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International Workshop on Data Integration in the Life Sciences

DILS 2006: Data Integration in the Life Sciences pp 152–167Cite as

On Querying OBO Ontologies Using a DAG Pattern Query Language

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Part of the Lecture Notes in Computer Science book series (LNBI,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.

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

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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
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  2. Simone Santini
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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

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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

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  • 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)

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