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Welcome to the myvariant.info wiki!

Roadmap

• Setup public server
• Add "data plugins" (importers) for available variant annotation resources
• Setup staging server for external "data plugin" contributors to test their code
• Complete REST API implementation
• Create Python and R native clients
• Investigate the possibility of using myvariant.info data as the backend for popupar variant annotation tools, like ANNOVAR, SNPEFF.

Variant resources

• dbSNP loaded
• COSMIC loaded
• MutDB loaded
• dbNSFP loaded
• SNPedia loaded
• gwassnps loaded (from ucsc)
• docm loaded (variant collections from Obi Griffith's group)
• EVS loaded
• 1000Genomes
• GRASP
• CADD loaded
• ClinVar loaded
• EMVclass loaded
• EVA
• ExAC

Guideline: JSON documents for variants

{
    "_id": <variant_id>,
    "attr1": <value_1>,
    "attr2": <value_2>
    ...
 }

• <variant_id> should follow HGVS standard.

• a real example:

    {
      '_id': u'chr1:g.35366C>T',
      'allele1': u'C',
      'allele2': u'T',
      'chrom': u'chr1',
      'chromEnd': 35367,
      'chromStart': 35366,
      'func': u'unknown',
      'rsid': u'rs71409357',
      'snpclass': u'single',
      'strand': u'-'
    }
  

Resources:

• MyGene.info

  • http://mygene.info

  • MyGene.info repos

    • https://bitbucket.org/sulab/mygene.hub/src (backend)
    • https://bitbucket.org/sulab/mygene.info/src (frontend)

• mutdb (Mooney lab)

  • missense mutations from COSMIC, UniProt, dbSNP
  • (Sean will send dumps, maybe expose an API)