APE

APE composes automated bioinformatics workflows by combining semantically annotated tools and domain ontologies to synthesize purpose-specific analysis pipelines.

Key Features:

• Domain Adaptability: Integrates a domain ontology and semantically annotated tools to configure workflows for new application domains.
• Semantic Annotations: Uses semantic annotations from the bio.tools registry and terms from EDAM (Extensible Data Annotation Model) to define data types, formats, and operations for tool integration.
• Automated Workflow Synthesis: Automatically generates workflows from specified available inputs, desired outputs, and constraints.
• Exploration of Tool Combinations: Systematically explores combinations of tools by accessing the repository of over 17,000 computational tools in bio.tools.
• Control Mechanisms for Workflow Quality: Applies tool filters, configuration options, and workflow constraints to mitigate variability in annotation quality and reduce erroneous combinations.

Scientific Applications:

• Proteomics: Composes multistep analysis workflows for proteomics data by integrating compatible tools and data formats.
• Cross-domain Life Sciences Research: Adapts workflow composition to diverse life sciences domains via domain ontologies and semantically annotated tool descriptions.

Methodology:

Represents tools and data using ontologies and semantic annotations (EDAM) from bio.tools, performs automated workflow synthesis from specified inputs, outputs, and constraints, systematically explores tool combinations, and applies tool filters, configuration options, and workflow constraints.