MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data

Irzam Sarfraz; Yichen Wang; Amulya Shastry; Wei Kheng Teh; Artem Sokolov; Brian R Herb; Heather H Creasy; Isaac Virshup; Ruben Dries; Kylee Degatano; Anup Mahurkar; Daniel J Schnell; Pedro Madrigal; Jason Hilton; Nils Gehlenborg; Timothy Tickle; Joshua D Campbell

doi:10.1186/s13059-024-03349-w

MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data

Genome Biol. 2024 Aug 1;25(1):205. doi: 10.1186/s13059-024-03349-w.

Authors

Irzam Sarfraz¹, Yichen Wang¹, Amulya Shastry¹, Wei Kheng Teh², Artem Sokolov³, Brian R Herb⁴, Heather H Creasy⁴, Isaac Virshup⁵, Ruben Dries¹, Kylee Degatano⁶, Anup Mahurkar⁴, Daniel J Schnell⁷, Pedro Madrigal², Jason Hilton⁸, Nils Gehlenborg⁹, Timothy Tickle⁶, Joshua D Campbell¹⁰

Affiliations

¹ Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
² European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK.
³ Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
⁴ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
⁵ Department of Computational Health, Helmholtz Munich, Oberschleißheim, Germany.
⁶ Data Sciences Platform, Broad Institute, Cambridge, MA, USA.
⁷ Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
⁸ Department of Genetics, Stanford University, Stanford, CA, USA.
⁹ Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
¹⁰ Department of Medicine, Boston University School of Medicine, Boston, MA, USA. [email protected].

Abstract

Many datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While biospecimen and experimental information is often captured, detailed metadata standards related to data matrices and analysis workflows are currently lacking. To address this, we develop the matrix and analysis metadata standards (MAMS) to serve as a resource for data centers, repositories, and tool developers. We define metadata fields for matrices and parameters commonly utilized in analytical workflows and developed the rmams package to extract MAMS from single-cell objects. Overall, MAMS promotes the harmonization, integration, and reproducibility of single-cell data across platforms.

MeSH terms

Humans
Metadata*
Reproducibility of Results
Single-Cell Analysis* / methods
Single-Cell Analysis* / standards
Software

Abstract

MeSH terms

Grants and funding