Frederic B. Bastian - scFAIR: Standardization and stewardship of single-cell metadata
Channel: Biocuration Conference 2023
Date: 21/06/2023

*Session:* April 25 - Fair 1 - 02

*Abstract:* Single-cell functional genomics is bringing major insight into the life sciences. Single-cell data are rapidly increasing both in quantity and in diversity, but lack method and metadata standardization. While some large projects have clear standards of reporting, most publicly available datasets have partial or non standardized metadata. This leads to multiple non-compatible “standards” across datasets, and limits reusability, which in turn presents challenges to make these data useful to an increasing community of specialists and non-specialists. Therefore, there is a need for a centralized, standardized repository where researchers can collaboratively upload, annotate, or access single-cell metadata. There is also a need for standards in the way single-cell data are stored and annotated, especially for cell type and other associated information. Indeed, metadata is critical to the capacity to use these large and potentially very informative datasets. It includes protocols, which constrain which transcripts were accessible or which normalizations are relevant, the association between barcodes and annotations, or the methods used to identify cell types. Existing ontologies and controlled vocabularies are not used systematically, even when information is reported. The project scFAIR has the aim of building a collaborative platform supporting and disseminating Open Research Data practices for the single-cell genomics community, including data stewardship, both for sharing datasets and their metadata. scFAIR is funded by the Swiss Confederation with the aim of anchoring existing Open Research Data practices and taking them to the next level. It is a collaboration between the labs developing Bgee (https://bgee.org/) and ASAP (https://asap.epfl.ch/). An important aspect is to provide data stewardship to help researchers make their data FAIR, rather than adding a new layer of under-used “standards”. In the first part of the project, we are gathering feedback, and learning from existing practices, in order to define a standard for single-cell data that can be widely adopted by researchers. The challenges identified include, e.g., for single-cell RNA-Seq data, the requirement to have access to barcode information, in relation to cluster information; or to have access to the pipeline analysis parameters allowing to reproduce the clustering step. The second part of this project will be to develop a collaborative platform, implementing this standard, to improve single-cell data availability and reusability. An essential aspect is to obtain the involvement of the research community, to support them in the data submission process, notably by providing helpful information about errors identified in their metadata, and to disseminate the use of this single-cell FAIR practice. At this Biocuration 2023 conference, we would like to make researchers aware of this funded Open Research Data initiative, and obtain a large involvement of the biocuration community. We believe scFAIR has strong potential to become a tool for biocurators. We will present the limitations already identified in existing metadata, and the solutions so far.