Padhoc

Padhoc generates custom biological pathway representations from user-provided keywords to reconstruct pathways tailored to the user's research context.

Key Features:

• Natural Language Processing (NLP): Interpret keywords for pathway generation.
• Database Knowledge Extraction: Gather relevant biological data from databases.
• Orthology Search Algorithms: Identify homologous genes across species.
• Graph Algorithms: Construct coherent pathway structures.

Scientific Applications:

• E. coli Pathways: Reconstruct well-established pathways for validation.
• New Organisms: Create novel pathways for model organisms and non-model species.

Methodology:

Padhoc integrates natural language processing, database knowledge extraction, orthology search algorithms, and graph algorithms to generate custom biological pathway representations from user-defined keywords.