Variation data representation and exchange

Abbreviation: VarioML

General Information

Data using the VarioML standard can be integrated with the global library of purely genetic data. VarioML is a central prerequisite for effective modelling of phenotype data and genotype-to-phenotype relationships. It removes the obstacles to the effective passing of variant data from discovery laboratories into the biomedical database world. Now all that is needed is the broad participation of the genotype-to-phenotype research community.

Homepage http://varioml.org

Countries that developed this resource European Union , United States

Taxonomic range

Homo sapiens

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: VarioML; Variation data representation and exchange; DOI: https://doi.org/10.25504/FAIRsharing.pxvkt0; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Apr 18 2021 5:41 p.m.

This record is maintained by jmuilu ORCID

Record updated: Nov. 21, 2018, 11:40 a.m. by The FAIRsharing Team.

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Edits to 'https://fairsharing.org/FAIRsharing.pxvkt0' by 'The FAIRsharing Team' at 11:40, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Deoxyribonucleic acid (DNA)
			Life Science
			Single nucleotide polymorphism (SNP)
		After:
			Deoxyribonucleic acid (DNA)
			Genetic polymorphism
			Life Science
			Single nucleotide polymorphism (SNP)
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			Genetic polymorphism
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	'miriam_id' has been modified:
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Edits to 'https://fairsharing.org/FAIRsharing.pxvkt0' by 'The FAIRsharing Team' at 18:51, 31 Oct 2018 (approved):

'contact' has been modified:
Before: Contact
After: General Contact

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'description' has been modified:
Before: A Locus-specific Database (LSDB) describes the variants discovered on a single gene or members of a gene family and other related functional elements. LSDBs are curated by experts on their respective loci, and as such are typically the best resources of such information available. But LSDBs vary widely in format and completeness, making data integration and exchange among them difficult and time-consuming. To address these difficulties, the VarioML format has been developed for the full range of variation data use-cases, providing semantically well-defined components which can be easily composed to fit specific needs.

Using VarioML, data owners can now efficiently enable the integration, federation, and exchange of their variant data. The discoverabiliaty, extensibility, and quality of variation data is immediately enhanced. Critical new avenues of research and knowledge discovery are opened, as data using the VarioML standard can be integrated with the global library of purely genetic data.

VarioML is a central prerequisite for effective modelling of phenotype data and genotype-to-phenotype relationships. It removes the long-standing technical obstacles to the effective passing of variant data from discovery laboratories into the biomedical database world. Now all that is needed is the broad participation of the genotype-to-phenotype research community.
After: Data using the VarioML standard can be integrated with the global library of purely genetic data. VarioML is a central prerequisite for effective modelling of phenotype data and genotype-to-phenotype relationships. It removes the obstacles to the effective passing of variant data from discovery laboratories into the biomedical database world. Now all that is needed is the broad participation of the genotype-to-phenotype research community.

Edits to 'https://fairsharing.org/FAIRsharing.pxvkt0' by 'The FAIRsharing Team' at 20:28, 24 Oct 2016 (approved):

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			Contact
			Domain list has changed: 
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			DNA|material|http://purl.org/obo/owl/GO#GO_0005574
			Single Nucleotide Polymorphisms (SNPs)||
			Variation||
			New values: 
			DNA|material|http://purl.org/obo/owl/GO#GO_0005574
			Single Nucleotide Polymorphisms (SNPs)||
			Variation||
			Life Science|domain|
			Standard|information content entity|
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			http://varioml.org/faq.htm
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Support

General

FAQ	http://varioml.org/faq.htm

Additional Information

Contact

General Contact

Tools

No tools defined

Schemas

Name: variome
Version: 1.0

Download

Access / Retrieve Data

Conditions of Use

Publications

VarioML framework for comprehensive variation data representation and exchange

Byrne M, Fokkema IF, Lancaster O, Adamusiak T, Ahonen-Bishopp A, Atlan D, Beroud C, Cornell M, Dalgleish R, Devereau A, Patrinos GP, Swertz MA, Taschner PE, Thorisson GA, Vihinen M, Brookes AJ, Muilu J
BMC Bioinformatics 2012

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (1)

Database of genomic structural VARiation
dbVar is a database of human genomic structural variation where users can search, view, and download data from submitted studies. dbVar stopped supporting data from non-human organisms in 2017, however existing non-human data remains available. In keeping with the common definition of structural variation, most variants are larger than 50 basepairs in length - however a handful of smaller variants may also be found. dbVar provides access to the raw data whenever available, as well as links to additional resources, from both NCBI and elsewhere. It can accept diverse types of events, including inversions, insertions and translocations. Additionally, both germline and somatic variants are accepted.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by jmuilu ORCID

Funds

European Commission FP7 (Government body)

Maintains

gen2phen (Consortium)

Grant Number(s)

200754 (European Commission FP7)

Variation data representation and exchange

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	lsdb.xsd
	cafe_variome.xsd