ontocount

ontocount counts and analyzes ontology terms in biological datasets to quantify and categorize ontology annotations within the EMBOSS framework.

Key Features:

• Integration with EMBOSS: Operates within the EMBOSS framework and integrates with its command-line applications.
• Extensible C programming libraries: Leverages EMBOSS C libraries to enable extension and development of new functionality.
• Customization via ACD files and API: Supports ACD file–based interface customization and EMBOSS API programming for application development.
• Database configuration and management: Provides procedures for database setup and configuration under EMBOSS to manage biological data used for ontology term analyses.

Scientific Applications:

• Gene expression studies: Quantifies and categorizes ontology annotations associated with gene expression datasets.
• Proteomics: Counts and organizes ontology terms linked to proteomics data annotations.
• Systems biology: Enables summarization of ontology-based annotations for systems-level analyses.

Methodology:

Runs within the EMBOSS framework using the EMBOSS command-line interface, leverages EMBOSS C programming libraries, supports ACD file–based customization, and uses EMBOSS database configuration procedures.