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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 T Cell Response (A) and B Cell Response (B) class.
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Figure 6: High-level classification of T Cell Response (A) and B Cell Response (B) class.

Mentions: The T Cell Response class captures all of the T cell mediated immunity-related information (Figure 6A). It has properties that are of type: Immunization, Effector Cells, Antigen Presenting Cell, Antigen, Assay Information, and Epitope-MHC-TCR Complex. The Effector Cell class describes the cells that are elicited upon immunization and that acquire measurable functions as a result. The B Cell Response class describes antibody responses that are related to the epitope (Figure 6B). This class has properties that are of type: Immunization, Antibody Molecule, Antigen, Assay Information, and Antigen-Antibody Complex. Because B cell responses do not require MHC binding and antigen presenting cells, the respective classes related to MHC Molecule and Antigen Presenting Cells are not used as restrictions on properties of the B Cell Response class.


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 T Cell Response (A) and B Cell Response (B) class.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: High-level classification of T Cell Response (A) and B Cell Response (B) class.
Mentions: The T Cell Response class captures all of the T cell mediated immunity-related information (Figure 6A). It has properties that are of type: Immunization, Effector Cells, Antigen Presenting Cell, Antigen, Assay Information, and Epitope-MHC-TCR Complex. The Effector Cell class describes the cells that are elicited upon immunization and that acquire measurable functions as a result. The B Cell Response class describes antibody responses that are related to the epitope (Figure 6B). This class has properties that are of type: Immunization, Antibody Molecule, Antigen, Assay Information, and Antigen-Antibody Complex. Because B cell responses do not require MHC binding and antigen presenting cells, the respective classes related to MHC Molecule and Antigen Presenting Cells are not used as restrictions on properties of the B Cell Response class.

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