Publication and archiving of data

Advantages of data publications

Data publications make research data findable and usable. They promote the traceability of research. The data is submitted to a  public repository, usually receives a DOI and can then be cited like articles. The advantages of data publications are:

  • Increase visibility and scientific impact.
  • Are already recognized as an independent scientific achievement in some disciplines.
  • Support Open Science and accelerate the overall progress of science.

 

Checklist for publishing data
  1. The data are clearly named and the identifiers do not contain any special characters.
  2. The  data format corresponds to the format required by the selected repository.
  3. All  metadata required by the repository has been recorded.
  4. Sufficient information is attached to the data to assess data quality and compliance with disciplinary standards.
  5. A  suitable license has been selected.

Information from Osnabrück University

 How to publish research data?

 osnaData - Research data repository of Osnabrück University

 OMERO - Image data repository of the Institute of Biology

Note

Until now, research data has often only been published as"supplementary material". The data is handed over to the publisher without being given its own permanent identifier. This approach is problematic as it prevents long-term archiving and compliance with the  FAIR principles!

General and subject-specific repositories

Public repositories secure research data in the long term with a focus on accessibility and reusability of data in accordance with the  FAIR principles.

In addition to general repositories that accept all data types and generic metadata, such as Zenodo, there are also subject-specific repositories that only accept certain data types with validated data formats and detailed, subject-specific metadata to enable precise description and analysis of the data within the subject area. Data structures and search functions are optimally adapted to the respective data type. Compliance with community standards also guarantees the quality of the research data.

Examples of specialized repositories in the field of biology are:

  • Sequence data: ENA, NCBI SRA, DDBJ
  • Proteome data: PRIDE
  • Metabolome data: MetaboLights, EMBL-EBI Metabolights
  • Mass spectrometry data: GNPS, MassIVE
  • Structural data: PDB

For biological imaging data, you will find a small overview of selected repositories below.

Repositories overview

Repository databases with filter function:

 re3data

 FAIRsharing

 Public repositories for image data (PNG) (2024)

The  RDM team will be happy to help you find a suitable repository for your data.

Data Publishing Databases
Overview specific repositories
Name Recommended usage drawing Interactivity Max. upload size Download Visualization Responsibility
OMERO.public Biological imaging data ✅ ✅ no limit ✅ ✅ Biology UOS
osnaData All formats ✅ ❌ no limit ✅ ❌ UOS Library
Zenodo All formats ✅ ❌ 50 GB ✅ ❌ CERN
IDR Biological imaging data ❌ ✅ no limit ✅ ✅ OME team
Bioimage Archive Biological imaging data ✅ ✅ no limit ✅ ✅ EMBL-EBI
Figshare All fomats ✅ ❌ 20 GB (more if charged) ✅ ✅ Figshare team
Procedure for finding a suitable repository
  1. Clarify the data/subject area: Categorize the data type (e.g. sequences, images, omics, logs, ...).
  2. Search for suitable repositories: Use e.g.  re3data or  FAIRsharing with suitable keywords.
  3. Check journal/funder requirements: Some publishers or funders stipulate certain repositories!
  4. Check community standards: Many subject communities have preferred repositories.
  5. Check additional requirements: E.g. access rights, data protection, DOI assignment, location, formats, data size, data structuring, metadata or licensing.

The Biology department offers its staff the free software  OMERO for managing image data. OMERO manages and archives image data in over 150 different formats on a central, secure image server with a database for metadata.

In its function as a  repository, OMERO also enables the  publication of image data. All image data are given persistent identifiers and can be cited in scientific articles.

Take a look at an  example of a data publication.

Procedure

  1. Requesting an OMERO group for your data publication

  2. Depositing the data in OMERO

  3. Depositing the metadata in OMERO

  4. Requesting a data DOI

For more information or if you have a specific publication request, please contact  Dr. Susanne Kunis.

Project results resulting from DFG-funded projects must be made available to the public in an appropriate manner. Publications must contain the following reference to DFG funding:

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project number(s)

If a publication refers to several projects, the project numbers must be separated by semicolons.

DFG project number

The DFG project number of the referenced project can be found in the letter of approval or in the DFG project information system  GEPRIS.

 DFG Funding Acknowledgements

How to decide on a license and overviews can be found at:

 

Information from Osnabrück University

 Terms of access & use and intellectual property rights

In the best case scenario, archiving research data should enable long-term availability and traceability as well as subsequent use of this data. For long-term archiving in accordance with the  FAIR principles, the files should therefore:

  • be unencrypted
  • not be compressed
  • not be proprietary/patented
  • use an open, documented standard with regard to  data format and  metadata
  • be clearly described

As a  storage location, please use the infrastructure provided by Osnabrück University or only recognized national or international (subject-specific)  repositories or archives.

It is also crucial that it is conclusively defined and publicly available (e.g. in a publication) how the archived data can be accessed.

Information from Osnabrück University

 Why archive research data?

Archive or repository?

Scientific archives preserve data for the long term and protect its authenticity through restricted access. Repositories store data with the aim of enabling long-term accessibility and reusability, in accordance with the  FAIR principles. The two can overlap, but not every repository is a full archive.