Evidence Repository API

This wiki presents the documentation for the ClinGen Evidence Repository JSON-LD REST API.

A.1. Interpretations

A.1.1 Interpretation by UUID

Get an interpretation record by the unique identifier in SEPIO supported JSON-LD format.

https://erepo.genome.network/evrepo/api/interpretation/{uuid}

Example - https://erepo.genome.network/evrepo/api/interpretation/fc9045f6-6b42-44b3-91a2-bb334c06b05f
Payload (truncated):


{
  "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA285292/MONDO:0008723/021",
  "id": "CG-PCER-VARINT:CA285292/MONDO:0008723/021",
  "type": "VariantPathogenicityInterpretation",
  "@context": "https://erepo.genome.network/evrepo/api/context",
  "uuid": "fc9045f6-6b42-44b3-91a2-bb334c06b05f",
  "metadata": {
    "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)",
    "contentVersionId": 9223372036854775807,
    "producedAtUTC": "Thu, 07 Jul 2022 12:40:27 -0000",
    "note": "DISCLAIMER: While the data/content in this document is approved by ClinGen expert panel(s), the SEPIO schema presented here is an initial prototype and has not been reviewed nor finalized by the ClinGen Data Exchange Modeling Team. We expect it to differ significantly from the final schema." 
  },
  "variant": {
    "@id": "https://reg.genome.network/allele/CA285292",
    "id": "CAR:CA285292",
    "type": "CAR",
    "relatedContextualAllele": [
      {
        "preferred": true,
        "alleleName": [
          {
            "name": "NM_000018.4:c.194C>T" 
          }
        ]
      }
    ],
    "relatedIdentifier": [
      {
        "label": "NM_000018.4(ACADVL):c.194C>T (p.Pro65Leu)" 
      }
    ]
  },
  "condition": {
    "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0008723",
    "id": "MONDO:0008723",
    "type": "GeneticCondition",
    "label": "very long chain acyl-CoA dehydrogenase deficiency" 
  },
  "statementOutcome": {
    "@id": "https://loinc.org/LA6675-8",
    "id": "LN:LA6675-8",
    "label": "Benign" 
  },
  "assertionMethod": {
    "@id": "https://obofoundry.org/sepio/0000193",
    "id": "AssertMeth331",
    "type": "VariantPathogenicityInterpretationGuideline",
    "version": "1.0",
    "description": "ACMG ISV guidelines 2015",
    "url": "https://clinicalgenome.org/site/assets/files/7380/clingen_acadvl_acmg_specifications_v1.pdf",
    "scoringAlgorithm": {
      "id": "SEPIO-CG:99300",
      "description": "This is the description of how the weighting of the satisfied criterion are typically evaluated to arrive at a specific clinical significance." 
    },
    "label": "ClinGen ACADVL Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1" 
  },
  "evidenceLine": [ ... ]

}

A.1.2 Interpretation by an allele context

Interpretation by an allele context (CAR, disease and specification ID)

https://erepo.genome.network/evrepo/api/interpretation/{contextID}

Example - https://erepo.genome.network/evrepo/api/interpretation/CA285292/MONDO:0008723/021

A.1.3 Interpretation by a combination of fields

Interpreations are also defined by one or more of the query parameters given below with the query string given in parenthesis:
  1. Allele Registry ID (caid)
  2. ClinVar ID (variationID)
  3. HGVS (hgvs)
  4. Gene (gene)
  5. Condition (condition)
  6. Assertion (assertion)
  7. Variant Curation Expert Panel (expertpanel)

Example to get all pathogenic interpretations for the gene CDH23

https://erepo.genome.network/evrepo/api/classifications?assertion=Pathogenic&matchMode=exact&gene=CDH23

