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Bioinformatics Advance Access originally published online on May 7, 2009
Bioinformatics 2009 25(16):2064-2070; doi:10.1093/bioinformatics/btp306
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining{dagger}

David S. DeLuca 1,2,*, Elena Beisswanger 3, Joachim Wermter 3, Peter A. Horn 4, Udo Hahn 3 and Rainer Blasczyk 1

1Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany, 2Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA, 3Jena University Language & Information Engineering (JULIE) Lab, Jena and 4Institute for Transfusion Medicine, University Hospital Essen, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: The high level of polymorphism associated with the major histocompatibility complex (MHC) poses a challenge to organizing associated bioinformatic data, particularly in the area of hematopoietic stem cell transplantation. Thus, this area of research has great potential to profit from the ongoing development of biomedical ontologies, which offer structure and definition to MHC-data related communication and portability issues.

Results: We introduce the design considerations, methodological foundations and implementational issues underlying MaHCO, an ontology which represents the alleles and encoded molecules of the major histocompatibility complex. Importantly for human immunogenetics, it includes a detailed level of human leukocyte antigen (HLA) classification. We then present an ontology browser, search interfaces for immunogenetic fact and document retrieval, and the specification of an annotation language for semantic metadata, based on MaHCO. These use cases are intended to demonstrate the utility of ontology-driven bioinformatics in the field of immunogenetics.

Availability and Implementation: The MaHCO Ontology is available via the BioPortal: http://www.bioontology.org/tools/portal/bioportal.html, and at: http://purl.org/stemnet/

Contact: david_deluca{at}dfci.harvard.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on February 12, 2009; revised on May 1, 2009; accepted on May 4, 2009

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