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- Schaafsma, Gerard, et al.
(author)
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VariOtator, A Software Tool for Variation Annotation with the Variation Ontology.
- 2016
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In: Human Mutation. - : Hindawi Limited. - 1059-7794. ; 37:4, s. 344-349
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Journal article (peer-reviewed)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.
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| 2. |
- Vihinen, Mauno, et al.
(author)
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Human Variome Project Quality Assessment Criteria for Variation Databases.
- 2016
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In: Human Mutation. - : Hindawi Limited. - 1059-7794. ; 37:6, s. 549-549
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Journal article (peer-reviewed)abstract
- Numerous databases containing information about DNA, RNA and protein variations are available. Gene-specific variant databases (locus specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. This article is protected by copyright. All rights reserved.
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