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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))

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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.

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© 2006 Springer-Verlag Berlin Heidelberg

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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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