Article thumbnail

VariOtator, A Software Tool for Variation Annotation with the Variation Ontology.

By Gerard Schaafsma and Mauno Vihinen

Abstract

The Variation Ontology (VariO) is used for describing and annotating types, effects, consequences and mechanisms of variations. To facilitate easy and consistent annotations, the online application VariOtator was developed. For variation type annotations VariOtator is fully automated, accepting variant descriptions in Human Genome Variation Society (HGVS) format, and generating VariO terms, either with or without full lineage, i.e. all parent terms. When a coding DNA variant description with a reference sequence is provided, VariOtator checks the description first with Mutalyzer and then generates the predicted RNA and protein descriptions with their respective VariO annotations. For the other sublevels - function, structure and property - annotations cannot be automated, and VariOtator generates annotation based on provided details. For VariO terms relating to structure and property, one can use attribute terms as modifiers and Evidence Code (ECO) terms for annotating experimental evidence. There is an online batch version, and stand-alone batch versions to be used with a Leiden Open Variation Database (LOVD) download file. A SOAP web service allows client programs to access VariOtator programmatically. Thus, systematic variation effect and type annotations can be efficiently generated to allow easy use and integration of variations and their consequences. This article is protected by copyright. All rights reserved

Topics: Biomedical Laboratory Science/Technology
Publisher: 'Wiley'
Year: 2016
DOI identifier: 10.1002/humu.22954
OAI identifier: oai:lup.lub.lu.se:a538a53f-49dc-40fc-8a2a-802a53f56ffe
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://dx.doi.org/10.1002/humu... (external link)
  • https://portal.research.lu.se/... (external link)
  • https://lup.lub.lu.se/record/8... (external link)
  • Suggested articles


    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.