supporting the integration, federation, and exchange of Variation Data
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README.md

VarioML

VarioML is a XML/RelaxNG based framework which can be used as a template for developing serialization formats for variation data focusing on the LSDB (Locus Specific Mutation Database) use cases. Translations for JSON and EXI are supported using Jackson and Excificient libraries. VarioML is flexible and provides common building blocks for different implementations, which should be fixed further using appropriate schema definition languages like Schematron. VarioML is developed in GEN2PHEN program and it based on an observation model developed there. Simplified UML mode is here

VarioML is a collaborative, community-driven specification in active development. Your first step should be to contact admin at varioml.org, as documentation is not yet complete.

Important:

  • All new implementations should use validation to ensure consistency with the core specification. Contact admin at varioml.org for help with generating validation scripts using Schematron.
  • Use standard ontologies for the content, such as the Sequence Ontology and VariO. Some LSDB specific terms are defined using SKOS vocabularies
  • Source attributes in database xrefs (such as gene and ref_seq) as well as ontology terms should use database abbreviations defined in the MIRIAM registry. For example, use hgnc.symbol for gene names, refseq for NCBI reference sequences, and obo.so for Sequence Ontology references.

VarioML is currently implemented in Café Variome.

More information on VarioML can be found at: http://varioml.org/

VarioML has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 - the GEN2PHEN project.

Apps

Demo applications can be found here https://github.com/VarioML/Apps. Also see validation tools here: https://github.com/VarioML/VarioML/tree/master/xml/cafe_variome/validator, and here: http:varioml.org/validator.htm

News

  • 10.9.2016 Libraries updated. NEMDB Examples added

  • 19.8.2012 Population changed to singleton in frequency. Do not have impact in existing XML implementations (property not used)

  • 8.8.2012 Gene has changed to list of genes. One mutation may have impact on more than one genes

  • 8.8.2012 EXI (http://www.w3.org/XML/EXI/) binary XML support added. EXI can reduce the size of memory usage by 3-~10 times, already even without compression.

  • 9.2.2012: JAXB / JSON (based on Jackson) API implementation is in org.varioml.jaxb folder. Code is not fully tested. SimpleXML implementation will be retired (support is possible though)

  • Note: Version 1.0 is now on a separate branch. The main trunk is heading towards release 2.0. The only difference between 1.0 and 2.0 is that the variant element can have haplotype elements containing variants which are in the cis position. Namespaces will be kept the same.

  • Comments/feedback: admin <> varioml.org. Please send email if you are using the software so that we can accommodate your requirements!