A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape

Area of Science:

• Plant genomics
• Bioinformatics
• Data science

Background:

• Integrating transcriptomic experiments for gene expression analysis is complex.
• A unified access point for diverse gene expression measurements is needed.
• Grapevine (Vitis vinifera) transcriptomic data is fragmented across platforms.

Purpose of the Study:

• To update VESPUCCI, an integrated database for grapevine gene expression data, to be FAIR-compliant.
• To provide a centralized and accessible repository for all public grapevine transcriptomic experiments.
• To facilitate flexible analysis of gene expression data through standardized access and normalization.

Main Methods:

• Updated VESPUCCI database to comply with FAIR data principles (Findable, Accessible, Interoperable, Reusable).
• Integrated all public grapevine gene expression data from microarray and RNA-seq platforms.
• Developed a COMPASS GraphQL interface for data querying.
• Implemented multiple data normalization methodologies.
• Manually curated sample annotations using standard formats and ontologies.

Main Results:

• VESPUCCI is now FAIR-compliant, enhancing data discoverability and reusability.
• The database integrates comprehensive public grapevine transcriptomic data.
• Flexible data access and analysis are enabled via the GraphQL interface and varied normalization options.
• Manually curated annotations ensure data quality and standardization.

Conclusions:

• The updated VESPUCCI database provides seamless querying and analysis of grapevine gene expression (meta)data.
• It can be integrated into existing bioinformatics workflows and tools.
• VESPUCCI is freely accessible, supporting diverse user needs and expertise levels for grapevine research.