Nucleic Acids Research Advance Access originally published online on April 1, 2007
Nucleic Acids Research 2007 35(8):2533-2543; doi:10.1093/nar/gkm054
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Nucleic Acids Research, 2007, Vol. 35, No. 8 2533-2543
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
1Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium, 2Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven, Belgium and 3Center for Medical Genetics, Ghent University Hospital, MRB 2nd floor, De Pintelaan 185, B-9000 Ghent, Belgium
*To whom correspondence should be addressed. Tel: +3216328654; Fax: +3216321970; Email: steven.vanvooren{at}esat.kuleuven.be
Received October 3, 2006. Revised October 27, 2006. Accepted January 18, 2007.
Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development and Gene Ontology branches. The association between a band (e.g. 4p16.3) and a concept (e.g. microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings and support researchers interested in human gene function. The method is available as a web application, aBandApart, at http://www.esat.kuleuven.be/abandapart/.