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An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities.

Sathiamurthy M, Peters B, Bui HH, Sidney J, Mokili J, Wilson SS, Fleri W, McGuinness DL, Bourne PE, Sette A - Immunome Res (2005)

Bottom Line: To effectively represent and communicate the information related to immune epitopes, a formal ontology was developed.The semantics of the epitope domain and related concepts were captured as a hierarchy of classes, which represent the general and specialized relationships between the various concepts.We anticipate that the development of this type of ontology and associated databases will facilitate rigorous description of data related to immune epitopes, and might ultimately lead to completely new methods for describing and modeling immune responses.

View Article: PubMed Central - HTML - PubMed

Affiliation: La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, California, 92109, USA. muthu@liai.org

ABSTRACT

Background: Epitopes can be defined as the molecular structures bound by specific receptors, which are recognized during immune responses. The Immune Epitope Database and Analysis Resource (IEDB) project will catalog and organize information regarding antibody and T cell epitopes from infectious pathogens, experimental antigens and self-antigens, with a priority on NIAID Category A-C pathogens (http://www2.niaid.nih.gov/Biodefense/bandc_priority.htm) and emerging/re-emerging infectious diseases. Both intrinsic structural and phylogenetic features, as well as information relating to the interactions of the epitopes with the host's immune system will be catalogued.

Description: To effectively represent and communicate the information related to immune epitopes, a formal ontology was developed. The semantics of the epitope domain and related concepts were captured as a hierarchy of classes, which represent the general and specialized relationships between the various concepts. A complete listing of classes and their properties can be found at http://www.immuneepitope.org/ontology/index.html.

Conclusion: The IEDB's ontology is the first ontology specifically designed to capture both intrinsic chemical and biochemical information relating to immune epitopes with information relating to the interaction of these structures with molecules derived from the host immune system. We anticipate that the development of this type of ontology and associated databases will facilitate rigorous description of data related to immune epitopes, and might ultimately lead to completely new methods for describing and modeling immune responses.

No MeSH data available.


Related in: MedlinePlus

High-level classification of Immunization (A), Antigen (B), and Antigen Presenting Cells (C) class.
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Figure 4: High-level classification of Immunization (A), Antigen (B), and Antigen Presenting Cells (C) class.

Mentions: As with Assay Information, the classes Immunization, Antigen, and Antigen Presenting Cell are used in multiple other class descriptions. Features relating to the induction of the immune response are captured in the Immunization class (Figure 4A). It has relationships to other classes like Immunized Species, Immunogen, In vivo Immunization, and In vitro Immunization. Immunized Species contains information relating to the host that is being immunized. The Immunogen class describes the molecules that induce the immune response and an associated carrier molecule, if present. Features relating to how the immunogen was introduced to the immunized species are captured under the In vivo and In vitro Immunization classes.


An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities.

Sathiamurthy M, Peters B, Bui HH, Sidney J, Mokili J, Wilson SS, Fleri W, McGuinness DL, Bourne PE, Sette A - Immunome Res (2005)

High-level classification of Immunization (A), Antigen (B), and Antigen Presenting Cells (C) class.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1287064&req=5

Figure 4: High-level classification of Immunization (A), Antigen (B), and Antigen Presenting Cells (C) class.
Mentions: As with Assay Information, the classes Immunization, Antigen, and Antigen Presenting Cell are used in multiple other class descriptions. Features relating to the induction of the immune response are captured in the Immunization class (Figure 4A). It has relationships to other classes like Immunized Species, Immunogen, In vivo Immunization, and In vitro Immunization. Immunized Species contains information relating to the host that is being immunized. The Immunogen class describes the molecules that induce the immune response and an associated carrier molecule, if present. Features relating to how the immunogen was introduced to the immunized species are captured under the In vivo and In vitro Immunization classes.

Bottom Line: To effectively represent and communicate the information related to immune epitopes, a formal ontology was developed.The semantics of the epitope domain and related concepts were captured as a hierarchy of classes, which represent the general and specialized relationships between the various concepts.We anticipate that the development of this type of ontology and associated databases will facilitate rigorous description of data related to immune epitopes, and might ultimately lead to completely new methods for describing and modeling immune responses.

View Article: PubMed Central - HTML - PubMed

Affiliation: La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, California, 92109, USA. muthu@liai.org

ABSTRACT

Background: Epitopes can be defined as the molecular structures bound by specific receptors, which are recognized during immune responses. The Immune Epitope Database and Analysis Resource (IEDB) project will catalog and organize information regarding antibody and T cell epitopes from infectious pathogens, experimental antigens and self-antigens, with a priority on NIAID Category A-C pathogens (http://www2.niaid.nih.gov/Biodefense/bandc_priority.htm) and emerging/re-emerging infectious diseases. Both intrinsic structural and phylogenetic features, as well as information relating to the interactions of the epitopes with the host's immune system will be catalogued.

Description: To effectively represent and communicate the information related to immune epitopes, a formal ontology was developed. The semantics of the epitope domain and related concepts were captured as a hierarchy of classes, which represent the general and specialized relationships between the various concepts. A complete listing of classes and their properties can be found at http://www.immuneepitope.org/ontology/index.html.

Conclusion: The IEDB's ontology is the first ontology specifically designed to capture both intrinsic chemical and biochemical information relating to immune epitopes with information relating to the interaction of these structures with molecules derived from the host immune system. We anticipate that the development of this type of ontology and associated databases will facilitate rigorous description of data related to immune epitopes, and might ultimately lead to completely new methods for describing and modeling immune responses.

No MeSH data available.


Related in: MedlinePlus