• Corpus ID: 90413454

Online Mendelian Inheritance in Animals (OMIA): inclusion of a hyperlinked table of likely causal variants for inherited disorders and traits

@inproceedings{Tammen2018OnlineMI,
  title={Online Mendelian Inheritance in Animals (OMIA): inclusion of a hyperlinked table of likely causal variants for inherited disorders and traits},
  author={Imke Tammen and Frank W. Nicholas},
  year={2018}
}

• I. Tammen, F. Nicholas
• Published 2018
• Computer Science

Online Mendelian Inheritance in Animals (OMIA) is a comprehensive, annotated catalogue of inherited disorders and other familial traits in animals other than humans, rats and mice. OMIA is modelled on and is complementary to Online Mendelian Inheritance in Man (OMIM). Starting with the very first report of a likely causal variant (for inherited goitre in cattle, published in 1987), the total number of likely causal variants in OMIA is now nearly 1000, with new variants being included at a rate of more than one per week. Until recently, information on these likely causal variants was imbedded in text fields in the OMIA database/website – a source of increasing frustration for researchers and chip designers who require a tabulated list in standard format. In 2013, one of us (FN) commenced placing information on likely causal variants from different sources in standard format in an Excel spreadsheet. In August 2017, work commenced incorporating the contents of the spreadsheet into appropriate new fields in the OMIA database, along with development of curation tools to enable new variants to be added as they are published. This will enable the presentation of all likely causal variants on the OMIA website in a standard tabular format that is readily sortable, and freely downloadable for one or more species. The other major challenge with documenting likely causal variants is that very few (around 4%) of those relevant to OMIA traits have been submitted to any variant database. Primarily this is because variant database submission tools were designed for batch submission of thousands of variants from genome-wide studies, rather than for the submission of one or two variants. Commencing in September 2017, all animal variants will reside only in the European Variant Archive (EVA). Accordingly, one of us (FN) has been collaborating with EVA personnel to devise an easy protocol for the submission of likely causal variant to EVA. When this protocol is fully operational, journal editors will be requested to require submission of any new likely causal variant to EVA as a condition of publication. A major advantage of submitting a variant to EVA is that its genomic location will automatically be updated to the latest version of the relevant genome assembly. For each variant submitted to EVA, OMIA will be able to extract all relevant information (including current genomic location and flanking sequence) via the variant ID, by means of an Application Programming Interface (API). The up-to-date table of likely causal variants that will be downloadable from OMIA will include hyperlinks from each variant to the relevant full entries in OMIA and EVA and to the original publication. This downloadable table should be of benefit to researchers, chip designers, diagnostic service providers, veterinarians and breed societies.