Xenbase - Curation

组件：固化 项目总结/摘要 Xenbase的任务是整理来自Xenopus研究的数据， 这个关键模式生物的参考数据集。为了完成这一任务，Xenbase中的数据 必须准确注释、全面和最新。Xenbase包含许多不同的 数据类型（基因组和基因、同源性、RNA、蛋白质、基因组数据（RNA/ChIP-seq）、基因 表达，基因功能，解剖学，试剂（MO和抗体），突变体和转基因系， 表型和疾病关联），数据来自已发表的文献， 提交和其他。我们使用本体（即， 标准化词汇表），这使得数据计算机可读并且符合FAIR。这 允许我们在Xenbase中将不同的数据类型相互关联，并将Xenopus数据与人类联系起来 和其他模式生物。我们的文献模块包含> 52，000篇非洲爪蟾研究论文。 我们已经策划了约4,800个这些主要是基因表达模式，转基因品系， 试剂，但我们估计约有10，000份额外的论文包含有价值的数据，包括 表型和GO，这是我们在这次更新中的两个主要策展重点。另一个主要目标是 在NCBI Gene中管理与Xenopus RNA-seq和ChIP-seq数据集相关的元数据 Expression Omnibus（GEO），以便我们可以处理数据并使其在Xenbase上可用。 我们支持单细胞转录组学的计划将是这次更新的第三个主要策展工作。 为了管理这一数量的新数据，我们的策展工作流程实现了几个创新的 半自动化管道，短信挖掘和机器学习。我们的策展目标是 与新出版物同步，清理待整理文件的积压（优先考虑那些 与人类疾病的表型/模型），并添加额外的数据类型，包括不同的组学 数据集。 目标1.继续管理非洲爪蟾的研究数据。 目标二。管理非洲爪蟾表型和人类疾病模型。 目标3。策划新的组学和细胞生物学数据。

Component: CURATION PROJECT SUMMARY/ABSTRACT Xenbase’s mandate is to curate the data from Xenopus research and generate the definitive reference dataset for this key model organism. In order to fulfill this mandate, the data in Xenbase must be accurately annotated, comprehensive, and up-to-date. Xenbase contains many different data types (genomes and genes, orthology, RNA, proteins, genomic data (RNA/ChIP-seq), gene expression, gene function, anatomy, reagents (MOs and antibodies), mutant and transgenic lines, phenotypes and disease associations) that data come from published literature, direct community submissions and from other. We curate, annotate and index data types using ontologies (i.e., standardized vocabularies), which make the data computer readable and FAIR compliant. This allows us to inter-relate different data types within Xenbase and to link Xenopus data to humans and other model organisms. Our literature module contains >52,000 Xenopus research papers. We have curated ~4,800 of these primarily for gene expression patterns, transgenic lines and reagents, yet we estimate that about 10,000 additional papers contain valuable data, including phenotypes and GO, two of our main curation priorities in this renewal. Another major goal is to curate the metadata associated with Xenopus RNA-seq and ChIP-seq datasets in the NCBI Gene Expression Omnibus (GEO) so that we can process the data and make it available on Xenbase. Our plan to support single cell transcriptomics will be a third major curation effort in this renewal. In order to manage this volume of new data, our curation workflow implements several innovative semi-automated pipelines, texting mining and machine learning. Our curation goals are to stay current with new publications, clear the backlog of to-be-curated papers (giving priority to those with phenotypes/models of human disease), and add additional data types, including diverse omic data sets. Aim 1. Continue curation of Xenopus research data. Aim 2. Curate Xenopus phenotypes and human disease models. Aim 3. Curate new omics and cell biological data.