Computer Science Department, University of Crete, Voutes Campus, 70013 Heraklion, Crete, Greece.
Gnosis Data Analysis PC, Palaiokapa 64, 71305 Heraklion, Crete, Greece.
Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay011.
Biotechnology revolution generates a plethora of omics data with an exponential growth pace. Therefore, biological data mining demands automatic, 'high quality' curation efforts to organize biomedical knowledge into online databases. BioDataome is a database of uniformly preprocessed and disease-annotated omics data with the aim to promote and accelerate the reuse of public data. We followed the same preprocessing pipeline for each biological mart (microarray gene expression, RNA-Seq gene expression and DNA methylation) to produce ready for downstream analysis datasets and automatically annotated them with disease-ontology terms. We also designate datasets that share common samples and automatically discover control samples in case-control studies. Currently, BioDataome includes ∼5600 datasets, ∼260 000 samples spanning ∼500 diseases and can be easily used in large-scale massive experiments and meta-analysis. All datasets are publicly available for querying and downloading via BioDataome web application. We demonstrate BioDataome's utility by presenting exploratory data analysis examples. We have also developed BioDataome R package found in: https://github.com/mensxmachina/BioDataome/.Database URL: http://dataome.mensxmachina.org/.
生物技术革命产生了大量的组学数据，其增长速度呈指数级增长。因此，生物数据挖掘需要自动的、“高质量”的策展工作，将生物医学知识组织到在线数据库中。BioDataome 是一个统一预处理和疾病注释的组学数据库，旨在促进和加速公共数据的再利用。我们对每个生物集市（微阵列基因表达、RNA-Seq 基因表达和 DNA 甲基化）都采用相同的预处理管道，生成可用于下游分析的数据集，并使用疾病本体论术语对其进行自动注释。我们还指定了共享共同样本的数据集，并在病例对照研究中自动发现对照样本。目前，BioDataome 包含约 5600 个数据集，约 260000 个样本，涵盖约 500 种疾病，可轻松用于大规模的大规模实验和荟萃分析。所有数据集均可通过 BioDataome 网络应用程序进行查询和下载。我们通过展示探索性数据分析示例来演示 BioDataome 的实用性。我们还开发了可在：https://github.com/mensxmachina/BioDataome/ 找到的 BioDataome R 包。数据库 URL：http://dataome.mensxmachina.org/。
