Spatial Transcriptomics for the Data-Minded: Blueprints for Developing Metadata Standards for Adoption by a Community
Date: TBA
Organised by: Mr Wei Kheng Teh
Overview:
"Spatial transcriptomics technologies reveal how the spatial organization of cells and tissues relates to cell types, gene functions, and biological effects. New technologies, analysis methodologies, and integration protocols are continually released, resulting in numerous file formats, metadata standards, and databases.
This workshop will be split into two parts: knowledge sharing and discussion
- Part 1: Share about existing structures in the spatial transcriptomics data landscape (file formats, metadata standards, databases), describe the EMBL-EBI metadata standard for spatial transcriptomics technologies, the advantages of archiving data using a unified submissions pathway, and common challenges and solutions for adopting metadata standards
- Part 2: Engage workshop participants to share about individual challenges relating to spatial data, metadata standards, and archiving. During the workshop, we will cluster these challenges and communally share existing resources (tools, organisations, working groups, websites) that lead to solutions. In the interests of respecting the participants time commitments, a collection of shared challenges, solutions, and resources will be shared with participants after the workshop.
Objectives:
- Discuss the advantages and disadvantages of different file formats, metadata standards, and analysis methodologies in imaging and spatial transcriptomics
- Describe the Human Cell Atlas metadata standard, and the developing spatial transcriptomics standard focusing on integration and reanalysis
- Cover existing archives for spatial transcriptomics data, their metadata and file format expectations
- Describe the FAIR data advantages to standardisation and utilising existing data infrastructure
- Share challenges and solutions in developing and adopting a metadata standard for a new technology
- Discuss and hear from workshop participants the challenges for projects based in Africa relating to spatial data, metadata standards, and data archiving
- Cluster challenges thematically and share resources, existing working groups, networks and tools for solving challenges
Learning Outcomes:
- Understand the advantages and disadvantages of the different metadata standards, file formats, and analysis methodologies in spatial transcriptomics
- Learn the metadata and data expectations of key spatial transcriptomics archives, and how to submit data to the archives
- Take advantage of personalised feedback for individual issues, be guided to solutions (tools, organisations, networks) for specific spatial data, metadata standard, and data archiving issues
Target Audience:
Researchers, data stewards, data managers generating, curating or integrating spatial transcriptomics data.
Prerequisites:
It would be advantageous to have an understanding of spatial transcriptomics or data archiving.
Capacity: 30
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