Title: Mapping Biomedical Concepts onto the Human Genome by Mining Literature on Chromosomal Aberrations
Authors: Van Vooren, Steven ×
Thienpont, Bernard
Menten, B
Speleman, F
De Moor, Bart
Vermeesch, Joris
Moreau, Yves #
Issue Date: Apr-2007
Publisher: Oxford University Press
Series Title: Nucleic Acids Research vol:35 issue:8 pages:2533-2543
Abstract: 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
Description: \emph{Nucleic Acids Research}, vol. Advance Access, no. 10.1093/nar/gkm054, Apr. 2007
ISSN: 0305-1048
Publication status: published
KU Leuven publication type: IT
Appears in Collections:ESAT - STADIUS, Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics
Clinical Genetics Section (-)
Department of Human Genetics - miscellaneous
× corresponding author
# (joint) last author

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