ZebrafishMine

ZebrafishMine integrates diverse zebrafish biological datasets from sources including ZFIN and Panther via the InterMIne data warehouse system to enable integrative analyses of gene function, development, physiology, and disease modeling.

Key Features:

• Data Integration and Extensibility: Uses the InterMIne data warehouse system to aggregate datasets from multiple sources including ZFIN and Panther and supports incorporation of new data types via an extensible data model.
• Customizable Query Facility: Provides a flexible query builder supporting genomic region searches and a set of widgets for statistical analyses across integrated datasets.
• Data Export Options: Exports query results in multiple commonly used file formats for downstream analysis.
• Extensible Framework and Web Services: Implements an extensible framework and exposes web services with client libraries available in five programming languages.

Scientific Applications:

• Gene Function Analysis: Facilitates integrative queries and cross-dataset analyses to investigate gene function in zebrafish.
• Developmental Biology: Supports analyses relevant to zebrafish development by combining relevant datasets.
• Physiological Studies: Enables exploration of physiological data in the context of integrated zebrafish datasets.
• Disease Modeling and Comparative Biology: Aids in disease modeling and evolutionary biology investigations using curated ZFIN and Panther data.

Methodology:

Aggregates heterogeneous biological datasets into a unified database using the InterMIne data warehouse system, employs an extensible data model to incorporate new data types, and exposes customizable query and statistical analysis tools.