!StemNet Ontologies
!!StemNet
The [[http://www.stemnet.de/|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 %target=_blank%
[[http://obofoundry.org/|OBO Foundry]], including the [[http://www.geneontology.org/|Gene Ontology]] and the [[http://obofoundry.org/cgi-bin/detail.cgi?id=cell|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 [[http://www.sequenceontology.org/|Sequence Ontology]].
!!!Viewing
There are different ways of browisng the ontologies contained in the OWL files below, but here are two options
#[[http://protege.stanford.edu/|Protégé]] is a java-based stand alone graphical user interface for viewing and editing ontologies. It is loaded with features.
#[[http://pellet.owldl.com/ontology-browser|OwlSight]] is a web-based ontology browser requiring no installation. To use it, go [[http://pellet.owldl.com/ontology-browser|here]],
click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and pase the following:
http://purl.org/stemnet/MHC/MaHCO.owl
into the "Ontolgy URI" field and click "Browse".
!!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
[[http://imgt.cines.fr/|international ImMunoGeneTics information system]] (IMGT), and the
[[http://www.ebi.ac.uk/ipd/|Immuno Polymorphism Database]] (IPD).
!!Files
a target='_new' href='./MHC/MaHCO.owl|MaHCO.owl]]
%target=_blank% [[MaHCO_upperClasses.png|Figure]] of upper classes of MaHCO (very large)
[[./MaHCO_subsetWithHLAAlleles.png|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|http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl]]
!!HLA Ontology
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
[[http://www.anthonynolan.org.uk/HIG/nomen/nomen_index.html|HLA Nomenclature Comittee]].
The official curated source of HLA sequences is the [[http://www.ebi.ac.uk/imgt/hla/|IMGT/HLA Database]].
The ]]HLA Dictionary]], as well as the [[http://www.anthonynolan.org.uk/HIG/|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
[[./HLA/MaHCO_HLA.owl|MaHCO_HLA.owl]]
[[./HLA/MaHCO_HLA.xml|MaHCO_HLA.xml]]
These files do not include serological nomenclature, and instead only use "Two Digit" HLA resolution:
[[./HLA/MaHCO_HLA_twodigit.owl|MaHCO_HLA_twodigit.owl]]
[[./HLA/MaHCO_HLA_twodigit.xml|MaHCO_HLA_twodigit.xml]]
!!!Date Changed
April 16th, 2008
!!!Dependencies
<ul>
<li>Dublin core: [[http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl|http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl]]
</ul>
!!Publications
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).
!!Applications
[[http://www.semedico.org|semedico]]
[[http://www.peptidecheck.org/jsp/explorer/|HLA Module Explorer]]