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dc.contributor.authorChen, Q
dc.contributor.authorZobel, J
dc.contributor.authorVerspoor, K
dc.date.accessioned2020-12-22T03:26:49Z
dc.date.available2020-12-22T03:26:49Z
dc.date.issued2017-01-10
dc.identifierpii: baw163
dc.identifier.citationChen, Q., Zobel, J. & Verspoor, K. (2017). Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2017 (1), https://doi.org/10.1093/database/baw163.
dc.identifier.issn1758-0463
dc.identifier.urihttp://hdl.handle.net/11343/257855
dc.description.abstractGenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed. Existing duplicate detection methods in bioinformatics only address specific duplicate types, with inconsistent assumptions; and the impact of duplicates in bioinformatics databases has not been carefully assessed, making it difficult to judge the value of such methods. Our goal is to assess the scale, kinds and impact of duplicates in bioinformatics databases, through a retrospective analysis of merged groups in INSDC databases. Our outcomes are threefold: (1) We analyse a benchmark dataset consisting of duplicates manually identified in INSDC-a dataset of 67 888 merged groups with 111 823 duplicate pairs across 21 organisms from INSDC databases - in terms of the prevalence, types and impacts of duplicates. (2) We categorize duplicates at both sequence and annotation level, with supporting quantitative statistics, showing that different organisms have different prevalence of distinct kinds of duplicate. (3) We show that the presence of duplicates has practical impact via a simple case study on duplicates, in terms of GC content and melting temperature. We demonstrate that duplicates not only introduce redundancy, but can lead to inconsistent results for certain tasks. Our findings lead to a better understanding of the problem of duplication in biological databases.Database URL: the merged records are available at https://cloudstor.aarnet.edu.au/plus/index.php/s/Xef2fvsebBEAv9w.
dc.languageEnglish
dc.publisherOXFORD UNIV PRESS
dc.titleDuplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study
dc.typeJournal Article
dc.identifier.doi10.1093/database/baw163
melbourne.affiliation.departmentChancellery Research
melbourne.affiliation.departmentComputing and Information Systems
melbourne.source.titleDatabase: the journal of biological databases and curation
melbourne.source.volume2017
melbourne.source.issue1
melbourne.identifier.arcDP150101550
dc.rights.licenseCC BY
melbourne.elementsid1179621
melbourne.contributor.authorZobel, Justin
melbourne.contributor.authorVerspoor, Cornelia
melbourne.contributor.authorChen, Qingyu
dc.identifier.eissn1758-0463
melbourne.identifier.fundernameidAUST RESEARCH COUNCIL, DP150101550
melbourne.accessrightsOpen Access


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