elastic

G2P VERSION 0.8

contents

ui: https://g2p-test.ddns.net elastic search backups: s3://g2p-test-snapshots "snapshot_20180125t1305" (contact for access) json files : s3://g2p-0.8 (public access)

Each file is contains evidence documents from the respective source. all.json contains the aggregations of all sources.

source	count
molecularmatch_trials	41148
jax	5754
brca	5717
oncokb	4048
civic	3497
molecularmatch	2079
cgi	1431
jax_trials	1173
pmkb	600
sage	69

evidence_label	count
C	33590
D	18764
B	7646
A	1715

changes

• ontology terms (environment & phenotype) now have 'source' itemized separately
• Evidence from brca no longer has "Unreviewed" variants
• Molecular match trials CONDITION is now filtered to remove hierarchy terms, which previously accounted for many records identical except for phenotype

structure

// An association between a phenotype('disease'), environment('drug')
// and genome(feature), harvested from a trusted knowledge base(source).
// For organization, the entrez name('genes') is included separately.
// For traceability, the document from the original source is included


message Evidence {
  string source = 1;
  repeated string genes = 2;

  // "ga4gh/sequence_annotations.proto"
  repeated google.protobuf.Struct features = 3;

  // "ga4gh/genotype_phenotype.proto"
  google.protobuf.Struct association = 4;

  // opaque source documents
  oneof opaque_source {
    google.protobuf.Struct cgi = 5;
    google.protobuf.Struct jax = 6;
    google.protobuf.Struct civic = 7;
    google.protobuf.Struct oncokb = 8;
    google.protobuf.Struct molecularmatch = 9;
    google.protobuf.Struct molecularmatch_trials = 10;
    google.protobuf.Struct jax_trials = 11;
    google.protobuf.Struct sage = 12;
  }  
}

_{Note: the feature and associations are based on ga4gh.feature and ga4gh.FeaturePhenotypeAssociation, but have evolved. Future phases will create a PR to the appropriate GA4GH repository}