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PLoS One. 2015 Aug 5;10(8):e0134693. doi: 10.1371/journal.pone.0134693. eCollection 2015.

FROG - Fingerprinting Genomic Variation Ontology.

Author information

1
Department of Bioinformatics, SASTRA University, Thanjavur, Tamil Nadu, India.
2
School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
3
Open Source Drug Discovery Unit, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110001, India.

Abstract

Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

PMID:
26244889
PMCID:
PMC4526677
DOI:
10.1371/journal.pone.0134693
[Indexed for MEDLINE]
Free PMC Article

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