PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science

Abstract

SummaryThe nature of taxonomic science and the scientific nomenclature system makes it difficult to use scientific names as identifiers without running into complications. To facilitate high-throughput analysis of biological data involving scientific names, we designed PhyloSophos, a Python package that takes into account the properties of scientific names and taxonomic systems to map name inputs to the entries within the reference database of choice. We would like to present three case-studies which demonstrates how our implementations, including rule-based pre-processing and recursive mapping could improve mapping performance and information availability. We expect PhyloSophos to help with the systematic processing of poorly digitized and curated biological data, such as biodiversity information and ethnopharmacological resources, thus enabling full-scale bioinformatics analysis using these data. Availability and implementationPhyloSophos is available at GitHub https://github.com/mhcho4096/phylosophos. Supplementary informationSupplementary data are available at Bioinformatics online.