Limits...
FROG - Fingerprinting Genomic Variation Ontology.

Abinaya E, Narang P, Bhardwaj A - PLoS ONE (2015)

Bottom Line: Genetic variations play a crucial role in differential phenotypic outcomes.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, SASTRA University, Thanjavur, Tamil Nadu, 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.

No MeSH data available.


The attributes, ontology terms and their relationship within (A) Variation and (B) Interaction level.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4526677&req=5

pone.0134693.g004: The attributes, ontology terms and their relationship within (A) Variation and (B) Interaction level.

Mentions: FROG is an organism independent fingerprinting system designed to tag genomic variation at various levels of resolution (Fig 1A). FROG has six levels to describe the variation annotation. The six levels are Chromosome, DNA, RNA, Protein, Variations and Interactions (Fig 1B). Each level is a conceptual aggregation of logically connected attributes (Figs 2–4). For example, Chromosome level has five attributes, namely, location of variation (Allosomes or Autosomes), variation kind (indel, deletion, insertion, substitution), number of variations (diploidy, polyploidy—set number, disomy, polysomy—number of variation etc.), repeats (micro- and mini-satellite expansion, tandem repeats, interspersed repeats etc.) and structural variation (complex changes like telomere changes and translocations like inter and intra chromosomal) as shown in Fig 2A. Each attribute is a set describing various properties of the variant. In all there are 38 properties in the Chromosome level. Similarly, the other levels have a set of attributes to annotate the variation data.


FROG - Fingerprinting Genomic Variation Ontology.

Abinaya E, Narang P, Bhardwaj A - PLoS ONE (2015)

The attributes, ontology terms and their relationship within (A) Variation and (B) Interaction level.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526677&req=5

pone.0134693.g004: The attributes, ontology terms and their relationship within (A) Variation and (B) Interaction level.
Mentions: FROG is an organism independent fingerprinting system designed to tag genomic variation at various levels of resolution (Fig 1A). FROG has six levels to describe the variation annotation. The six levels are Chromosome, DNA, RNA, Protein, Variations and Interactions (Fig 1B). Each level is a conceptual aggregation of logically connected attributes (Figs 2–4). For example, Chromosome level has five attributes, namely, location of variation (Allosomes or Autosomes), variation kind (indel, deletion, insertion, substitution), number of variations (diploidy, polyploidy—set number, disomy, polysomy—number of variation etc.), repeats (micro- and mini-satellite expansion, tandem repeats, interspersed repeats etc.) and structural variation (complex changes like telomere changes and translocations like inter and intra chromosomal) as shown in Fig 2A. Each attribute is a set describing various properties of the variant. In all there are 38 properties in the Chromosome level. Similarly, the other levels have a set of attributes to annotate the variation data.

Bottom Line: Genetic variations play a crucial role in differential phenotypic outcomes.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, SASTRA University, Thanjavur, Tamil Nadu, 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.

No MeSH data available.