Variation Ontology for annotation of variation effects and mechanisms

Vihinen, Mauno

doi:10.1101/gr.157495.113

Cited by 57 publications

(70 citation statements)

References 34 publications

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“…Existing ontologies, such as the Human Phenotype Ontology (HPO) [30], Sequence Ontology (SO) [31], and Variation Ontology (VariO) [32], can be used with VarioML. Separate SKOS (Simple Knowledge Organization System) [33] vocabularies have been provided for elements which do not have online definitions.…”

Section: Methodsmentioning

confidence: 99%

VarioML framework for comprehensive variation data representation and exchange

et al. 2012

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BackgroundSharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement.ResultsThe GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components.ConclusionsVarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

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Section: Methodsmentioning

confidence: 99%

VarioML framework for comprehensive variation data representation and exchange

et al. 2012

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“…This applies also to variation information. Recently, VariO (http://www.variationontology.org/) was introduced for the systematic description of variation effects, consequences and mechanisms (Vihinen 2014a). The ontology is used to annotate information in databases at the three molecular levels: DNA, RNA and protein.…”

Section: Variation Ontologymentioning

confidence: 99%

“…In this article, effects of protein variations are discussed mainly in relation to diseases and in the framework of the Variation Ontology (VariO) (Vihinen 2014a), which allows systematic description of variation effects, consequences and mechanisms whether of experimental or of predicted origin. Examples are included to highlight the different features of variants.…”

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confidence: 99%

Types and effects of protein variations

Vihinen

2015

Hum Genet

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Types and effects of protein variations. Vihinen, MaunoPublished in: Human Genetics DOI: 10.1007/s00439-015-1529-6Published: 2015-01-01Link to publication Citation for published version (APA): Vihinen, M. (2015). Types and effects of protein variations. Human Genetics, 134(4), 405-421. DOI: 10.1007405-421. DOI: 10. /s00439-015-1529 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. for all variation types, a more detailed description can be made by explaining changes to protein function, structure and properties. Examples are provided for the effects and mechanisms, usually in relation to human diseases. In addition, the examples are selected so that protein 3D structural changes, when relevant, are included and visualized. Here, systematics is described for protein variants based on VariO. It will benefit the unequivocal description of variations and their effects and further reuse and integration of data from different sources. 1 TYPES AND EFFECTS OF PROTEIN VARIATIONS

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“…These include the Human Genome Variation Society (HGVS) nomenclature [2], articles [3] including the American College of Medical Genetics guidelines [4], and Variation Ontology (VariO) [5] (Box 1).…”

Section: Mutation Versus Variationmentioning

confidence: 99%

“…To address this, VariO translates systematic descriptions of variation type into short English terms for variations, such as DNA substitution or protein truncation [5] (Box 1). The VariOtator tool (http://variationontology.org/VariOtator.php) provides VariO variation-type annotations automatically from the sequence and variation details.…”

Section: Variation In Naming Systematicsmentioning

confidence: 99%

Muddled genetic terms miss and mess the message

Vihinen

2015

Trends in Genetics

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Muddled genetic terms miss and mess the message. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Vihinen, Mauno• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Muddled genetic terms miss and mess the message Mauno VihinenDepartment of Experimental Medical Science, Lund University, BMC D10, SE-22184 Lund, Sweden A critical aspect of science is the clear communication of complicated matters. However, language is often ambiguous, and the message can get lost in the telling. In particular, genetic terms can have different meanings for different people. Here, I discuss this problem and suggest remedies to clarify the message.

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Variation Ontology for annotation of variation effects and mechanisms

Cited by 57 publications

References 34 publications

VarioML framework for comprehensive variation data representation and exchange

VarioML framework for comprehensive variation data representation and exchange

Types and effects of protein variations

Muddled genetic terms miss and mess the message

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