Skip to main content
SpringerLink
Log in

On Querying OBO Ontologies Using a DAG Pattern Query Language

  • Conference paper
Data Integration in the Life Sciences (DILS 2006)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4075))

Included in the following conference series:

  • 520 Accesses

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.

Supported in part by NSF ITR Grant EIA-0205061, and the NLADR grant from NSF.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  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. 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. 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. 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)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  7. Fernandez, M.F., Florescu, D., Levy, A.Y., Suciu, D.: Declarative specification of web sites with strudel. VLDB Journal 9, 38–55 (2000)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  9. Seaborne, A.: SPARQL query language for RDF. W3C Working Draft 21 (2005)

    Google Scholar 

  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)

    Chapter  Google Scholar 

  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)

    Chapter  Google Scholar 

  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)

    Chapter  Google Scholar 

  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. 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. 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. 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. 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. Bang-Jensen, J., Gutin, G.: Digraphs: Theory, Algorithms and Applications. Springer, London (2001)

    MATH  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA

    Amarnath Gupta & Simone Santini

Authors
  1. Amarnath Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Simone Santini
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Humboldt-Universität zu Berlin,  

    Ulf Leser

  2. Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany

    Felix Naumann

  3. IBM Application and Integration Middleware, 1475 Phoenixville Pike, 19380, West Chester, PA, USA

    Barbara Eckman

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Gupta, A., Santini, S. (2006). On Querying OBO Ontologies Using a DAG Pattern Query Language. In: Leser, U., Naumann, F., Eckman, B. (eds) Data Integration in the Life Sciences. DILS 2006. Lecture Notes in Computer Science(), vol 4075. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11799511_14

Download citation

  • DOI: https://doi.org/10.1007/11799511_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-36593-8

  • Online ISBN: 978-3-540-36595-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation