The Life Science Database Archive (LSDB Archive, https://dbarchive.biosciencedbc.jp/ ) is a service to collect, preserve and provide databases generated by life-science researchers in Japan. As of September 2015, the LSDB Archive includes 103 databases and all the databases can be downloadable with appropriate licenses and metadata. Although a simple keyword search tool is available for the databases, more exible retrieval system to obtain relevant data from heterogeneous databases is required. Therefore, we rst converted the databases into RDF datasets, uploaded in a triple store. Then, we developed a prototype of retrieval system using SPARQL Builder. Because SPARQL Builder assists users in writing queries, the prototype enables users without knowledge of RDF to access the datasets.
In life sciences, many kinds of data have been generated as results of
experimental research. Although they are often organized and provided as databases,
we found that many databases in Japan were not maintained anymore after
fundings of projects end as of 2006 [
Although a simple keyword search tool is available for the databases, more
exible retrieval system to obtain relevant data from heterogeneous databases
is required. To do so, we decided to use semantic web technologies to integrate
the databases. We converted the databases into RDF datasets, and uploaded in
a triple store with a SPARQL endpoint as a trial. However, a SPARQL query
construct is intractable to users who are unfamiliar with semantic web
technologies although a SPARQL endpoint is very exible retrieval system. As a system
for assisting users to write SPARQL query, we employed SPARQL Builder [
Method and Result
To generate initial RDF datasets from databases in LSDB Archive, we used
TogoDB [
We then developed a prototype of a search interface on RDFized LSDB Archive using SPARQL Builder. Using this interface, by selecting two classes and a relationship between the two classes, users can search for desired data using SPARQL query from combined heterogenious RDF datasets in LSDB archive. Acknowledgments. This work was supported by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).