IDSM ChemWebRDF: SPARQLing small-molecule datasets

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/.

Annotation of biologically relevant ligands in UniProtKB using ChEBI

“…It now supports queries for ligand binding site annotations using identifiers, names, synonyms and chemical structure data from ChEBI. We demonstrate this capability using a federated SPARQL query that combines the UniProt SPARQL endpoint and that of the Integrated Database of Small Molecules (IDSM) (Galgonek and Vondrasek, 2021; Kratochvil, et al, 2019). IDSM supports fingerprint-guided chemical similarity and substructure searches in a number of chemical datasets, including ChEBI, using Sachem, a high performance open source chemical cartridge (Kratochvil, et al, 2018).…”

From Platform to Knowledge Graph: Evolution of Laboratory Automation

“… 105 However, the Resource Description Framework (RDF) version of these databases did not come with officially supported SPARQL Protocols and RDF Query Language (SPARQL) endpoint. Galgonek and Vondrášek 145 recently addressed this issue by integrating PubChem, ChEMBL, and ChEBI data sets as a PostgreSQL database and exposing that to support SPARQL queries. This enabled fast access to chemical data from different sources.…”

Chemical reaction network knowledge graphs: the OntoRXN ontology

“…The application of these triple patterns to an RDF graph provides a RDF subgraph including only the triples matched by the query, which can be employed either to effecively add new statements to the main graph (CONSTRUCT query) or to isolate these subsets to answer questions (SELECT query). Several SPARQL endpoints to semantically-organized chemical databases, such as RHEA [ 42 ] or the Integrated Database of Small Molecules [ 43 ] (IDSM), have been proposed.…”