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developing shared terminology and specifications for exchanging sequence variation
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Latest commit 0864123 Oct 15, 2019

README.md

DOI

The GA4GH Variation Representation Specification provides a comprehensive framework for the computational representation of biological sequence variation. VR-Spec is the result of a collaboration among contributors representing national information resource providers, major international public initiatives, and diagnostic testing laboratories.

NOTE: vr-spec is under very active development. The priorities and roadmap are available at the VR 2019 Project.

Specific goals:

  • Develop common language- and protocol-neutral information models and nomenclature for biological sequence variation.
  • From the information models, develop data schemas. The current schema is defined in JSON Schema, but other formats are expected.
  • Provide algorithmic guidance and conventions to minimize representational ambiguity.
  • Define a globally unique computed identifier for covered data classes.
  • Develop an implementation to facilitate adoption.
  • Develop validation tests to ensure consistency of implementations.

The VR model is the product of the GA4GH Variation Representation group.

Using the schema

The schema is available in the schema/ directory, in both yaml and json versions. It conforms to json schema draft-07. For a list of libraries that support json schema, see JSON Schema>Implementations.

Contributing to the schema

VR uses yaml as the source document for json schema

To convert vr.yaml to vr.json:

make vr.json

You'll probably have to pip install pyyaml first.

To watch for changes and update automatically:

make -C schema watch &

Contributing docs

The VR specification documentation is written in reStructuredText and located in docs/source/. Commits to this repo are built automatically at vr-spec.readthedocs.io__.

To build documentation locally, type:

make -C docs clean watch &

Then, open docs/build/html/index.html. The above make command should build docs when source changes. (Some types of changes require recleaning and building.)

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