Linked Open Data (LOD) is being increasingly used when publishing life science databases. To facilitate the exible use of such databases, we employ a method that uses federated query search along a path of class-class relationships. To demonstrate our strategy, we implemented a prototype system accessible via a web API as a preliminary trial. We have been collecting SPARQL Builder Metadata (SBM) that describe a data schema for each SPARQL endpoint. Employing the SBM, we constructed a graph of the class-class relationships in LOD. Using this graph, our system can provide the information required to construct a federated search query, such as the SPARQL endpoints that include a class{class relationship, and paths of the class-class relationships between two classes.
LOD Surfer is a search system that discovers data along paths of class{class
relationships over life sciences Linked Open Data (LOD) provided by di erent
SPARQL endpoints. A user can interactively obtain desired data by inputting
data or class, and selecting an output class and a path of class{class
relationships between the classes. In a previous study [
In this study, we implemented a web API for LOD Surfer as a preliminary trial, using technologies developed for SPARQL Builder such as SBM and class graphs. This enables exible data acquisition from multiple SPARQL endpoints for users who do not have detailed information for data schema over LOD. 2
LOD Surfer API The LOD Surfer API is designed to easily develop a search system, such as LOD Surfer. Using this API, a list of SPARQL endpoints, classes reachable using links from a given class, and Fig. 1. Overview of the architecture of the LOD Surfer API paths between two given classes can be obtained in JSON format along with a federated SPARQL query and result obtained for a given path by a simple HTTP GET request. Figure 1 shows the overview of the architecture of the LOD Surfer API. From the SBM collected by the LOD crawler, a single graph with 14147 nodes that corresponds to the classes appearing in LOD is constructed. Using this graph, the output generator can e ciently compute the output of this API. For example, from the connected components of the graph, a list of classes reachable from a given class can be instantly obtained. A typical example of the usage for this API is obtaining related data typed by some other classes (e.g., Disease, Protein, etc) from various datasets for a set of IDs typed by a class (e.g. Gene). The code for this web API can be accessed at https://github.com/LODSurfer/lodsurfer-api. This system is an early prototype and will be improved to make it more practical for users. In addition, the development for an application using this API will be the focus of our future work.
Acknowledgments This work was supported by JSPS KAKENHI grant numbers 17K00434, 17K00424 and 17H01789 and by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).