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On Querying OBO Ontologies Using a DAG Pattern Query Language

  • Amarnath Gupta
  • Simone Santini
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4075)

Abstract

The Open Biomedical Ontologies (OBO) is a consortium that serves as a repository of ontologies that are structured like directed acyclic graphs. In this paper we present a language DQL for querying a database of directed acyclic graphs. The query language has a comprehension style syntax and contains a pattern specification sub-language DPL. DPL can be viewed as an extension of tree-pattern query language like XPath. The language allows extraction of nodes, paths and subgraphs from DAGs, and permits construction of result structures by composing them. We show that using such a language on OBO ontologies (such as the gene ontology), we can express more complex and scientifically valuable queries.

Keywords

Gene Ontology Directed Acyclic Graph Query Language Pattern Language XPath Query 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Consens, M.P.: Graphlog: Real life recursive queries using graphs. Master’s thesis, Dept. of Computer Science, University of Toronto (1989)Google Scholar
  2. 2.
    Agrawal, R., Jagadish, H.V.: Direct algorithms for computing the transitive closure of database relations. In: Proc. 13th Int. Conf. on VLDB, pp. 255–266 (1987)Google Scholar
  3. 3.
    Subramanian, B., Zdonik, S.B., Leung, T.W., Vandenberg, S.L.: Ordered types in the aqua data model. In: Proc. of the 4th Int. Workshop on Database Programming Languages (DBPL), London, UK, pp. 115–135. Springer, Heidelberg (1994)Google Scholar
  4. 4.
    Gyssens, M., Paredaens, J., den Bussche, J.V., van Gucht, D.: A graph-oriented object database model. IEEE Transactions on Knowledge and Data Engineering 6, 572–586 (1994)CrossRefGoogle Scholar
  5. 5.
    Poulovassilis, A., Levene, M.: A nested-graph model for the representation and manipulation of complex objects. ACM Trans. Inf. Syst. 12, 35–68 (1994)CrossRefGoogle Scholar
  6. 6.
    McHugh, J., Abiteboul, S., Goldman, R., Quass, D., Widom, J.: Lore: a database management system for semistructured data. SIGMOD Rec. 26, 54–66 (1997)CrossRefGoogle Scholar
  7. 7.
    Fernandez, M.F., Florescu, D., Levy, A.Y., Suciu, D.: Declarative specification of web sites with strudel. VLDB Journal 9, 38–55 (2000)CrossRefGoogle Scholar
  8. 8.
    Buneman, P., Fernandez, M., Suciu, D.: Unql: a query language and algebra for semistructured data based on structural recursion. The VLDB Journal 9, 76–110 (2000)CrossRefGoogle Scholar
  9. 9.
    Seaborne, A.: SPARQL query language for RDF. W3C Working Draft 21 (2005)Google Scholar
  10. 10.
    Zimányi, E., Gabouje, S.S.d.: Semantic visualization of biochemical databases. In: Bouzeghoub, M., Goble, C.A., Kashyap, V., Spaccapietra, S. (eds.) ICSNW 2004. LNCS, vol. 3226, pp. 199–214. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  11. 11.
    Yan, X., Yu, P.S., Han, J.: Substructure similarity search in graph databases. In: Proc. ACM SIGMOD International Conference on Management of Data, pp. 766–777. ACM Press, New York (2005)CrossRefGoogle Scholar
  12. 12.
    Trissl, S., Leser, U.: Querying ontologies in relational database systems. In: Ludäscher, B., Raschid, L. (eds.) DILS 2005. LNCS (LNBI), vol. 3615, pp. 63–79. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  13. 13.
    Fegaras, L., Maier, D.: Towards an effective calculus for object query languages. In: ACM SIGMOD International Conference on Management of Data, pp. 47–58. ACM, San Jose (1995)Google Scholar
  14. 14.
    Chen, L., Gupta, A., Kurul, M.E.: Stack-based algorithms for pattern matching on dags. In: Proc. 31st Int. Conf. on Very Large Databases (VLDB), Stockholm, pp. 493–504 (2005)Google Scholar
  15. 15.
    Vagena, Z., Moro, M.M., Tsotras, V.J.: Twig query processing over graph-structured XML data. In: WebDB 2004: Proc. of the 7th International Workshop on the Web and Databases, pp. 43–48 (2004)Google Scholar
  16. 16.
    Wang, H., He, H., Yang, J., Yu, P., Yu, J.X.: Dual labeling: Answering graph reachability queries in constant time. In: ICDE 2006: Proc. of the 22nd International Conference on Data Engineering (to appear, 2006)Google Scholar
  17. 17.
    Fegaras, L., Elmasri, R.: Query engines for web-accessible XML data. In: Proceedings of the 27th Int. Conf. on Very Large Data Bases (VLDB), pp. 251–260. Morgan Kaufmann Publishers Inc., San Francisco (2001)Google Scholar
  18. 18.
    Bang-Jensen, J., Gutin, G.: Digraphs: Theory, Algorithms and Applications. Springer, London (2001)MATHGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Amarnath Gupta
    • 1
  • Simone Santini
    • 1
  1. 1.San Diego Supercomputer CenterUniversity of CaliforniaSan Diego, La JollaUSA

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