Padhoc: a computational pipeline for pathway reconstruction on the fly

Salvador Casaní-Galdón, Cecile Pereira, Ana Conesa
2020 Bioinformatics  
Motivation Molecular pathway databases represent cellular processes in a structured and standardized way. These databases support the community-wide utilization of pathway information in biological research and the computational analysis of high-throughput biochemical data. Although pathway databases are critical in genomics research, the fast progress of biomedical sciences prevents databases from staying up-to-date. Moreover, the compartmentalization of cellular reactions into defined
more » ... reflects arbitrary choices that might not always be aligned with the needs of the researcher. Today, no tool exists that allow the easy creation of user-defined pathway representations. Results Here we present Padhoc, a pipeline for pathway ad hoc reconstruction. Based on a set of user-provided keywords, Padhoc combines natural language processing, database knowledge extraction, orthology search and powerful graph algorithms to create navigable pathways tailored to the user's needs. We validate Padhoc with a set of well-established Escherichia coli pathways and demonstrate usability to create not-yet-available pathways in model (human) and non-model (sweet orange) organisms. Availability and implementation Padhoc is freely available at https://github.com/ConesaLab/padhoc. Supplementary information Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btaa811 pmid:33381819 fatcat:e7te5paykvegvdvdq3mclmssa4