BioCarian: search engine for exploratory searches in heterogeneous biological databases

BMC Bioinformatics

Software

Nazar Zaki¹  Chandana Tennakoon¹ 

[1] Department of Comp. Science and Software Engineering, College of Info. Technology, United Arab Emirates University (UAEU), PO Box 15551, Al Ain, United Arab Emirates;

关键词: Search engine;    Exploratory search;    Biological databases;    Heterogeneous databases;    RDF;    SPARQL;   

DOI  :  10.1186/s12859-017-1840-4

 received in 2017-04-06, accepted in 2017-09-21,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThere are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community.ResultsWe present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com.ConclusionsWe have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

【 授权许可】

CC BY   
© The Author(s) 2017

【 图 表 】

12944_2023_1927_Article_IEq7.gif

12944_2023_1927_Article_IEq6.gif

Fig. 9

Fig. 1

12951_2015_155_Article_IEq34.gif

12951_2015_155_Article_IEq33.gif

Fig. 2

Fig. 1