scFAIR: Single-Cell Genomics Data Standardization Initiative

Overview

scFAIR is an initiative to standardize single-cell genomics data and promote findable, accessible, interoperable, and reusable (FAIR) single-cell data. Our goal is to build a collaborative platform that supports and disseminates open research data (ORD) practices within the single-cell genomics community. This platform will enable researchers to upload, annotate, and access single-cell data and associated metadata, ensuring that these data are useful to an increasing community of specialists and non-specialists.

Background

Single-cell genomics has emerged as a transformative field within molecular biology, revolutionizing our understanding of cellular heterogeneity and paving the way for unprecedented insights into complex biological systems. As the quantity and diversity of single-cell data rapidly increase, the lack of clear reporting standards has led to multiple non-compatible datasets, limiting reusability. This presents challenges in making these data useful to the broader scientific community.

Need for Standardization

To address these challenges, there is a critical need for:

• A centralized, standardized repository where researchers can collaboratively upload, annotate, and access single-cell data and associated metadata.
• Standardized methods for storing and annotating single-cell data, particularly regarding essential metadata. This includes:
  • Protocols
  • Normalization and pipeline characteristics
  • Cell type classifications and the methods used to classify them
  • Association between barcodes and annotations

Adopting systematic data-sharing practices and standards is integral to fostering transparency, reproducibility, and effective utilization of single-cell genomics data.

Objectives

• Build a collaborative platform for sharing datasets and their metadata.
• Standardize the way data are shared across datasets.
• Promote communication and outreach to increase the relevance and implementation of these standards within the single-cell genomics community.

Getting Started

To set up the project, follow these steps:

1. Create a /data folder in the root directory of the project.
2. Download the composite metazoan ontology file from the following link: http://purl.obolibrary.org/obo/uberon/composite-metazoan.obo.
3. Place the downloaded file in the /data folder.

After setting up the /data folder and placing the ontology file, run the following Rake commands in sequence:

rake obo:parse[/data/composite-metazoan.obo]
rake obo:update_adjacency_lists
rake api_updates

These commands will parse the ontology file, update the adjacency lists, and finally, update the API.

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Thank you for being part of the scFAIR initiative! Together, we can make single-cell genomics data more findable, accessible, interoperable, and reusable.