OMD Curation Toolkit: a workflow for in-house curation of public omics datasets

• Published in: BMC bioinformatics Vol. 25; no. 1; pp. 184 - 7
• Main Authors: Piquer-Esteban, Samuel, Arnau, Vicente, Diaz, Wladimiro, Moya, Andrés
• Format: Journal Article
• Language: English
• Published: London BioMed Central 09.05.2024; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Archives & records; Bioinformatics; Biomedical and Life Sciences; Computational Biology - methods; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Curation tools; Data Curation - methods; Data integration; Databases, Genetic; Datasets; Dictionaries; ENA; Genomics - methods; Information management; Life Sciences; Medical research; Medicine, Experimental; Metadata; Microarrays; Nucleotides; Omics data; Python; Sequencing data; Software; Toolkits; Variables; Workflow; Spain; Metadata; ENA; Curation tools; Sequencing data; Data integration; Omics data
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05803-9

Background Major advances in sequencing technologies and the sharing of data and metadata in science have resulted in a wealth of publicly available datasets. However, working with and especially curating public omics datasets remains challenging despite these efforts. While a growing number of initiatives aim to re-use previous results, these present limitations that often lead to the need for further in-house curation and processing. Results Here, we present the Omics Dataset Curation Toolkit (OMD Curation Toolkit), a python3 package designed to accompany and guide the researcher during the curation process of metadata and fastq files of public omics datasets. This workflow provides a standardized framework with multiple capabilities (collection, control check, treatment and integration) to facilitate the arduous task of curating public sequencing data projects. While centered on the European Nucleotide Archive (ENA), the majority of the provided tools are generic and can be used to curate datasets from different sources. Conclusions Thus, it offers valuable tools for the in-house curation previously needed to re-use public omics data. Due to its workflow structure and capabilities, it can be easily used and benefit investigators in developing novel omics meta-analyses based on sequencing data.