Abstract
Many databases in life science are provided in Resource Description Framework (RDF) model with SPARQL Protocol and RDF Query Language (SPARQL) endpoints. However, it may be difficult for users who are not familiar with Semantic Web technologies to write a SPARQL query. Therefore, assisting users to build SPARQL queries is important task to expand the range of users of RDF databases. We developed a web application called SPARQL Builder (http://sparqlbuilder.org/) that enables users to access life-science RDF datasets by assisting them in writing SPARQL queries. One of the key technologies used in SPARQL Builder is to extract possible relationships in an RDF dataset between two classes of input and output data. We express such relationships by paths on a labeled graph called class graph representing class–predicate–class relations in a dataset. In addition, we present an efficient algorithm to compute all the possible paths between two classes on a class graph. To show the performance of the proposed algorithm, we compared our algorithm with a naive method using RDF datasets of various class sizes and confirmed that our algorithm runs much faster when the numbers of classes and relations are relatively large.
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References
Linked Data. http://www.w3.org/DesignIssues/LinkedData.html
The UniProt Consortium: Reorganizing the protein space at the Universal ProteinResource (UniProt). Nucl. Acids Res. 40(D1), D71–D75 (2012)
Belleau, F., Nolin, M.A., Tourigny, N., Rigault, P., Morissette, J.: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inform. 41(5), 706–716 (2008)
Jupp, S., Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., Gaulton, A., Gehant, S., Laibe, C., Redaschi, N., Wimalaratne, S.M., Martin, M., Le Novére, N., Parkinson, H., Birney, E., Jenkinson, A.M.: The EBI RDF platform: linked open data for the life sciences. Bioinform. 30(9), 1338–1339 (2014)
Yamaguchi, A., Kozaki, K., Lenz, K., Wu, H., Kobayashi, N.: An Intelligent SPARQL Query Builder for Exploration of Various Life-science Databases. In: CEUR Workshop Proceedings 1279 of the 3rd International Workshop on Intelligent Exploration of Semantic Data (IESD 2014), Riva del Garda, Italy.(1279)
Ferré, S., Hermann, A.: Reconciling faceted search and query languages for the semantic web. IJMSO 7(1), 37–54 (2012)
Guyonvarch, J., Ferré, S.: Scalewelis: a scalable query-based faceted search elena work. Multilingual Question Answering over Linked Data (QALD-3), Valencia, Spain (2013)
Russell, A., Smart, P.R., Braines, D., Shadbolt, N.R.: NITELIGHT: a graphical tool for semantic query construction. In: Semantic Web User Interaction Workshop (SWUI 2008), Florence, Italy (2008)
Hogenboom, F., Milea, V., Frasincar, F., Kaymak, U.: RDF-GL: A SPARQL-based graphical query language for RDF. In: Chbeir, R., Badr, Y., Abraham, A., Hassanien, A.-E. (eds.) Emergent Web Intelligence: Advanced Information Retrieval, pp. 87–116. Springer, London (2010)
Popov, I.O., Schraefel, M.C., Hall, W., Shadbolt, N.: Connecting the dots: a multi-pivot approach to data exploration. In: Aroyo, L., Welty, C., Alani, H., Taylor, J., Bernstein, A., Kagal, L., Noy, N., Blomqvist, E. (eds.) ISWC 2011, Part I. LNCS, vol. 7031, pp. 553–568. Springer, Heidelberg (2011)
Kozaki, K., Hirota, T., Mizoguchi, R.: Understanding an ontology through divergent exploration. In: Grobelnik, M., Simperl, E., Parsia, B., Plexousakis, D., Leenheer, P., Pan, J., Antoniou, G. (eds.) ESWC 2011, Part I. LNCS, vol. 6643, pp. 305–320. Springer, Heidelberg (2011)
Li, F., Le, W., Duan, S., Kementsietsidis, A.: Scalable keyword search on large RDF data. IEEE Trans. Knowl. Data Eng. 26, 2774–2788 (2014). doi:10.1109/TKDE.2014.2302294
Tran, T., Ladwig, G., Rudolph, S.: Managing structured and semistructured RDF data using structure indexes. IEEE Trans. Knowl. Data Eng. 25(9), 2076–2089 (2013)
Kobayashi, N., Toyoda, T.: BioSPARQL: ontology-based smart building of SPARQL queries for biological linked open data. In: SWAT4LS, pp. 47–49, London, UK (2011)
Grossi, R.: Enumeration of paths, cycles, and spanning trees. In: Kao, M.Y. (ed.) Encyclopedia of Algorithms, pp. 1–7. Springer, New York (2015)
Zhang, H., Li, Y., Tan, H.B.K.: Measuring design complexity of semantic web ontologies. J. Syst. Softw. 83, 803–814 (2010)
Yamamoto, Y., Yamaguchi, A., Bono, H., Takagi, T.: Allie: a database and a search service of abbreviations and long forms. Database (2011). doi:10.1093/database/bar013
Acknowledgments
This work was supported by JSPS KAKENHI Grant Number 25280081, 24120002 and the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).
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Yamaguchi, A., Kozaki, K., Lenz, K., Wu, H., Yamamoto, Y., Kobayashi, N. (2016). Efficiently Finding Paths Between Classes to Build a SPARQL Query for Life-Science Databases. In: Qi, G., Kozaki, K., Pan, J., Yu, S. (eds) Semantic Technology. JIST 2015. Lecture Notes in Computer Science(), vol 9544. Springer, Cham. https://doi.org/10.1007/978-3-319-31676-5_24
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DOI: https://doi.org/10.1007/978-3-319-31676-5_24
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