Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

OMICS studies: How about metadata checklist and data publications?

Data fully utilized by the community resources promote progress rather than repetition. Effective data sharing can accelerate the transition from data to actionable knowledge, yet barriers to data sharing remain, both technological and procedural. The DELSA community has tackled the sharing barrier by creating a multi-omics metadata checklist for the life sciences. The checklist and associated data publication examples are now jointly published in Big Data and OMICS: A Journal of Integrative Biology. The checklist will enable diverse datasets to be easily harmonized and reused for richer analyses. It will facilitate data deposits, stand alone as a data publication, and grant appropriate credit to researchers. We invite the broader life sciences community to test the checklist for feedback and improvements.

MOPED enables discoveries through consistently processed proteomics data

The Model Organism Protein Expression Database (MOPED, http://moped.proteinspire.org) is an expanding proteomics resource to enable biological and biomedical discoveries. MOPED aggregates simple, standardized and consistently processed summaries of protein expression and metadata from proteomics (mass spectrometry) experiments from human and model organisms (mouse, worm, and yeast). The latest version of MOPED adds new estimates of protein abundance and concentration as well as relative (differential) expression data. MOPED provides a new updated query interface that allows users to explore information by organism, tissue, localization, condition, experiment, or keyword. MOPED supports the Human Proteome Project's efforts to generate chromosome- and diseases-specific proteomes by providing links from proteins to chromosome and disease information as well as many complementary resources. MOPED supports a new omics metadata checklist to harmonize data integration, analysis, and use. MOPED's development is driven by the user community, which spans 90 countries and guides future development that will transform MOPED into a multiomics resource. MOPED encourages users to submit data in a simple format. They can use the metadata checklist to generate a data publication for this submission. As a result, MOPED will provide even greater insights into complex biological processes and systems and enable deeper and more comprehensive biological and biomedical discoveries.

Metadata Checklist for the Integrated Personal Omics Study: Proteomics and Metabolomics Experiments

The integrative personal omics profiling study introduced a novel, integrative approach based on personalized, longitudinal, multi-omics data. The study collected genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14-month period. The results revealed various medical risks and extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. The current article is a data publication that provides the checklists for the metadata of the proteomics (see Table 1 ) and metabolomics (see Table 2 ) datasets of the study. The proposed checklist was recently developed and endorsed by the Data-Enabled Life Sciences Alliance (DELSA Global). We call for the broader use of data publications using the metadata checklist to make omics data more discoverable, interpretable, and reusable, while enabling appropriate attribution to data generators and infrastructure science builders.