{"@context":"https://erepo.genome.network/evrepo/api/context/light","variantInterpretations":[{"evidenceLinks":[{"@id":"https://www.ncbi.nlm.nih.gov/pubmed/30367262"},{"@id":"https://www.ncbi.nlm.nih.gov/pubmed/24164807"},{"@id":"https://www.ncbi.nlm.nih.gov/pubmed/26264712"},{"@id":"https://www.ncbi.nlm.nih.gov/pubmed/22899989"},{"@id":"https://www.ncbi.nlm.nih.gov/pubmed/17850630"},{"@id":"https://www.ncbi.nlm.nih.gov/pubmed/25963016"},{"@id":"https://www.ncbi.nlm.nih.gov/pubmed/24618850"}],"publishedDate":"2019-10-17","uuid":"bdc50191-a305-4375-b8cc-89088a4e5cac","@id":"https://erepo.genome.network/evrepo/api/interpretation/CA253338/MONDO:0019497/005","warnings":null,"caid":"CAR:CA253338","condition":{"@id":"MONDO:0019497","label":"nonsyndromic genetic deafness"},"hgvs":["NM_022124.5:c.719C>T","NC_000010.11:g.71570884C>T","CM000672.2:g.71570884C>T","NC_000010.10:g.73330641C>T","CM000672.1:g.73330641C>T","NC_000010.9:g.73000647C>T","NG_008835.1:g.178938C>T","NM_001171930.1:c.719C>T","NM_001171931.1:c.719C>T","NM_001171932.1:c.719C>T","NM_052836.3:c.719C>T","XM_006717940.2:c.854C>T","XM_006717942.2:c.854C>T","XM_011540039.1:c.854C>T","XM_011540040.1:c.854C>T","XM_011540041.1:c.854C>T","XM_011540042.1:c.854C>T","XM_011540043.1:c.854C>T","XM_011540044.1:c.719C>T","XM_011540045.1:c.854C>T","XM_011540046.1:c.314C>T","XM_011540048.1:c.854C>T","XM_011540049.1:c.854C>T","XM_011540050.1:c.854C>T","XM_011540051.1:c.854C>T","XM_011540053.1:c.854C>T","XM_011540054.1:c.854C>T","XR_246128.2:n.162-5750G>A","XR_945796.1:n.1097C>T","ENST00000224721.10:c.734C>T","ENST00000299366.11:c.719C>T","ENST00000398809.8:c.719C>T","ENST00000398842.7:c.470C>T","ENST00000461841.7:c.719C>T","ENST00000466757.7:n.90C>T","ENST00000616684.4:c.719C>T","ENST00000622827.4:c.719C>T","NM_022124.5(CDH23):c.719C>T (p.Pro240Leu)"],"gene":{"label":"CDH23","NCBI_id":"64072"},"guidelines":[{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN005","label":"Hearing Loss Variant Curation Expert Panel","outcome":{"@id":"LN:LA6668-3","label":"Pathogenic"},"agents":[{"@id":"CG-PCER-AGENT:CG_50007_EP.1551907997.58139","label":"CG_50007 EP","evidenceCodes":[{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN005/tag/BP4","label":"BP4","status":"Not Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN005/tag/PS4","label":"PS4","status":"Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN005/tag/PP3","label":"PP3","status":"Not Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN005/tag/PP1_Strong","label":"PP1_Strong","status":"Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN005/tag/PM2_Supporting","label":"PM2_Supporting","status":"Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN005/tag/PM3_Strong","label":"PM3_Strong","status":"Met"}],"affiliation":"Hearing Loss VCEP","outcome":{"@id":"LN:LA6668-3","label":"Pathogenic"}}]}],"variationId":"4928"}]}

Another example to get intepretations from the Hereditary Breast, Ovarian and Pancreatic Cancer VCEP. Note: by default it returns the first 25 entries.
https://erepo.genome.network/evrepo/api/classifications?matchMode=exact&expertpanel=Hereditary%20Breast,%20Ovarian%20and%20Pancreatic%20Cancer%20VCEP

Use the matchLimit parameter to the limit or get all the interpretations
Example, limit by 2 interpretations

https://erepo.genome.network/evrepo/api/classifications?matchMode=exact&expertpanel=Hereditary%20Breast,%20Ovarian%20and%20Pancreatic%20Cancer%20VCEP&matchLimit=2

