IDSM ChemWebRDF: SPARQLing small-molecule datasets

Jakub Galgonek,Jiří Vondrášek

doi:10.1186/s13321-021-00515-1

Abstract

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/.

Highlights

The role of information has become crucially important in many aspects of human activities, including in life science research
We focus on the development of a web application named ChemWebRDF that allows users to write SPARQL queries and to explore data in a user-friendly way
We take advantage of the fact that both datasets are loaded in one SPARQL service, and we employ a set of SPARQL queries to examine how thoroughly the data from ChEMBL are included in the PubChem datasets

Summary

Introduction

The role of information has become crucially important in many aspects of human activities, including in life science research. One of the approaches that can be used to improve the interoperability of datasets produced by heterogeneous providers is to adopt Linked Data principles [1] According to these principles, things should be identified by uniform identifiers, connected with useful information accessible from the Internet in standard formats over the HTTP protocol and interlinked with other relevant things. The framework is intended to represent information about resources where a resource is an abstraction of an entity in the world In this framework, each piece of information is expressed as a subject-predicate-object triple denoting that the subject is related to the object, where the relation is denoted by the predicate. A set of triples is often visualised as a connected graph with nodes representing subjects and objects and with labelled arcs representing predicates

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Results

Conclusion