Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peerreview and increases the impact of datasets by enhancing their visibility, accessibility, and re-usability.
We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivise researchers to publish well-described data sets, we created a prototype workflow for streamlined import of genomics metadata from the European Nucleotide Archive directly into a data paper manuscript.
An omics data paper template was designed by defining key article sections which encourage the description of omics datasets and methodologies. A metadata import workflow, based on REpresentational State Transfer services and Xpath, was prototyped to extract information from the European Nucleotide Archive, ArrayExpress and BioSamples databases.
The template and workflow for automatic import of standard-compliant metadata into an omics data paper manuscript provide a mechanism for enhancing existing metadata through publishing.
The omics data paper structure and workflow for import of genomics metadata help to bring genomic and other omics datasets into the spotlight. Promoting enhanced metadata descriptions and enforcing manuscript peer review and data auditing of the underlying datasets brings additional quality to datasets. We hope that streamlined metadata re-use for scholarly publishing encourages authors to create enhanced metadata descriptions in the form of data papers to improve both the quality of their metadata and its findability and accessibility.

Keywords:

• omics
• genomics
• metadata
• workflow
• standards
• fair principles
• mixs
• minseqe

Read the peer-reviewed publication(s):

(PubMed: 33983435)

Additional information:

https://scicrunch.org/resolver/RRID:SCR_019809

https://bio.tools/omics-data-paper-shinyapp-golem

https://mdmtrv.shinyapps.io/Omics_data_paper/

Github links:

https://github.com/pensoft/omicsdatapaper