VarioML

    What is the VarioML data format?

    The VarioML data format supports data exchange between locus specific databases (LSDBs) and central repositories and HTP data. Use cases include exchanging data between partners in the context of specific phenotype extensions. External invited participants from the epidemiology, medical genetics, ontology development and model organism communities provided expertise and use cases beyond those of Gen2Phen Partners.

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    Is there a published account of VarioML that I can read?

    The VarioML paper has been published - read it here

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    Where can I get more information about VarioML?

    More information is available from: [ top ]   

    Who is the final arbiter of VarioML content?

    VarioML is the product of European scientists collaborating through the Gen2Pgen project. See the Gen2Phen Knowledge Center for more information.

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Variant Reporting Standards

    Will I have to learn a new variant nomenclature?

    No, standard HGVS Nomenclature is used. HGNC names (symbols) should be used to name genes.

    Example source:

    • HGNC

    Example accession:

    • BRACA2

    Examples:

    <gene source="HGNC" accession="BRACA2"/>
    
    <gene source="HGNC" accession="BRACA2"> 
    	<db_xref accession="600185" uri="http://www.ncbi.nlm.nih.gov/omim/600185" source="OMIM"/>
    	<db_xref accession="BRACA2" source="HGNC" uri="http://www.genenames.org/data/hgnc_data.php?hgnc_id=1101"/>
    </gene>
    


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    What are current best practices in variation nomenclature?

    See our Nomenclature page here.


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    How do I find out if an LSDB already exists for my gene of interest?

    Search the Gen2Phen LSDB listing here.

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    If none yet exists, how do I request the creation of an LSDB?

    You can request the creation of an LSDB for your gene of interest by contacting us here.

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Using LSDBs

    What are the differences between the VarioML data format and the Leiden Open Variation Database (LOVD) format?

    See LSDB compared to LOVD.

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    What do I need to view a VarioML LSDB?

    Browser-based tools and other applications to view VarioML LSDBs and use different facets of the VarioML data model are forthcoming. Subscribe to the VarioML RSS feed to receive notification of tools as they become available.

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Software support for LSDBs

    What free software currently supports LSDBs?

    Are there any third-party applications that support the VarioML LSDB format?

    VarioML can be used with these leading tools: [ top ]   

    Can I write my own application?

    Anybody can write an application to make use of VarioML. The VarioML format is open and the schema is freely available here. Technical support for the schema is available at help@gen2phen.org. We would encourage you to make your software free and open and to let us know about it so that we can provide links to your application.

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    Are there pre-written support modules for programming languages?

    We are not aware of any at present. However, we hope that there will eventually be modules to support VarioML in the commonly used scripting languages such as Perl, Python, PHP, Ruby etc.

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Specifications and standards

    Where can I get a copy of the VarioML specification?

    The current version of the technical specification document is available here: VarioML data format specification. A technical reference to the specification is here.

    Are VarioML LSDBs formatted as GenBank records or as EMBL records?

    VarioML uses XML as this provides many technical advantages.

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    If LSDBs are written in XML, are they not difficult to read?

    Style sheets are being created to transform the VartioML XML files into a human readable format.

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    Is the VarioML XML schema available?

    The VarioML XML schema can be downloaded here.

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    Can I create my own VarioML LSDB?

    For an LSDB to be an international standard, it must be accessioned by the collaborating groups. If you would like to request a VarioML LSDB, please contact us here.

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    Can I request new features for the VarioML schema?

    Requests for changes to the schema should be made to us here.

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    What is an LSDB?

    from Wikipedia:LOVD entry:

    A database to collect and display variants in the DNA sequence.

    The focus of an LSDB is usually the combination between a gene and a genetic (heritable) disease. All sequence variants found in individuals are collected in the database, together with information about whether they could be causally connected to the disease (i.e. a disease-causing variant or mutation) or not (i.e. a non-disease causing variant). Specialized doctors (clinical geneticists) use LSDBs to diagnose and advise patients carrying a genetic disease. Ideally, if a patient has been screened for mutations and one has been found, information in LSDB can predict the progress of the disease. In contrast to human genome databases, showing information on all DNA variants, LSDBs include information about the individuals in which the variants were found. This patient information is only accessible for registered users.

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    Are there published accounts of LSDBs I can read?

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Administrative Issues

    What is the role of GEN2PHEN in VarioML?

    The VarioML data format is being developed within the GEN2PHEN project (http://www.gen2phen.org/) which is funded for five years under the European Community's Seventh Framework Programme (FP7: http://cordis.europa.eu/fp7/).

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    What will happen when the GEN2PHEN project funding ends?

    Although funding for GEN2PHEN ends in December 2012, only the initial development of the LSDB data format concept is supported by GEN2PHEN.

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