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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

Overview of IEDB Class Hierarchy.
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Figure 1: Overview of IEDB Class Hierarchy.

Mentions: We have previously described some of the general concepts relating to the IEDB design [1,2]. More information relating to various aspects of the project can be accessed at . Herein, we report a detailed description of the novel aspects of the IEDB ontology. In designing our application architecture, we have followed the common system engineering practice of first determining the scope and nature of the data involved. A first essential step is to understand the semantics of the domain and to capture that knowledge in an agreed-upon format. Arranging the domain concepts in a taxonomy is one of the initial organizing steps in the ontology design process. The class hierarchy represents the generalization and specialization relationships between the various classes of objects in a domain [6]. Briefly, classes describe concepts in the domain. Subclasses represent concepts (classes) that are more specific than the superclass and these subclasses can have their own unique properties. Slots represent properties of the classes. For example, in Figure 1, we see that there is a class named Reference and three more specific subclasses of Reference: Journal Article, Patent Application, and Direct Submission. Figure 1 also shows that the class Epitope has a number of properties (slots) associated with it such as "has Epitope Structure" and "has Epitope Source".


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)

Overview of IEDB Class Hierarchy.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Overview of IEDB Class Hierarchy.
Mentions: We have previously described some of the general concepts relating to the IEDB design [1,2]. More information relating to various aspects of the project can be accessed at . Herein, we report a detailed description of the novel aspects of the IEDB ontology. In designing our application architecture, we have followed the common system engineering practice of first determining the scope and nature of the data involved. A first essential step is to understand the semantics of the domain and to capture that knowledge in an agreed-upon format. Arranging the domain concepts in a taxonomy is one of the initial organizing steps in the ontology design process. The class hierarchy represents the generalization and specialization relationships between the various classes of objects in a domain [6]. Briefly, classes describe concepts in the domain. Subclasses represent concepts (classes) that are more specific than the superclass and these subclasses can have their own unique properties. Slots represent properties of the classes. For example, in Figure 1, we see that there is a class named Reference and three more specific subclasses of Reference: Journal Article, Patent Application, and Direct Submission. Figure 1 also shows that the class Epitope has a number of properties (slots) associated with it such as "has Epitope Structure" and "has Epitope Source".

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