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Author: tpoisot

manuscript.typ

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 *Abstract*:
 
-`NCBITaxonomy.jl` is a Julia package designed to address the complex challenges of taxonomic name reconciliation using a local copy of the NCBI taxonomic backbone @Federhen2012NcbTax @Schoch2020NcbTax. The package provides advanced name matching capabilities that handle common issues in taxonomic data, including synonyms, homonyms, vernacular names, nomenclatural changes, and typographical errors. Core functionalities include case-insensitive search, customizable fuzzy string matching, and taxonomically-restricted searches. The package implements a robust exception system that explicitly handles ambiguous matches without interrupting workflow execution, enabling automated processing of large datasets. `NCBITaxonomy.jl` works with Julia 1.6 and up, uses Apache Arrow format for efficient local storage. It provides lineage navigation and taxonomic distance functions. The package has been successfully deployed in large-scale projects for automated name reconcilation and cleaning, demonstrating its effectiveness for high-throughput name reconciliation across heterogeneous biological datasets. The design prioritizes programmatic access over command-line usage, making it well-suited for integration into bioinformatics pipelines requiring reliable taxonomic standardization.
+`NCBITaxonomy.jl` is a Julia package designed to address the complex challenges of taxonomic name reconciliation using a local copy of the NCBI taxonomic backbone @Federhen2012NcbTax @Schoch2020NcbTax. The package provides advanced name matching capabilities that handle common issues in taxonomic data, including synonyms, homonyms, vernacular names, nomenclatural changes, and typographical errors. Core functionalities include case-insensitive search, customizable fuzzy string matching, and taxonomically-restricted searches. The package implements a robust exception system that explicitly handles ambiguous matches without interrupting workflow execution, enabling automated processing of large datasets. `NCBITaxonomy.jl` works with Julia 1.6 and up, uses Apache Arrow format for efficient local storage. It provides lineage navigation and taxonomic distance functions. The package has been successfully deployed in large-scale projects for automated name reconciliation and cleaning, demonstrating its effectiveness for high-throughput name reconciliation across heterogeneous biological datasets. The design prioritizes programmatic access over command-line usage, making it well-suited for integration into bioinformatics pipelines requiring reliable taxonomic standardization.
 
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