Comprehensive, Flexible and FAIR Tools for the HuBMAP HIVE

摘要 人类生物分子图谱计划(HuBMAP)将重新定义我们对人类的理解 通过恢复多尺度的组织结构--解剖学、组织学和分子学，在 史无前例的分辨率，通过计算集成各种实验 测量。我们建议开发计算方法和工具，以便能够使用 HuBMAP收集了财团参与者、国际研究界和 大型软件和方法开发社区。我们的建议集中在三个关键方面 工具组成部分的说明：(1)社区参与：开发储存库， API、接口和架构，支持托管、发现和集成工具 由我们和其他人开发的图书馆。我们将特别强调确保这一点 流程是高效的，减少了重复工作，并使 一般开发人员社区。所有工具都将作为开放源码软件开发。(2) 创新工具开发：虽然我们打算尽可能多地依赖和使用现有工具 可能的话，我们还建议开发一套全面的创新工具，用于特定的 HuBMAP的长期愿景和数据带来的挑战。其中包括用于查询的工具 以及检索由HUBMAP、表情和图像分析方法收集的数据以及 库、用于分析地图的空间和时间数据的工具以及用于建模的工具 以及数据集成，以实现HuBMAP数据与海量数据的集成 其他可公开获得的生物数据。(3)灵活性：我们期待技术的改进 而组织测绘中心的具体计划的差异将导致额外的类型 过去我们没有为之设计工具的数据。因此，我们召集了一位经验丰富的 和不同的调查小组，他们都在工具开发方面拥有丰富的经验， 总而言之，它们跨越了潜在数据类型的范围。 我们的建议包括详细的计划，以确保我们开发和实施的工具 可查找、可访问、可互操作和可重复使用(公平)，并解决与验证相关的问题 工具的准确性和有用性、数据保密性和可重复性。工具组件可以正常工作 与其他配置单元组件紧密协作，以分发工具并与 开发商和国际研究界。

Abstract The Human BioMolecular Atlas Program (HuBMAP) will redefine our understanding of the human body by recovering multi-scale tissue organization -- anatomical, histological, and molecular, at unprecedented resolution, through computational integration of diverse experimental measurements. We propose to develop computational methods and tools to enable the use of HuBMAP collected data by consortium participants, the international research community and the large software and method development community. Our proposal is focused on three key directions for the Tools Component: (1) Community involvement: Development of repositories, APIs, interfaces and schemas to enable the hosting, discovery and integration of tools and libraries developed by us and others. We would put specific emphasis on making sure that this process is efficient, reduces duplicated efforts and transparent enabling involvement of the general developer community. All tools would be developed as open source software. (2) Innovative tool development: While we intend to rely and use existing tools as much as possible, we also propose to develop a comprehensive set of innovative tools for the specific challenges presented by the HuBMAP long term vision and data. These include tools for querying and retrieving data collected by the HUBMAP, expression and image analysis methods and libraries, tools for the analysis of spatial and temporal data from the MAP and tools for modeling and data integration which would enable the integration of HuBMAP data with the vast amounts of other publicly available biological data. (3) Flexibility: We expect that improved technology and variance in the specific plans of the Tissue Mapping Centers would lead to additional types of data that we have not designed tools for in the past. We have thus assembled an experienced and diverse group of investigators, all with significant experience in tool development that, together, span the spectrum of potential types of data. Our proposal includes detailed plans for ensuring that the tools we develop and implement are findable, accessible, interoperable and reusable (FAIR) and addresses issues related to validation of tool accuracy and usefulness, data privacy and reproducibly. The Tools component would work very closely with other HIVE components to disseminate the tools and to connect with both the developers and the international research communities.