{"@context":"https://erepo.genome.network/evrepo/api/context/light","variantInterpretations":[{"evidenceLinks":[],"publishedDate":"2022-03-09","uuid":"f902c885-8b6e-4e29-a3bb-2b52a3a53330","@id":"https://erepo.genome.network/evrepo/api/interpretation/CA165678/MONDO:0016419/020","warnings":[],"caid":"CAR:CA165678","condition":{"@id":"MONDO:0016419","label":"hereditary breast cancer"},"hgvs":["NM_000051.3:c.3284G>A","NC_000011.10:g.108272852G>A","CM000673.2:g.108272852G>A","NC_000011.9:g.108143579G>A","CM000673.1:g.108143579G>A","NC_000011.8:g.107648789G>A","NG_009830.1:g.55021G>A","LRG_135:g.55021G>A","ENST00000527805.6:c.3284G>A","ENST00000675595.1:c.3119G>A","ENST00000675843.1:c.3284G>A","ENST00000278616.8:c.3284G>A","ENST00000452508.6:c.3284G>A","ENST00000527805.5:c.3284G>A","LRG_135t1:c.3284G>A","XM_005271561.3:c.3284G>A","XM_005271562.3:c.3284G>A","XM_006718843.2:c.3284G>A","XM_011542840.1:c.3284G>A","XM_011542841.1:c.3284G>A","XM_011542842.1:c.3119G>A","XM_011542843.1:c.3284G>A","XM_011542844.1:c.2240G>A","XM_011542845.1:c.1976G>A","XM_011542846.1:c.3284G>A","NM_001351834.1:c.3284G>A","XM_005271562.5:c.3284G>A","XM_006718843.4:c.3284G>A","XM_011542840.3:c.3284G>A","XM_011542842.3:c.3119G>A","XM_011542843.2:c.3284G>A","XM_011542844.3:c.2240G>A","XM_011542845.2:c.1976G>A","XM_017017789.2:c.3284G>A","XM_017017790.2:c.3284G>A","XM_017017791.1:c.3284G>A","XM_017017792.2:c.3284G>A","XR_002957150.1:n.4017G>A","NM_001351834.2:c.3284G>A","NM_000051.4:c.3284G>A","NM_000051.4(ATM):c.3284G>A (p.Arg1095Lys)","NM_000051.3(ATM):c.3284G>A (p.Arg1095Lys)"],"gene":{"label":"ATM","NCBI_id":"472"},"guidelines":[{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020","label":"Hereditary Breast, Ovarian and Pancreatic Cancer (HBOP)","outcome":{"@id":"LN:LA26333-7","label":"Uncertain Significance"},"agents":[{"@id":"CG-PCER-AGENT:CG_50039_EP.1646807360.3834","label":"CG_50039 EP","evidenceCodes":[{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020/tag/PP3","label":"PP3","status":"Not Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020/tag/PVS1_Strong","label":"PVS1_Strong","status":"Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020/tag/PM2_Supporting","label":"PM2_Supporting","status":"Met"}],"affiliation":"Hereditary Breast, Ovarian and Pancreatic Cancer VCEP","outcome":{"@id":"LN:LA26333-7","label":"Uncertain Significance - Insufficient Evidence"}}]}],"variationId":"141522"},{"evidenceLinks":[],"publishedDate":"2022-03-09","uuid":"b031a823-83d4-4852-b057-ff7333023650","@id":"https://erepo.genome.network/evrepo/api/interpretation/CV453341/MONDO:0016419/020","warnings":[{"warningId":{"value":"message-gene-missing","properties":{"msg":{"value":"There was no gene found in the curated document received from the VCI/VCEP"}}}},{"warningId":{"value":"missing-message-gene-derived-from-ClinVarCAR","properties":{"msg":{"value":"Gene listed was thus derived from ClinVar and/or CAR"}}}}],"caid":"","condition":{"@id":"MONDO:0016419","label":"hereditary breast cancer"},"hgvs":["NC_000011.10:g.(?_108287594)_(108287721_?)del"],"gene":{"label":"ATM"},"guidelines":[{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020","label":"Hereditary Breast, Ovarian and Pancreatic Cancer (HBOP)","outcome":{"@id":"LN:LA6668-3","label":"Pathogenic"},"agents":[{"@id":"CG-PCER-AGENT:CG_50039_EP.1646807360.3834","label":"CG_50039 EP","evidenceCodes":[{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020/tag/PVS1","label":"PVS1","status":"Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020/tag/PM2_Supporting","label":"PM2_Supporting","status":"Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020/tag/PM5_Supporting","label":"PM5_Supporting","status":"Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020/tag/BA1","label":"BA1","status":"Not Met"},{"@id":"https://erepo.genome.network/evrepo/api/guideline/GN020/tag/BS1","label":"BS1","status":"Not Met"}],"affiliation":"Hereditary Breast, Ovarian and Pancreatic Cancer VCEP","outcome":{"@id":"LN:LA6668-3","label":"Pathogenic"}}]}],"variationId":"453341"}]}

To get all the interpretaions use the matchLimit query string with the value all
For example. get all interpretations where the assertion is Benign or expertpanel is ACADVL VCEP
https://erepo.genome.network/evrepo/api/classifications?assertion=Benign&matchMode=exact&expertpanel=ACADVL%20VCEP&matchLimit=all

A.1.4 Download interpretations

Download interpretations in tab limited text format by using the query parameter format as given below: 

https://erepo.genome.network/evrepo/api/classifications/all?format=tabbed&matchSkip=0&assertion=Pathogenic&matchLimit=25&gene=ACADVL&matchMode=exact

A.1.5 Fetch all the interpretations

Get all the interpretation records in a tab limited format via this GET API:

https://erepo.clinicalgenome.org/evrepo/api/classifications/all?format=tabbed