Determining the semantic similarities of GO terms based on their existence dependencies

Kamal Taha

doi:10.1109/CyberneticsCom.2012.6381630

Determining the semantic similarities of GO terms based on their existence dependencies

Kamal Taha

Electrical Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

We introduce in this paper a system called EDGT, which determines the semantic relationships among Gene Ontology terms. EDGT accepts Keyword-based queries with the form Q ("t₁", "t₂", .., "t_n") and Loosely Structured queries with the form Q( "t₁",..., "t_n", R₁?,..., R_n?), where t_i denotes a GO search term and R_i denotes a return/result GO term. The result of the Keyword-based query Q("t₁", "t₂") is a set of GO terms, where each term in the set is semantically related to both t₁ and t₂. The framework of EDGT determines the relationships among GO terms using the concept of existence dependency. EDGT resides between user application and Gene Ontology database. We experimentally evaluated EDGT and compared it with four existing methods. The results showed marked improvement.

Original language	British English
Title of host publication	Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012
Pages	118-122
Number of pages	5
DOIs	https://doi.org/10.1109/CyberneticsCom.2012.6381630
State	Published - 2012
Event	2012 1st IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012 - Bali, Indonesia Duration: 12 Jul 2012 → 14 Jul 2012

Publication series

Name	Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012

Conference

Conference	2012 1st IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012
Country/Territory	Indonesia
City	Bali
Period	12/07/12 → 14/07/12

Keywords

Gene Ontology
gene products
semantic similarity

Access to Document

10.1109/CyberneticsCom.2012.6381630

Cite this

Taha, K. (2012). Determining the semantic similarities of GO terms based on their existence dependencies. In Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012 (pp. 118-122). Article 6381630 (Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012). https://doi.org/10.1109/CyberneticsCom.2012.6381630

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title = "Determining the semantic similarities of GO terms based on their existence dependencies",

abstract = "We introduce in this paper a system called EDGT, which determines the semantic relationships among Gene Ontology terms. EDGT accepts Keyword-based queries with the form Q ({"}t1{"}, {"}t2{"}, .., {"}tn{"}) and Loosely Structured queries with the form Q( {"}t1{"},..., {"}tn{"}, R1?,..., Rn?), where ti denotes a GO search term and Ri denotes a return/result GO term. The result of the Keyword-based query Q({"}t1{"}, {"}t2{"}) is a set of GO terms, where each term in the set is semantically related to both t1 and t2. The framework of EDGT determines the relationships among GO terms using the concept of existence dependency. EDGT resides between user application and Gene Ontology database. We experimentally evaluated EDGT and compared it with four existing methods. The results showed marked improvement.",

keywords = "Gene Ontology, gene products, semantic similarity",

author = "Kamal Taha",

year = "2012",

doi = "10.1109/CyberneticsCom.2012.6381630",

language = "British English",

isbn = "9781467308922",

series = "Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012",

pages = "118--122",

booktitle = "Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012",

note = "2012 1st IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012 ; Conference date: 12-07-2012 Through 14-07-2012",

}

Taha, K 2012, Determining the semantic similarities of GO terms based on their existence dependencies. in Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012., 6381630, Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012, pp. 118-122, 2012 1st IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012, Bali, Indonesia, 12/07/12. https://doi.org/10.1109/CyberneticsCom.2012.6381630

Determining the semantic similarities of GO terms based on their existence dependencies. / Taha, Kamal.
Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012. 2012. p. 118-122 6381630 (Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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T1 - Determining the semantic similarities of GO terms based on their existence dependencies

AU - Taha, Kamal

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N2 - We introduce in this paper a system called EDGT, which determines the semantic relationships among Gene Ontology terms. EDGT accepts Keyword-based queries with the form Q ("t1", "t2", .., "tn") and Loosely Structured queries with the form Q( "t1",..., "tn", R1?,..., Rn?), where ti denotes a GO search term and Ri denotes a return/result GO term. The result of the Keyword-based query Q("t1", "t2") is a set of GO terms, where each term in the set is semantically related to both t1 and t2. The framework of EDGT determines the relationships among GO terms using the concept of existence dependency. EDGT resides between user application and Gene Ontology database. We experimentally evaluated EDGT and compared it with four existing methods. The results showed marked improvement.

AB - We introduce in this paper a system called EDGT, which determines the semantic relationships among Gene Ontology terms. EDGT accepts Keyword-based queries with the form Q ("t1", "t2", .., "tn") and Loosely Structured queries with the form Q( "t1",..., "tn", R1?,..., Rn?), where ti denotes a GO search term and Ri denotes a return/result GO term. The result of the Keyword-based query Q("t1", "t2") is a set of GO terms, where each term in the set is semantically related to both t1 and t2. The framework of EDGT determines the relationships among GO terms using the concept of existence dependency. EDGT resides between user application and Gene Ontology database. We experimentally evaluated EDGT and compared it with four existing methods. The results showed marked improvement.

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KW - gene products

KW - semantic similarity

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DO - 10.1109/CyberneticsCom.2012.6381630

M3 - Conference contribution

AN - SCOPUS:84874581135

SN - 9781467308922

T3 - Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012

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BT - Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012

T2 - 2012 1st IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012

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ER -

Taha K. Determining the semantic similarities of GO terms based on their existence dependencies. In Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012. 2012. p. 118-122. 6381630. (Proceeding - 2012 IEEE International Conference on Computational Intelligence and Cybernetics, CyberneticsCom 2012). doi: 10.1109/CyberneticsCom.2012.6381630

Determining the semantic similarities of GO terms based on their existence dependencies

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