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

Content Provider	PubMed Central
Author	Rees, Tony
Editor	Diego, Fontaneto
Copyright Year	2014
Abstract	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.
Related Links	http://dx.doi.org/10.1371/journal.pone.0107510
Starting Page	107510
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	9
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-09-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

Quantifying the Consistency of Scientific Databases

A Hybrid CPU/GPU Pattern-Matching Algorithm for Deep Packet Inspection

A Novel Tracking Algorithm via Feature Points Matching

Using an Improved SIFT Algorithm and Fuzzy Closed-Loop Control Strategy for Object Recognition in Cluttered Scenes

WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online Taxonomic Backbone data

Dispec: A Novel Peptide Scoring Algorithm Based on Peptide Matching Discriminability

AliquotG: An Improved Heuristic Algorithm for Genome Aliquoting

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

Similar Documents

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

Quantifying the Consistency of Scientific Databases

A Hybrid CPU/GPU Pattern-Matching Algorithm for Deep Packet Inspection

A Novel Tracking Algorithm via Feature Points Matching

Using an Improved SIFT Algorithm and Fuzzy Closed-Loop Control Strategy for Object Recognition in Cluttered Scenes

WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online Taxonomic Backbone data

Dispec: A Novel Peptide Scoring Algorithm Based on Peptide Matching Discriminability

AliquotG: An Improved Heuristic Algorithm for Genome Aliquoting

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