BioExtract

BioExtract enables creation, execution, and preservation of reproducible bioinformatic workflows that integrate distributed biomolecular databases and analytic tools for genomic data analysis.

Key Features:

• Workflow Creation: Records a series of analysis tasks including querying data sources, saving query results as searchable extracts, and executing local and web-accessible analytic tools.
• Data Integration: Integrates with NCBI nucleotide and protein databases, EMBL-Bank non-redundant nucleotide database, UniProt, and UniRef to consolidate biomolecular data.
• Analytic Tools Access: Provides access to preinstalled curated analytic tools and web services such as EMBOSS, BioMoby, and KEGG, and supports integration of local command-line tools via a client-side Java applet.
• Data Querying and Processing: Allows specification of data sources, execution of flexible queries, application of analytic tools to query results, and download and storage of result sets for reuse.
• Workflow Preservation: Automatically saves each analysis step and preserves sequences of steps as named, described, reproducible workflows that can be re-executed with original or modified inputs and parameters.
• Multi-format Interoperability: Supports multiple query languages and formats to enable use of outputs from one tool as inputs for another.
• Data Mash-up Consolidation: Consolidates and serves data in a mash-up format to integrate distributed sources for downstream analysis.

Scientific Applications:

• In silico genomic investigations: Integration of heterogeneous biomolecular databases for comparative and exploratory analyses.
• Workflow-based analyses: Construction and reuse of reproducible analysis pipelines that chain queries and analytic tools across resources.
• Reproducibility and reuse: Generation of shareable workflows that improve reproducibility and enable variant-parameter reanalysis in bioinformatics studies.

Methodology:

Operates as a data integration application that consolidates and serves data in a mash-up format, records executed tasks to create workflows, allows specification of data sources and execution of queries, applies analytic tools to query results, manages and stores result sets, and enables workflow re-execution with original or modified inputs and parameters.