Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets

TL;DR

This paper presents an integrated system that enables scientists to enter experiment metadata via spreadsheets while ensuring compliance with community standards and improving data quality through validation tools.

Contribution

It introduces a comprehensive approach combining customizable templates, controlled vocabularies, and an interactive web tool to enhance spreadsheet-based metadata entry and validation.

Findings

Successful deployment in the HuBMAP consortium

Improved metadata consistency and standard adherence

Enhanced error detection and correction in spreadsheets

Abstract

Scientists increasingly recognize the importance of providing rich, standards-adherent metadata to describe their experimental results. Despite the availability of sophisticated tools to assist in the process of data annotation, investigators generally seem to prefer to use spreadsheets when supplying metadata, despite the limitations of spreadsheets in ensuring metadata consistency and compliance with formal specifications. In this paper, we describe an end-to-end approach that supports spreadsheet-based entry of metadata, while ensuring rigorous adherence to community-based metadata standards and providing quality control. Our methods employ several key components, including customizable templates that represent metadata standards and that can inform the spreadsheets that investigators use to author metadata, controlled terminologies and ontologies for defining metadata values that can be accessed directly from a spreadsheet, and an interactive Web-based tool that allows users to rapidly identify and fix errors in their spreadsheet-based metadata. We demonstrate how this approach is being deployed in a biomedical consortium known as HuBMAP to define and collect metadata about a wide range of biological assays.