-term archive
  • Recommended publication formats for research data: see “Recommended preservation formats for research data” on this page

Steps to deposit data in the FRL

  1. Contact forschungsdaten@zbmed.de.
  2. You will receive:
    • The terms of use that you need to sign and send back.
    • A record sheet that you need to fill in with your metadata and send back.
  3. Your metadata will be checked, entered into the FRL and assigned a DOI.
  4. Send your data and supplementary materials to the FRL team.
  5. Your data will be added to the metadata record already created in the FRL.
  6. You will receive a publication notice with the DOI.

Benefits

  • The FRL provides Open Access to its data (in specific cases, you can set an embargo period of up to 24 months).
  • There are no charges to publish, archive or use scientific texts and research data from the FRL.
  • The FRL supports the FAIR data principles (e.g. by assigning DOIs, by offering life science-specific metadata).
  • You can publish your metadata in the FRL and receive a DOI in advance of publishing your data.
  • You can publish large datasets in the FRL.
  • The FRL is permanently accessible online.
  • The FRL is indexed in re3data.
  • The FRL is findable via Google search and indexed in BASE, DataCite Search and LIVIVO - ZB MED Search Portal for Life Sciences.

Drawbacks

  • The FRL is not suitable for sensitive data.
  • The FRL can be browsed only in German.

Data publishing in Zenodo

Repository details

  • Data types: all research outputs, positive and negative results
  • Open Access: yes
  • Terms of use & License: yes
  • PID system: yes (DOI)
  • Certification or repository standard: no
  • Policy: yes (see here)
  • Archiving: yes
  • Costs: free of charge
  • Data curation & quality control: by the repository itself or by communities
  • Data guarantee: availability for the lifetime of the repository
  • Recommended publication formats for research data: any file format

Steps to deposit data in Zenodo

  1. Upload files.
  2. Describe your content so others can find it.
  3. Publish your content.

For more details, see this guide.

Benefits

  • Zenodo provides Open Access to its data (files may be deposited under closed, open or embargoed access).
  • There are no charges to publish, archive or use content.
  • Zenodo supports the FAIR data principles (e.g. by assigning DOIs).
  • Zenodo is permanently accessible online.
  • Zenodo is indexed in re3data.
  • Zenodo is findable via Google search and indexed in BASE and DataCite Search.

Drawbacks

  • Zenodo might not be suitable for sensitive data that might have to stay in their country of origin.
  • Zenodo has a size limit of 50 GB per record. For bigger size, a request has to be made.

Repository finders

Further Resources

Get Help

If you have any further questions about the management and analysis of your microbial research data, please contact us: helpdesk@nfdi4microbiota.de (by emailing us you agree to the privacy policy on our website: Contact)

References

  • Engelhardt, C., Biernacka, K., Coffey, A., Cornet, R., Danciu, A., Demchenko, Y., Downes, S., Erdmann, C., Garbuglia, F., Germer, K., Helbig, K., Hellström, M., Hettne, K., Hibbert, D., Jetten, M., Karimova, Y., Kryger Hansen, K., Kuusniemi, M. E., Letizia, V., … Zhou, B. (2022). D7.4 How to be FAIR with your data. A teaching and training handbook for higher education institutions (V1.2.1). Zenodo. https://doi.org/10.5281/ZENODO.6674301
  • Lindlar, M., Rudnik, P., Horton, L., & Jones, S. (2020). “You say potato, I say potato” - Mapping Digital Preservation and Research Data Management Concepts towards Collective Curation and Preservation Strategies. https://doi.org/10.5281/ZENODO.3672773
  • Rathmann T. et al. 2021-10. Workshop on Research Data Management. FoDaKo and ZB MED - Information Centre for Life Sciences. Google Slides.

Citation

National Research Data Infrastructure for Microbiota Research (NFDI4Microbiota). (2024, September 30). Data Repositories. NFDI4Microbiota Knowledge Base.