Omics Data Paper Generator

The Omics Data Paper Generator is an R Shiny app, installable as a golem, which imports (gen)omics metadata from EMBL's ENA and associated records from ArrayExpress and BioSamples into a data paper manuscript according to Pensoft's Biodiversity Data Journal omics data paper manuscript template. The manuscript can be downloaded as HTML or JATS XML. The goal of the tool is to enable (gen)omic data sharing and reuse through facilitating the authoring of genomics data papers. The workflow implemented in the Omics Data Paper Generator has been integrated inside Pensoft's ARPHA platform for authoring and reviewing scholarly articles. There, via this workflow, genomic data papers manuscripts can be generated by providing an ENA Study of Project identifier. Authors are then encouraged to improve their manuscripts through additional metadata and narrative. In addition to running this tool to use the workflow, it can be used via a web application: https://mdmtrv.shinyapps.io/Omics_data_paper/