GenoSurf

GenoSurf enables unified semantic search across integrated genomic metadata to support precise discovery of datasets for genomic, clinical, and epigenomic analyses.

Key Features:

• Multi-Ontology Semantic Search: Enriches metadata values using multiple ontologies and supports configurable levels of ontological enrichment to improve search precision.
• Consolidated Metadata Access: Aggregates approximately 40 million metadata entries from data providers including The Cancer Genome Atlas (TCGA), Encyclopedia of DNA Elements (ENCODE), Roadmap Epigenomics, GENCODE, and RefSeq.
• Combined Attribute and Keyword Search: Supports integrated attribute-based and keyword-based search modalities for flexible queries over metadata.
• Dataset Linking and Integration: Maps metadata to original accession IDs and source URLs and can serve as a component for executing complex queries over genomic regions and associated metadata.

Scientific Applications:

• Secondary data discovery: Facilitates identification of existing genomic datasets for reuse in secondary analyses.
• Clinical genomics: Enables retrieval of clinical datasets (for example from TCGA) relevant to translational and clinical research.
• Functional and experimental genomics: Supports locating experimental datasets from resources such as ENCODE and Roadmap Epigenomics for functional studies.
• Genomic annotation: Assists selection and comparison of annotation-related datasets that reference GENCODE and RefSeq.
• Epigenomic investigations: Supports retrieval of epigenomic datasets for analyses of chromatin and regulatory features.

Methodology:

Aggregates metadata from multiple genomic data sources and performs semantic enrichment of metadata values using multiple ontologies to enable attribute- and keyword-based search and mapping to source accession IDs and URLs.