Datasets2Tools

Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated “canned" analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets. The Datasets2Tools repository also contains the indexing of 4,901 published bioinformatics software tools, and all the analyzed datasets. Datasets2Tools enables users to rapidly find datasets, tools, and canned analyses through an intuitive web interface, a Google Chrome extension, and an API. Furthermore, Datasets2Tools provides a platform for contributing canned analyses, datasets, and tools, as well as evaluating these digital objects according to their compliance with the findable, accessible, interoperable, and reusable (FAIR) principles. By incorporating community engagement, Datasets2Tools promotes sharing of digital resources to stimulate the extraction of knowledge from biomedical research data.

诸如基因表达综合数据库（Gene Expression Omnibus，GEO）这类生物医学数据存储库，可支持用户检索并发现相关的生物医学数字数据对象。类似地，诸如OMICtools这类组学工具资源，可为能够从上述数字数据对象中提取知识的生物信息学工具构建索引。然而，目前尚无系统化的访问途径，可获取由生物信息学工具针对生物医学数字数据对象预先生成的“预制”分析成果。Datasets2Tools是一个索引存储库，可为应用于6431个数据集的31473项预制生物信息学分析成果编制索引。该存储库同时还收录了4901款已发表的生物信息学软件工具的索引信息，以及所有经分析的数据集。Datasets2Tools支持用户通过直观的网页界面、谷歌浏览器（Google Chrome）扩展程序以及应用程序编程接口（API），快速检索数据集、工具及预制分析成果。此外，Datasets2Tools还搭建了一个平台，可供用户提交预制分析成果、数据集及工具，并依据可发现、可访问、可互操作、可重用（Findable, Accessible, Interoperable, Reusable，FAIR）原则，对这些数字对象进行合规性评估。通过吸纳社区参与，Datasets2Tools推动了数字资源的共享，以促进从生物医学研究数据中提取知识的工作。

搜集汇总

背景与挑战

背景概述

Datasets2Tools是一个生物信息学索引仓库，集成了超过31,500个预生成分析、6,800多个数据集和4,900多个工具，支持用户通过多种方式搜索和贡献资源。该仓库还提供了一个平台，用于评估这些数字对象是否符合FAIR原则，以促进生物医学研究数据的知识提取和共享。