MaHCO - An MHC Ontology
StemNet
The StemNet project aims to improve the treatment of cancer patients based on a sepcial form of stem cell transplantation (HSCT). To accelerate research in this area, the project uses text mining techniques, such as automated test annotation to form structured databases out of unstructured scientific literature.
Ontologies
An important tool for
the StemNet project is the ontology. StemNet utilizes ontologies from the OBO Foundry, including the Gene Ontology and the Cell Ontology.
An ontology which is arising directly out of the StemNet project is MaHCO the MaHCO-HLA Ontology is a sub-domain. The long-term goal is the full integration of these ontologies into the Sequence Ontology.
MaHCO
MHC, or major histocompatibility complex is a gene complex found in jawed vertebrates. The genes found on this region of the genome include several important genes which encode proteins which are responsible for presenting peptides on the cell surface for inspection by cells of the immune system. In human, such genes are called HLA (human leukocyte antigen). MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans. Important resources include the international ImMunoGeneTics information system (IMGT), and the Immuno Polymorphism Database (IPD).
Files
- MaHCO.owl
- Figure of upper classes of MaHCO (very large)
- Figure of a subset of classes including HLA allele examples (also very large)
Date Changed
April 13th, 2009
Dependencies
- Note that MaHCO.owl uses an import statement to include the classes found in MaHCO_HLA.owl. Please download both files if you intend to work offline.
- Dublin core: http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl
MaHCO-HLA
Human MHC genes, or HLA genes, have major clinical relevance for transplantation and other blood and immune system related illnesses. Because of the high level of polymorphism found in these genes in the human population, thousands of variants have been identified. A systematic and official standard for the organization of HLA sequences has been provide by the HLA Nomenclature Comittee. The official curated source of HLA sequences is the IMGT/HLA Database. The HLA Dictionary, as well as the HLA Informatics Group website include other important resources.
The HLA Ontology is an attempt to apply the logical principles on ontologies to help combine the aforementioned resources into a universal structured source of HLA information. HLA research, as well as clinical processes, requires complicated software systems to process HLA data. This ontology is a resource for such software developers who need a formalized structure for their databases and systems which is maintained and up-to-date with the latest IMGT/HLA database releases.
Files
These files do not include serological nomenclature, and instead only use "Two Digit" HLA resolution:
Date Changed
August 24th, 2009
Dependencies
Community and Development
Forums
Feel free to start a discussion, ask a question, or request a feature at the MaHCO group forum: http://www.bioinformatics.org/forums/?group_id=950
There are two categories:
- Open Discussion: post messages here if you would like to make a feature request, start a discussion about conceptual matters, suggest changes, or point out any major problems (i.e. those requiring changes in ontology structure, or significant changes in term definitions, etc). For minor errors, such as typos or discrepancies, use the "Bug tracker".
- Help: post messages here if you have questions about working with the ontology.
Bug Tracking
Bug Tracking: If you find any minor errors (i.e. typos or mistakes in definitions, etc.) you can submit a bug instead of opening a forum discussion. When logged into the the bioinformatics.org webiste, this option my be found by clicking the little red beetle in the menu in the upper right of the page.
Applications
semedico
HLA Module Explorer
Publications
Original Paper
DeLuca DS, Beisswanger E, Wermter J, Horn PA, Hahn U and Blasczyk R. MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining, Bioinformatics (Oxford, England), 25, 2064-2070, 2009.
Conference Proceedings
Beisswanger E, DeLuca DS, Blasczyk R, Hahn U.
An Ontology for Major Histocompatibility Complex (MHC) Alleles and Molecules.
Proceedings of the AMIA 2007 Annual Symposium, Chicago, IL, USA, Nov. 10-14, 2007.
DeLuca DS, Beisswanger E, Hahn U, Blasczyk R. An automatically curated MHC ontology for intelligent immunogenetic information retrieval. J Immunol 178, LB9- 2007.
Changes to MaHCO
| Date | Description |
|---|
| 2003-04-13 | Corrected erroneous user of 'none-classical' in definition of HLA:HLA_Class_Ia_Allele |
| 2003-04-13 | MHC.owl has been renamed to MaHCO.owl |
Changes to MaHCO-HLA
Note, that MaHCO-HLA is updated regularly, in accordance with IMGT/HLA database updates. The current version incorporated in MaHCO-HLA is IMGT/HLA 2.26.0, 17 July 2009
| Date | Description |
|---|
| 2003-04-13 | HLA.owl has been renamed to MaHCO_HLA.owl |
| 2003-04-13 | HLA.xml has been renamed to MaHCO_HLA.xml |
Files
HLA Resources
Ontology Resources
Applications using MaHCO