Penn TMC: Data Analysis Core

Penn TMC：数据分析核心

• 批准号: 10269927
• 负责人: Alison Marie Pouch
• 金额: $ 19.37万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-24 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10269927
• 关键词: 3-Dimensional; Anatomic Models; Anatomy; Area; Cells; Cellular biology; Clinical; Communities; Computational Biology; Controlled Vocabulary; Data; Data Analyses; Data Provenance; Data Set; Databases; Deposition; Generations; Genome; Goals; Human; Human BioMolecular Atlas Program; Image; Individual; Informatics; Institutes; Maps; Metadata; Methods; Modeling; Molecular; National Human Genome Research Institute; Ontology; Organ; Output; Periodicity; Procedures; Process; Protocols documentation; Quality Control; Reagent; Resources; Sampling; Support System; System; Tissues; United States National Institutes of Health; Work; analysis pipeline; biobank; computational anatomy; computer infrastructure; computerized data processing; data curation; data modeling; data repository; data submission; digital models; experience; female reproductive system; frontier; genome sciences; image processing; imaging system; indexing; metadata standards; molecular scale; multimodal data; multimodality; operation; programs; public repository; spatial integration; success; transcriptomics

The proper curation of data and processes for a large-scale public resource generation project is critical to the success of projects like the HuBMAP TMCs. The goal of the Data Analysis Core is to support the resource generation operations of the Penn Center for Multiscale Molecular Map of the Female Reproductive System with data coordination. We will provide computational infrastructure to process all data, implement Quality Control (QC) procedures, and enable data provenance. We will develop metadata and provenance models of the clinical procedures, molecular procedures, and informatics procedures. We will also develop QC methods for all processes and implement automatic systems for QC checks. We will process all primary data, such as sequencing and image data, and prepare the data for deposition to HuBMAP HIVE groups and other public repositories. We will also provide analyses for the Center, including multi-modal integration and spatial integration. We will carry out data normalization, batch correction, alignments between datasets and across scales, as well as integration of multi-modal data types. We will develop a 3D digital model of the female reproductive system and use the model to guide spatial indexing of the samples as well as to align the molecular data to their spatial contexts. We will provide additional analytics specific to the project such as reconstructing periodic temporal dynamics. Finally, we will coordinate with HIVE to deposit and disseminate data, programs and analysis outputs, and material reagents. We will work with the HuBMAP HIVE groups to transform and QC the data to the standards of the consortium and deposit the data with the consortium. We will also work with the consortium to develop metadata standards, controlled vocabularies, ontologies, and other community standards. We will also document all protocols, reagents, tissue biobanks, programs, and analysis pipelines with data models and provide a public database for all associated information of the Penn Center.

大规模公共资源生成项目的数据和流程的正确管理至关重要 HuBMAP TMC 等项目的成功。数据分析核心的目标是支持 宾夕法尼亚大学女性多尺度分子图谱中心的资源生成操作 具有数据协调的生殖系统。我们将提供计算基础设施来处理所有 数据、实施质量控制 (QC) 程序并启用数据来源。我们将开发 临床程序、分子程序和信息学的元数据和来源模型 程序。我们还将开发所有流程的质量控制方法，并实施自动化系统 质量控制检查。我们将处理所有原始数据，例如测序和图像数据，并准备数据 用于存放到 HuBMAP HIVE 组和其他公共存储库。我们还将提供分析 中心包括多模态整合和空间整合。我们将进行数据标准化， 批量校正、数据集之间和跨尺度的对齐以及多模式集成 数据类型。我们将开发女性生殖系统的 3D 数字模型，并使用该模型 指导样本的空间索引以及将分子数据与其空间背景对齐。我们 将提供特定于该项目的额外分析，例如重建周期性时间动态。 最后，我们将与HIVE协调来存储和传播数据、程序和分析输出， 和材料试剂。我们将与 HuBMAP HIVE 小组合作，将数据转换和质量控制到 联合体标准，并将数据存入联合体。我们还将与 开发元数据标准、受控词汇、本体和其他社区的联盟 标准。我们还将记录所有方案、试剂、组织生物库、程序和分析 具有数据模型的管道，并为宾夕法尼亚大学的所有相关信息提供公共数据库 中心。