BioThings Explorer: A platform for distributed knowledge integration across biomedical APIs

BioThings Explorer：跨生物医学 API 的分布式知识集成平台

• 批准号: 10705399
• 负责人: ANDREW I SU
• 金额: $ 106.27万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-01-24 至 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10705399
• 关键词: Address; Adoption; Automation; Bypass; Client; Communities; Data; Databases; Ecosystem; Failure; Gatekeeping; Individual; Infrastructure; Knowledge; Methods; Modeling; Output; Provider; Pythons; Registries; Resources; Running; Schedule; Semantics; Sorting; Source; Structure; System; Thinness; application programming interface; data ingestion; data integration; data resource; improved; knowledge graph; knowledge integration; non-compliance; web app

This proposal describes the BioThings Explorer (BTE) platform as an Autonomous Relay Agent (ARA). Most data integration efforts (including many being pursued within Translator) are based on building centralized data resources. These efforts typically involve building resourcespecific data ingestion parsers, the outputs of which are assembled into knowledge graphs and loaded into a local database (with neo4j being a popular option within Translator). The BTE platform takes a complementary approach to data integration, focusing on a distributed network of knowledge providers connected by application programming interfaces (APIs). A proof-of-concept implementation of BTE is now complete (with demos available in [1,2]). This implementation has three components (Figure 1): a distributed knowledge graph (distributed-KG) based on many individual web APIs "in the wild", a meta-knowledge graph (meta-KG) that describes compatibility of inputs and outputs between each API, and a BTE python client that automates the planning and execution of queries across the API network. Relative to centralized solutions, this distributed model offers several advantages. First, the API ecosystem is easily extensible by the community since there is no gatekeeper controlling access to a centralized resource. The scope and output of the BTE system will continuously and automatically improve as the community-maintained registry of API components continues to grow. Second, the data retrieved are always up-to-date with the source and not dependent on having a frequent synchronization schedule. Third, the distributed model is more scalable to heavy usage since the BTE client is run on each user's own computing infrastructure, bypassing any centralized component that could become a single point of failure. BTE also distinguishes itself from other federated API solutions by using semantically-precise annotations of APIs as they exist, rather than mandating any changes to the API itself. These API annotations describe API inputs and outputs in enough detail to support initiating the API call and interpreting the result. In contrast, other federated approaches (including some within Translator) require APIs to conform to a common API structure. However, requirements like these have historically been significant barriers to widespread adoption, and thin API "wrappers" around non-compliant APIs introduce additional complexity and technical points of failure. The strengths of the current BTE implementation are the ease of adding new resources and the automation of the query planning and execution. The critical challenge that we address in this proposal is developing new methods to rank and sort the query path results that are retrieved from BTE queries.

该提案将BioThings Explorer （BTE）平台描述为自治中继