Dataset Information

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.

ABSTRACT: GenBank, 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.

SUBMITTER: Chen Q

PROVIDER: S-EPMC5225397 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.

Chen Qingyu Q Zobel Justin J Verspoor Karin K

Database : the journal of biological databases and curation 20170110

GenBank, 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, ...[more]

PMID: 28077566

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Project description:BackgroundFinding duplicates is an important phase of systematic review. However, no consensus regarding the methods to find duplicates has been provided. This study aims to describe a pragmatic strategy of combining auto- and hand-searching duplicates in systematic review and to evaluate the prevalence and characteristics of duplicates.Methods and findingsLiteratures regarding portal vein thrombosis (PVT) and Budd-Chiari syndrome (BCS) were searched by the PubMed, EMBASE, and Cochrane library databases. Duplicates included one index paper and one or more redundant papers. They were divided into type-I (duplicates among different databases) and type-II (duplicate publications in different journals/issues) duplicates. For type-I duplicates, reference items were further compared between index and redundant papers. Of 10936 papers regarding PVT, 2399 and 1307 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 11.0% (1201/10936) and 6.1% (665/10936), respectively. They included 3431 type-I and 275 type-II duplicates. Of 11403 papers regarding BCS, 3275 and 2064 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 14.4% (1640/11403) and 9.1% (1039/11403), respectively. They included 5053 type-I and 286 type-II duplicates. Most of type-I duplicates were identified by auto-searching method (69.5%, 2385/3431 in PVT literatures; 64.6%, 3263/5053 in BCS literatures). Nearly all type-II duplicates were identified by hand-searching method (94.9%, 261/275 in PVT literatures; 95.8%, 274/286 in BCS literatures). Compared with those identified by auto-searching method, type-I duplicates identified by hand-searching method had a significantly higher prevalence of wrong items (47/2385 versus 498/1046, p<0.0001 in PVT literatures; 30/3263 versus 778/1790, p<0.0001 in BCS literatures). Most of wrong items originated from EMBASE database.ConclusionGiven the inadequacy of a single strategy of auto-searching method, a combined strategy of auto- and hand-searching methods should be employed to find duplicates in systematic review.

Project description:IntroductionAntibiotics are the most commonly prescribed drug class in children. Real-world data mining on the paediatric population showed potential associations between antibiotic use and acute liver injury.ObjectiveWe assessed risk estimates of liver injury associated with antibiotic use in children and adolescent outpatients.MethodsA large, multi-database, population-based, case-control study was performed in people <18 years of age from two European countries (Italy and The Netherlands) during the period 2000-2008. All potential cases of liver injury were automatically extracted from three databases and then manually validated based on Council for International Organizations of Medical Sciences (CIOMS) criteria and by exclusion of all competing causes for liver injury. Up to 100 control participants were sampled for each case and were matched on index date of the event, age, sex and database. Based on prescription data, antibiotic exposure was categorized as current, recent or past use by calculating the time period between the end of prescription and the index date. Multivariate conditional logistic regression analyses were applied to calculate odds ratios (ORs) as a measure of the association (with 95% confidence interval [CI]).ResultsWe identified 938 cases of liver injury and matched to 93,665 controls. Current use of overall antibiotics is associated with a threefold increased risk of liver injury compared with past use (adjusted OR [ORadj] 3.22, 95% CI 2.57-4.03). With regard to individual antibiotics, the risk is significantly increased for current use of each antibiotic (p < 0.005), except for azithromycin. Risk estimates vary from the lowest ORadj of 1.86 (95% CI 1.08-3.21) for amoxicillin to the highest ORadj of 24.16 (95% CI 11.78-49.54) for cotrimoxazole (i.e. sulphamethoxazole/trimethoprim) and 26.70 (95% CI 12.09-58.96) for ceftriaxone. Sensitivity analyses confirm the associations for ceftriaxone, cotrimoxazole, and clarithromycin.ConclusionAntibiotic-induced liver injury in children is heterogeneous across the use of individual antibiotics. When prescribing ceftriaxone, cotrimoxazole and clarithromycin in children, paediatricians should definitely be aware of their potential risk of liver injury, even if for short periods.

Dataset Information

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.

Publications

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study.

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