Padhoc: a computational pipeline for pathway reconstruction on the fly

Area of Science:

• Bioinformatics
• Computational Biology
• Systems Biology

Background:

• Molecular pathway databases are crucial for biological research and analyzing high-throughput data.
• Existing databases struggle to stay current with rapid biomedical advancements.
• Current pathway representations may not align with specific researcher needs, lacking user-defined flexibility.

Purpose of the Study:

• To introduce Padhoc, a novel pipeline for the ad hoc reconstruction of molecular pathways.
• To provide researchers with a tool for creating customized pathway representations tailored to their specific needs.
• To overcome the limitations of static, pre-defined pathway databases.

Main Methods:

• Padhoc utilizes user-provided keywords to initiate pathway reconstruction.
• The pipeline integrates natural language processing, database knowledge extraction, and orthology search.
• Advanced graph algorithms are employed to construct navigable pathways.

Main Results:

• Padhoc successfully reconstructs well-established pathways in *Escherichia coli*.
• The tool demonstrates usability for creating novel pathways in model (human) and non-model (sweet orange) organisms.
• Generated pathways are tailored to user-defined keywords and research requirements.

Conclusions:

• Padhoc offers a flexible solution for creating user-defined molecular pathways.
• The pipeline enhances the utility of pathway information for diverse biological research applications.
• Padhoc facilitates the exploration of biological pathways beyond the scope of existing databases.