BBMRI-NL catalog

BBMRI-NL catalog provides a MOLGENIS-based database to manage and enable access to collections of biomaterials and associated omics data for biomedical research including next-generation sequencing, genome-wide association studies (GWAS), quantitative trait loci (QTL) analysis, proteomics, and biobanking.

Key Features:

• Model-Driven Development: Uses the MOLGENIS model-driven approach to define biological data structures and translate concise models into software components.
• Automated Code Generation: The MOLGENIS generator suite converts XML model definitions into databases, exchange formats, and scriptable interfaces, automating software component creation.
• Customization and Flexibility: Supports a plug-in mechanism to customize both the generator suite and generated products.
• Optimized Database Backend: Generates an optimized database backend for efficient biomedical data management and retrieval.
• Programming Interfaces: Provides programmatic access via R, Java, SOAP, REST/JSON, and RDF.
• Data Exchange Formats: Supports tab-delimited file formats for data upload and exchange.
• Enhanced Existing Databases: Includes the ExtractModel procedure to integrate MOLGENIS-generated interfaces into existing databases.

Scientific Applications:

• Next-Generation Sequencing: Supports management and prototyping of next-generation sequencing datasets.
• Genome-Wide Association Studies (GWAS): Facilitates data management and prototype systems for GWAS.
• Quantitative Trait Loci (QTL) Analysis: Supports data management and prototyping for QTL analysis.
• Proteomics: Enables management and prototyping of proteomics datasets.
• Biobanking: Supports cataloging and access to biobanking specimens and associated metadata.

Methodology:

Implements the MOLGENIS model-driven approach and generator suite to translate XML-defined models into databases, exchange formats, and scriptable interfaces, reusing shared modeling languages and generators for quality assurance and including the ExtractModel procedure for existing databases.