Taxamatch, an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases

• Published in: PloS one Vol. 9; no. 9; p. e107510
• Main Author: Rees, Tony
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 23.09.2014; Public Library of Science (PLoS)
• Subjects: Algorithms; Archives & records; Biodiversity; Biology and Life Sciences; Classification - methods; Computer and Information Sciences; Data systems; Databases, Factual; Dictionaries; Dynamic programming; First principles; Genera; Matching; N-Gram language models; Names; Phonetics; Physical Sciences; Ports; Product development; Recall; Species; Spelling errors; Taxonomy
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0107510

Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical.