The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF data and to explore links between them. Among other useful features, SPARQL supports federated queries that combine multiple independent data source endpoints. This allows users to obtain insights that are not possible using only a single data source. Owing to all of these useful features, many biological and chemical databases present their data in RDF, and support SPARQL querying. In our project, we primary focused on PubChem, ChEMBL and ChEBI small-molecule datasets. These datasets are already being exported to RDF by their creators. However, none of them has an official and currently supported SPARQL endpoint. This omission makes it difficult to construct complex or federated queries that could access all of the datasets, thus underutilising the main advantage of the availability of RDF data. Our goal is to address this gap by integrating the datasets into one database called the Integrated Database of Small Molecules (IDSM) that will be accessible through a SPARQL endpoint. Beyond that, we will also focus on increasing mutual interoperability of the datasets. To realise the endpoint, we decided to implement an in-house developed SPARQL engine based on the PostgreSQL relational database for data storage. In our approach, data are stored in the traditional relational form, and the SPARQL engine translates incoming SPARQL queries into equivalent SQL queries. An important feature of the engine is that it optimises the resulting SQL queries. Together with optimisations performed by PostgreSQL, this allows efficient evaluations of SPARQL queries. The endpoint provides not only querying in the dataset, but also the compound substructure and similarity search supported by our Sachem project. Although the endpoint is accessible from an internet browser, it is mainly intended to be used for programmatic access by other services, for example as a part of federated queries. For regular users, we offer a rich web application called ChemWebRDF using the endpoint. The application is publicly available at https://idsm.elixir-czech.cz/chemweb/ .

中文翻译：

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IDSM ChemWebRDF：SPARQLing小分子数据集

资源描述框架（RDF）与定义明确的本体一起极大地提高了数据的互操作性和可用性。引入了SPARQL查询语言来检索请求的RDF数据并探索它们之间的链接。在其他有用的功能中，SPARQL支持结合了多个独立数据源端点的联合查询。这使用户可以获得仅使用单个数据源无法获得的见解。由于所有这些有用的功能，许多生物和化学数据库以RDF形式显示其数据，并支持SPARQL查询。在我们的项目中，我们主要关注PubChem，ChEMBL和ChEBI小分子数据集。这些数据集的创建者已经将其导出到RDF。但是，它们都没有官方的且当前受支持的SPARQL端点。这种遗漏使得难以构造可以访问所有数据集的复杂查询或联合查询，从而未充分利用RDF数据可用性的主要优势。我们的目标是通过将数据集集成到一个可通过SPARQL端点访问的称为小分子集成数据库（IDSM）的数据库中来解决这一差距。除此之外，我们还将集中精力提高数据集的互操作性。为了实现该端点，我们决定基于PostgreSQL关系数据库实现内部开发的SPARQL引擎，以进行数据存储。在我们的方法中，数据以传统的关系形式存储，并且SPARQL引擎将传入的SPARQL查询转换为等效的SQL查询。该引擎的一个重要功能是它优化了生成的SQL查询。结合PostgreSQL进行的优化，可以有效评估SPARQL查询。端点不仅提供数据集中的查询，而且还提供我们的Sachem项目支持的复合子结构和相似性搜索。尽管可以从Internet浏览器访问该端点，但是该端点主要用于其他服务的编程访问，例如，作为联合查询的一部分。对于普通用户，我们使用端点提供了一个名为ChemWebRDF的富Web应用程序。该应用程序可从https://idsm.elixir-czech.cz/chemweb/公开获得。尽管可以从Internet浏览器访问该端点，但是该端点主要用于其他服务的编程访问，例如，作为联合查询的一部分。对于普通用户，我们使用端点提供了一个名为ChemWebRDF的富Web应用程序。该应用程序可从https://idsm.elixir-czech.cz/chemweb/公开获得。尽管可以从Internet浏览器访问该端点，但是该端点主要用于其他服务的编程访问，例如，作为联合查询的一部分。对于普通用户，我们使用端点提供了一个名为ChemWebRDF的富Web应用程序。该应用程序可从https://idsm.elixir-czech.cz/chemweb/公开获得。