Searching Biomedical Literature with Anatomy Ontologies

  • Thomas Wächter
  • Dimitra Alexopoulou
  • Heiko Dietze
  • Jörg Hakenberg
  • Michael Schroeder
Part of the Computational Biology book series (COBO, volume 6)


Many ontologies and vocabularies have been designed to annotate genes and gene products based on evidence from literature. They are also useful to search literature systematically. GoPubMed is such an ontology-based literature search engine. It allows users to explore PubMed search results with hierarchical vocabularies such as the Gene Ontology or MeSH.We demonstrate the use of GoPubMed and MeshPubMed to answer questions relating to anatomy. Then, we discuss MousePubMed, the adaption of GoPubMed to vocabularies used in the Edinburgh Mouse Atlas with genes, tissues, and developmental stages. We develop a specific text mining algorithm for MousePubMed and demonstrate its usefulness by evaluating it on the Mouse Atlas. For nearly 1500 genes and over 10.000 triples of gene, tissue and stage, we are able to reconstruct with MousePubMed 37% of genes, 31% of gene-tissue associations and 13% of gene-tissue-stage associations from PubMed abstracts. These figures are encouraging as only abstracts are used.


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Copyright information

© Albert Burger, Duncan Davidson, Richard Baldock 2008

Authors and Affiliations

  • Thomas Wächter
  • Dimitra Alexopoulou
  • Heiko Dietze
  • Jörg Hakenberg
  • Michael Schroeder

There are no affiliations available

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