MEDFORD: A human and machine readable metadata markup language

TL;DR

MEDFORD is a new metadata markup language designed to improve the recording and sharing of detailed research information, enhancing reproducibility in computational biology.

Contribution

It introduces MEDFORD, a human-readable, editable, and templatable language for comprehensive research metadata documentation.

Findings

Applied to coral research, including RNA-seq and photo data.

Facilitates detailed, reproducible research documentation.

Enhances ease of use and data sharing for scientists.

Abstract

Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle, or perhaps not noted at all. Much work is being done on the database and storage side of things, ensuring that there exists a space to store experiment-specific details, but current mechanisms for recording details are cumbersome for scientists to use. We propose a new metadata description language, named MEDFORD, in which scientists can record all details relevant to their research. Human-readable, easily-editable, and templatable, MEDFORD serves as a collection point for all notes that a researcher could find relevant to their research, be it for internal use or for future replication. MEDFORD has been applied to coral research, documenting research from RNA-seq analyses to photo collections.