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)


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.


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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© 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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