LIRICAL JSON Output

Lirical outputs results in a JSON format if --output-format json option is included in the command-line:

lirical phenopacket -p LDS2.v2.json \
  --output-format json

The JSON document contains three sections, the sections are described in the following text along with examples.

Examples of each section are provided below:

Analysis data

analysisData contains the analysis inputs (e.g. sample ID, age, present/excluded phenotypic features):

"analysisData" : {
  "sampleId" : "EXAMPLE",
  "age" : "P1Y2M3D",
  "sex" : "MALE",
  "observedPhenotypicFeatures" : [ "HP:0000001", "HP:0000002" ],
  "excludedPhenotypicFeatures" : [ "HP:0000003" ]
}

Analysis metadata

analysisMetadata includes user-provided options, analysis date, resource versions, etc.

"analysisMetadata" : {
  "liricalVersion" : "liricalVersion",
  "hpoVersion" : "hpoVersion",
  "transcriptDatabase" : "transcriptDatabase",
  "analysisDate" : "2022-12-29T14:02:58.653929682",
  "sampleName" : "sampleId",
  "isGlobalAnalysisMode" : true
}

Analysis results

analysisResults has a list of TestResults for each of the tested diseases.

Here we show an example for a made-up disease OMIM:1234567.

"analysisResults" : [ {
  "diseaseId" : "OMIM:1234567",
  "pretestProbability" : 1.2,
  "observedPhenotypicFeatures" : [ {
    "query" : "HP:0000001",
    "match" : "HP:0000002",
    "matchType" : "EXACT_MATCH",
    "lr" : 1.34,
    "explanation" : "EXPLANATION"
  } ],
  "excludedPhenotypicFeatures" : [ {
    "query" : "HP:0000001",
    "match" : "HP:0000003",
    "matchType" : "EXCLUDED_QUERY_TERM_NOT_PRESENT_IN_DISEASE",
    "lr" : 1.23,
    "explanation" : "EXCLUDED_EXPLANATION"
  } ],
  "genotypeLR" : {
    "geneId" : {
      "id" : "NCBIGene:1234",
      "symbol" : "GENE_SYMBOL"
    },
    "lr" : 1.23,
    "explanation" : "GENE_EXPLANATION"
  },
  "compositeLR" : 2.027286,
  "posttestProbability" : 1.0895759082370065
} ]