Advanced SPARQL querying in small molecule databases.
BACKGROUND
In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better interoperability of various data sources and powerful searching facilities. However, we identified several deficiencies that make usage of such RDF databases restrictive or challenging for common users.


RESULTS
We extended a SPARQL engine to be able to use special procedures inside SPARQL queries. This allows the user to work with data that cannot be simply precomputed and thus cannot be directly stored in the database. We designed an algorithm that checks a query against data ontology to identify possible user errors. This greatly improves query debugging. We also introduced an approach to visualize retrieved data in a user-friendly way, based on templates describing visualizations of resource classes. To integrate all of our approaches, we developed a simple web application.


CONCLUSIONS
Our system was implemented successfully, and we demonstrated its usability on the ChEBI database transformed into RDF form. To demonstrate procedure call functions, we employed compound similarity searching based on OrChem. The application is publicly available at https://bioinfo.uochb.cas.cz/projects/chemRDF.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
Jakub
J
Galgonek
Faculty of Mathematics and Physics, Charles University in Prague, Malostranské nám. 25, 118 00 Prague 1, Czech Republic.
Tomáš
T
Hurt
Faculty of Mathematics and Physics, Charles University in Prague, Malostranské nám. 25, 118 00 Prague 1, Czech Republic.
Vendula
V
Michlíková
Faculty of Mathematics and Physics, Charles University in Prague, Malostranské nám. 25, 118 00 Prague 1, Czech Republic.
Petr
P
Onderka
Faculty of Mathematics and Physics, Charles University in Prague, Malostranské nám. 25, 118 00 Prague 1, Czech Republic.
Jan
J
Schwarz
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
Jiří
J
Vondrášek
Database of small molecules; Resource Description Framework; SPARQL query language