Investigating Schema Definitions Using RDFS and OWL 2 for RDF Databases in Life Sciences

Abstract

With the development of measuring instruments, life science databases are becoming larger and more heterogeneous. As a step towards providing integrated databases, many life science databases have been published as Linked Open Data (LOD). To utilize such databases efficiently, it is desirable that the schema, such as class–class relations, can be acquired in advance from SPARQL Protocol and RDF Query Language (SPARQL) endpoints. However, a SPARQL query to obtain the schema from a SPARQL endpoint often fails because it is time consuming and places an excessive load on the server. On the other hand, many datasets include the definitions using standard vocabularies, such as RDF Schema 1.1 and OWL 2. If the database schema is properly described and provided using RDF Schema 1.1 or OWL 2, it is no longer necessary to obtain it by exhaustively crawling the SPARQL endpoints. Therefore, we investigated the extent of the schema definitions in life sciences databases, focusing on seven specific patterns related to properties using RDF Schema 1.1 or OWL 2. We found that for some datasets, the patterns of domain and range definitions using RDF Schema 1.1, are relatively well defined for properties. However, there are few patterns using OWL 2 as schema definitions for properties. Additionally, we validated RDF datasets by restricting the patterns of domain and range definitions of RDF Schema 1.1. Subsequently, we found that RDF datasets follow these restrictions.