Dataset Information

Expanded and updated data and a query pipeline for iBeetle-Base.

ABSTRACT: The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/.

SUBMITTER: Donitz J

PROVIDER: S-EPMC5753255 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Expanded and updated data and a query pipeline for iBeetle-Base.

Dönitz Jürgen J Gerischer Lizzy L Hahnke Stefan S Pfeiffer Stefan S Bucher Gregor G

Nucleic acids research 20180101 D1

The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages o ...[more]

PMID: 29069517

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Project description:BackgroundPatient decision aids should help people make evidence-informed decisions aligned with their values. There is limited guidance about how to achieve such alignment.PurposeTo describe the range of values clarification methods available to patient decision aid developers, synthesize evidence regarding their relative merits, and foster collection of evidence by offering researchers a proposed set of outcomes to report when evaluating the effects of values clarification methods.Data sourcesMEDLINE, EMBASE, PubMed, Web of Science, the Cochrane Library, and CINAHL.Study selectionWe included articles that described randomized trials of 1 or more explicit values clarification methods. From 30,648 records screened, we identified 33 articles describing trials of 43 values clarification methods.Data extractionTwo independent reviewers extracted details about each values clarification method and its evaluation.Data synthesisCompared to control conditions or to implicit values clarification methods, explicit values clarification methods decreased the frequency of values-incongruent choices (risk difference, -0.04; 95% confidence interval [CI], -0.06 to -0.02; P < 0.001) and decisional conflict (standardized mean difference, -0.20; 95% CI, -0.29 to -0.11; P < 0.001). Multicriteria decision analysis led to more values-congruent decisions than other values clarification methods (χ2 = 9.25, P = 0.01). There were no differences between different values clarification methods regarding decisional conflict (χ2 = 6.08, P = 0.05).LimitationsSome meta-analyses had high heterogeneity. We grouped values clarification methods into broad categories.ConclusionsCurrent evidence suggests patient decision aids should include an explicit values clarification method. Developers may wish to specifically consider multicriteria decision analysis. Future evaluations of values clarification methods should report their effects on decisional conflict, decisions made, values congruence, and decisional regret.

Dataset Information

Expanded and updated data and a query pipeline for iBeetle-Base.

Publications

Expanded and updated data and a query pipeline for iBeetle-Base.

Similar Datasets

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