An ontology-based search engine for protein-protein interactions.

BMC Bioinformatics
Byungkyu Park, Kyungsook Han

Abstract

Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often mi...Continue Reading

References

Jan 10, 2003·Nucleic Acids Research·Gary D BaderChristopher W V Hogue
May 1, 2004·Bioinformatics·Kyungsook HanJong Park
Mar 14, 2007·Molecular Systems Biology·Roded SharanRon Shamir
Apr 14, 2007·BMC Bioinformatics·Claudio CorsiRoberto Marangoni
Dec 21, 1928·Science·F Cajori
Nov 7, 2007·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Nov 15, 2007·Nucleic Acids Research·Bobby-Joe BreitkreutzMike Tyers
Dec 26, 2007·Nucleic Acids Research·H W MewesT Rattei
Jul 17, 2008·Comparative and Functional Genomics·David MilwardJulie Barnes
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Nov 8, 2008·Nucleic Acids Research·T S Keshava PrasadAkhilesh Pandey
Nov 28, 2008·Nucleic Acids Research·Derek WilsonJulian Gough

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Citations

Feb 10, 2012·Computer Methods in Biomechanics and Biomedical Engineering·Byungkyu ParkKyungsook Han
Jun 12, 2012·Biochimica Et Biophysica Acta·Yi-Tsung Tang, Hung-Yu Kao

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Methods Mentioned

BETA
two-hybrid

Software Mentioned

BOND
Java BigInteger
OWL Web Ontology
Cytoscape
HPRD

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