Xenbase - Curation

组件：策展 项目摘要/摘要 Xenbase的任务是整理Xenopus研究的数据并生成最终的 此关键模式生物体的参考数据集。为了完成这项任务，Xenbase中的数据 必须是准确的、全面的和最新的注释。Xenbase包含许多不同的 数据类型(基因组和基因、正构学、RNA、蛋白质、基因组数据(RNA/芯片序列)、基因 表达，基因功能，解剖，试剂(MO和抗体)，突变和转基因株系， 表型和疾病关联)，数据来自已发表的文献、直接社区 提交的材料和其他材料。我们使用本体来管理、注释和索引数据类型(即， 标准化词汇表)，这使数据在计算机上可读并符合公允标准。这 允许我们将Xenbase内的不同数据类型相互关联，并将Xenopus数据链接到人类 和其他模式生物。我们的文献模块包含52,000篇非洲爪哇研究论文。 我们已经管理了大约4800个主要用于基因表达模式、转基因品系和 试剂，但我们估计大约有10,000篇额外的论文包含有价值的数据，包括 表型和围棋，这是我们在这次更新中的两个主要管理优先事项。另一个主要目标是 整理与NCBI基因中的非洲爪哇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的计划将是这次更新中的第三个主要策划工作。 为了管理大量的新数据，我们的管理工作流实现了几项创新 半自动管道、文本挖掘和机器学习。我们的策划目标是留下来 目前有了新的出版物，清理积压的有待整理的论文(优先考虑 人类疾病的表型/模型)，并添加额外的数据类型，包括不同的基因组 数据集。 目的1.继续整理非洲爪哇研究数据。 目的2.研究非洲爪哇的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.