Ten quick tips for biocuration

Tang, Y. Amy; Pichler, Klemens; Füllgrabe, Anja; Lomax, Jane; Malone, James; Muñoz-Torres, Monica; Vasant, Drashtti; Williams, Eleanor; Haendel, Melissa

doi:10.1371/journal.pcbi.1006906

Cited by 28 publications

(14 citation statements)

References 17 publications

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“…Because gene expression is complex, we need to be careful at all steps of this sharing: how the data is curated, how it is analysed, and how it is presented to users. Expert manual curation is at the core of providing trustworthy information [66][67][68][69] . It is key to certify that expression data is from healthy wild-type samples, and to annotate precisely and accurately to anatomy, stage, sex and strain.…”

Section: Discussionmentioning

confidence: 99%

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Bastian

Roux

Niknejad³

et al. 2020

Preprint

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Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as "healthy" or not). Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Several tools are available, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.

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Section: Discussionmentioning

confidence: 99%

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Bastian

Roux

Niknejad³

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…A restrictive license, in this context, is any license that places additional requirements or caveats on use of the data. Investment in data citation, data publication, microannotation, and nanopublication [ 39 – 44 ] will reduce the need for the restrictive licenses and nonstandard use agreements that are often in place to track reuse and impact. A global system of interconnected data with automated methods of tracking use and apportioning credit requires standardized, machine-readable licensing and data use agreements.…”

Section: Foundational Infrastructure Componentsmentioning

confidence: 99%

From Reductionism to Reintegration: Solving society’s most pressing problems requires building bridges between data types across the life sciences

et al. 2021

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Decades of reductionist approaches in biology have achieved spectacular progress, but the proliferation of subdisciplines, each with its own technical and social practices regarding data, impedes the growth of the multidisciplinary and interdisciplinary approaches now needed to address pressing societal challenges. Data integration is key to a reintegrated biology able to address global issues such as climate change, biodiversity loss, and sustainable ecosystem management. We identify major challenges to data integration and present a vision for a “Data as a Service”-oriented architecture to promote reuse of data for discovery. The proposed architecture includes standards development, new tools and services, and strategies for career-development and sustainability.

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“…Принцип 1. Один уникальный изолят -одна строка таблицы В современных условиях рекомендуется максимально использовать автоматическую обработку данных [16]. Большинство программ требует, чтобы в исходных та блицах заголовочная строка была одноуровневая, без слияния ячеек [17].…”

Section: базовые принципы и рекомендации для организации данных монитunclassified

Data handling as a basis for local antimicrobial resistance surveillance

Vinogradova

Kuzmenkov

2020

CMAC

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Continuing trends of antimicrobial resistance growth require a set of countermeasures, of which antimicrobial resistance surveillance at the global, national, and local levels plays one of the most important roles. Local surveillance systems are the most significant in controlling the changes in susceptibility of microorganisms in specific settings and contribute to the necessary activities, including prevention of epidemics. This paper presents basic principles and recommendations for handling antimicrobial resistance surveillance data, provides examples of table completion and metadata quick guide. A focus is made on specific issues and problems associated with surveillance data handling and the ways to resolve those problems are proposed.

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Ten quick tips for biocuration

Cited by 28 publications

References 17 publications

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

From Reductionism to Reintegration: Solving society’s most pressing problems requires building bridges between data types across the life sciences

Data handling as a basis for local antimicrobial resistance surveillance

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