Towards Visualizing the Alignment of Large Biomedical Ontologies

  • Catia Pesquita
  • Daniel Faria
  • Emanuel Santos
  • Jean-Marc Neefs
  • Francisco M. Couto
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8574)


To successfully integrate biomedical data it is crucial to establish meaningful relationships between the ontologies used to annotate this data. Recent developments in ontology alignment techniques, including our AgreementMakerLight system, have been successful in matching very large biomedical ontologies. However the visualization of these alignments is still a challenge.

We have developed a graphical user interface for AgreementMakerLight that follows its core focus on computational efficiency and the handling of very large ontologies. It allows non-expert users to easily align biomedical ontologies, offering a wide selection of matching strategies and algorithms, with a particular focus on the use of external background knowledge. The visualization of the resulting alignment is based on linked subgraphs which are generated according to search queries over the full graph composed by the matched ontologies and the mappings between them. This strategy decreases the need for computational resources and improves the visualization experience, by letting the user focus on selected areas of the alignment.


Ontology Matching Ontology Alignment Alignment Visualization Large Ontologies Biomedical Ontologies 


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Catia Pesquita
    • 1
  • Daniel Faria
    • 1
  • Emanuel Santos
    • 1
  • Jean-Marc Neefs
    • 2
  • Francisco M. Couto
    • 1
  1. 1.Dept. de Informática, Faculdade de CiênciasUniversidade de LisboaPortugal
  2. 2.Janssen Pharmaceutical Companies of Johnson & JohnsonPortugal

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