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/.
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/.
Authors: Randi Vita; Apurva Mody; James A Overton; Soren Buus; Stephen T Haley; Alessandro Sette; Vamsee Mallajosyula; Mark M Davis; Dale L Long; Richard A Willis; Bjoern Peters; John D Altman Journal: J Immunol Date: 2022-02-01 Impact factor: 5.426
Authors: Christopher Funk; William Baumgartner; Benjamin Garcia; Christophe Roeder; Michael Bada; K Bretonnel Cohen; Lawrence E Hunter; Karin Verspoor Journal: BMC Bioinformatics Date: 2014-02-26 Impact factor: 3.169
Authors: Randi Vita; James A Overton; Emily Seymour; John Sidney; Jim Kaufman; Rebecca L Tallmadge; Shirley Ellis; John Hammond; Geoff W Butcher; Alessandro Sette; Bjoern Peters Journal: J Biomed Semantics Date: 2016-01-11