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
Author Information
Irzam Sarfraz: Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
Yichen Wang: Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
Amulya Shastry: Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
Wei Kheng Teh: European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK.
Artem Sokolov: Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
Brian R Herb: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Heather H Creasy: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Isaac Virshup: Department of Computational Health, Helmholtz Munich, Oberschleißheim, Germany.
Ruben Dries: Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
Kylee Degatano: Data Sciences Platform, Broad Institute, Cambridge, MA, USA.
Anup Mahurkar: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Daniel J Schnell: Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Pedro Madrigal: European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK.
Jason Hilton: Department of Genetics, Stanford University, Stanford, CA, USA.
Nils Gehlenborg: Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Timothy Tickle: Data Sciences Platform, Broad Institute, Cambridge, MA, USA.
Joshua D Campbell: Department of Medicine, Boston University School of Medicine, Boston, MA, USA. camp@bu.edu. ORCID
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.
References
Nucleic Acids Res. 2021 Jan 8;49(D1):D1502-D1506
[PMID: 33211879]
