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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

Detailed listing of properties of Epitope Structure (A), Epitope Source (B), and Assay Information (C) class.
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Figure 3: Detailed listing of properties of Epitope Structure (A), Epitope Source (B), and Assay Information (C) class.

Mentions: The Epitope Structure and Epitope Source classes capture intrinsic features of an epitope. The Epitope Structure class captures the physical and chemical features of an epitope. Virtually any molecular structure may provoke an immune response, such as proteins, carbohydrates, DNA, and lipids. In the Epitope Structure class, structural information relating to linear sequences and 2-D structures of the epitope, if available, are catalogued. The Epitope Source class captures the phylogenetic source of an epitope, including species of origin, gene name, protein name, and links to other databases for more detailed information about proteins and genes. Figures 3A and 3B show the listings of properties (slots/fields) encompassing the Epitope Structure and Epitope Source 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)

Detailed listing of properties of Epitope Structure (A), Epitope Source (B), and Assay Information (C) class.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Detailed listing of properties of Epitope Structure (A), Epitope Source (B), and Assay Information (C) class.
Mentions: The Epitope Structure and Epitope Source classes capture intrinsic features of an epitope. The Epitope Structure class captures the physical and chemical features of an epitope. Virtually any molecular structure may provoke an immune response, such as proteins, carbohydrates, DNA, and lipids. In the Epitope Structure class, structural information relating to linear sequences and 2-D structures of the epitope, if available, are catalogued. The Epitope Source class captures the phylogenetic source of an epitope, including species of origin, gene name, protein name, and links to other databases for more detailed information about proteins and genes. Figures 3A and 3B show the listings of properties (slots/fields) encompassing the Epitope Structure and Epitope Source 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