Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relationships between genotype and phenotype.
An ontology for standardized, systematic description of effects, consequences and mechanisms of variations. VariO allows unambiguous description of variation effects as well as computerized analyses over databases utilizing the ontology for annotation. VariO is a position specific ontology that can be used to describe effects of variations on DNA, RNA and/or protein level, whatever is appropriate.
Recommendations for the description of sequence variants. HGVS-nomenclature is used to report and exchange information regarding variants found in DNA, RNA and protein sequences and serves as an international standard in DNA diagnostics. HGVS-nomenclature is authorised by the Human Genome Variation Society (HGVS), the Human Variome Project (HVP) and the HUman Genome Organization (HUGO). The HGVS recommendations are designed to be stable, meaningful, memorable, and unequivocal.
Enables the generic representation of genomic feature and variation data. GFVO specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations.
A semantic approach 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. FROG is a unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis.
Provides a timely, robust, and useful data model, sufficiently developed and tested to justify formal registration and deployment to the many and various communities engaged in genotype-phenotype data handling. PaGE-OM has been tested and implemented in conjunction with several major databases, and approved as a standard by the Object Management Group (OMG). PaGE-OM is open-source, ready for use by the wider community, and can be further developed as needs arise. It will help to improve information management, assist data integration, and simplify the task of informatics resource design and construction for genotype and phenotype data projects.