A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F23%3A00573624" target="_blank" >RIV/61388963:_____/23:00573624 - isvavai.cz</a>

Result on the web

<a href="https://doi.org/10.1186/s13321-023-00729-5" target="_blank" >https://doi.org/10.1186/s13321-023-00729-5</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13321-023-00729-5" target="_blank" >10.1186/s13321-023-00729-5</a>

Result language

angličtina

Original language name

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL

Original language description

Current biological and chemical research is increasingly dependent on the reusability of previously acquired data, which typically come from various sources. Consequently, there is a growing need for database systems and databases stored in them to be interoperable with each other. One of the possible solutions to address this issue is to use systems based on Semantic Web technologies, namely on the Resource Description Framework (RDF) to express data and on the SPARQL query language to retrieve the data. Many existing biological and chemical databases are stored in the form of a relational database (RDB). Converting a relational database into the RDF form and storing it in a native RDF database system may not be desirable in many cases. It may be necessary to preserve the original database form, and having two versions of the same data may not be convenient. A solution may be to use a system mapping the relational database to the RDF form. Such a system keeps data in their original relational form and translates incoming SPARQL queries to equivalent SQL queries, which are evaluated by a relational-database system. This review compares different RDB-to-RDF mapping systems with a primary focus on those that can be used free of charge. In addition, it compares different approaches to expressing RDB-to-RDF mappings. The review shows that these systems represent a viable method providing sufficient performance. Their real-life performance is demonstrated on data and queries coming from the neXtProt project.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/LM2018131" target="_blank" >LM2018131: Czech National Infrastructure for Biological Data</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Cheminformatics

ISSN

1758-2946

e-ISSN

1758-2946

Volume of the periodical

15

Issue of the periodical within the volume

1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

14

Pages from-to

61

UT code for WoS article

001012034200001

EID of the result in the Scopus database

2-s2.0-85162890008