From 9814e8bc0e7182edc34a49b083898f561300d0f4 Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 19 Sep 2024 09:28:50 +0200 Subject: [PATCH] Change content of demo json submission to include a demo submission from ClinVar --- preClinVar/demo/__init__.py | 4 +- ...clinical_significance_hgvs_submission.json | 52 +++++ preClinVar/demo/submission.json | 200 ------------------ 3 files changed, 54 insertions(+), 202 deletions(-) create mode 100644 preClinVar/demo/sample_clinical_significance_hgvs_submission.json delete mode 100644 preClinVar/demo/submission.json diff --git a/preClinVar/demo/__init__.py b/preClinVar/demo/__init__.py index 867fcee..4a71074 100644 --- a/preClinVar/demo/__init__.py +++ b/preClinVar/demo/__init__.py @@ -22,5 +22,5 @@ variants_sv_range_coords_csv_path = str(files(BASE_PATH).joinpath(variants_sv_range_coords_csv)) ###### Example of a json file submission ###### -subm_json = "submission.json" -subm_json_path = str(files(BASE_PATH).joinpath(subm_json)) +clinsig_subm_json = "sample_clinical_significance_hgvs_submission.json" +subm_json_path = str(files(BASE_PATH).joinpath(clinsig_subm_json)) diff --git a/preClinVar/demo/sample_clinical_significance_hgvs_submission.json b/preClinVar/demo/sample_clinical_significance_hgvs_submission.json new file mode 100644 index 0000000..9ad8603 --- /dev/null +++ b/preClinVar/demo/sample_clinical_significance_hgvs_submission.json @@ -0,0 +1,52 @@ +{ + "clinvarSubmissionReleaseStatus": "hold until published", + "assertionCriteria":{ + "db": "PubMed", + "id": "25741868" + }, + "clinvarSubmission":[{ + "recordStatus": "novel", + "clinicalSignificance": { + "clinicalSignificanceDescription": "Pathogenic", + "dateLastEvaluated": "2018-04-28", + "comment": "This comment explains the rationale for classifying this PDE6B variant as pathogenic for Retinitis pigmentosa-40.", + "citation": [{ + "db": "PubMed", + "id": "PMID:11295882" + + }, + { + "db": "PubMed", + "id": "PMID:1363786" + + }, + { + "url": "https://yourdatabaselink.org" + }], + "modeOfInheritance":"Autosomal dominant inheritance" + }, + "observedIn":[ { + "alleleOrigin": "germline", + "affectedStatus": "yes", + "collectionMethod": "clinical testing", + "numberOfIndividuals": 1 + }], + "variantSet": { + "variant": [{ + "hgvs":"NM_000283.3:c.3645A>T", + "gene":[ { + "id":2 + }] + }]}, + "conditionSet": { + "condition": [{ + "db": "OMIM", + "id": "613801" + }] + + } + + +} +] +} \ No newline at end of file diff --git a/preClinVar/demo/submission.json b/preClinVar/demo/submission.json deleted file mode 100644 index c6a32aa..0000000 --- a/preClinVar/demo/submission.json +++ /dev/null @@ -1,200 +0,0 @@ -{ - "assertionCriteria": { - "db": "PubMed", - "id": "25741868" - }, - "clinvarSubmission": [ - { - "clinicalSignificance": { - "clinicalSignificanceDescription": "Pathogenic", - "dateLastEvaluated": "2021-03-16", - "modeOfInheritance": "Autosomal recessive inheritance" - }, - "conditionSet": { - "condition": [ - { - "db": "OMIM", - "id": "248600" - } - ] - }, - "localID": "7b7a372ea54e1c0de9ec6af4ebebd14a", - "localKey": "7b7a372ea54e1c0de9ec6af4ebebd14a", - "observedIn": [ - { - "affectedStatus": "yes", - "alleleOrigin": "germline", - "collectionMethod": "clinical testing" - } - ], - "variantSet": { - "variant": [ - { - "hgvs": "c.832G>A", - "gene": [ - { - "symbol": "BCKDHB" - } - ] - } - ] - }, - "recordStatus": "novel" - }, - { - "clinicalSignificance": { - "clinicalSignificanceDescription": "Pathogenic", - "dateLastEvaluated": "2021-03-12", - "modeOfInheritance": "Autosomal recessive inheritance" - }, - "conditionSet": { - "condition": [ - { - "db": "OMIM", - "id": "278300" - } - ] - }, - "localID": "1d9ce6ebf2f82d913cfbe20c5085947b", - "localKey": "1d9ce6ebf2f82d913cfbe20c5085947b", - "observedIn": [ - { - "affectedStatus": "yes", - "alleleOrigin": "germline", - "collectionMethod": "clinical testing" - } - ], - "variantSet": { - "variant": [ - { - "hgvs": "c.2751del", - "gene": [ - { - "symbol": "XDH" - } - ] - } - ] - }, - "recordStatus": "novel" - }, - { - "clinicalSignificance": { - "clinicalSignificanceDescription": "Pathogenic", - "dateLastEvaluated": "2021-03-16", - "modeOfInheritance": "Autosomal recessive inheritance" - }, - "conditionSet": { - "condition": [ - { - "db": "OMIM", - "id": "606054" - } - ] - }, - "localID": "69b138a4c5caf211d796a59a7b46e40d", - "localKey": "69b138a4c5caf211d796a59a7b46e40d", - "observedIn": [ - { - "affectedStatus": "yes", - "alleleOrigin": "germline", - "collectionMethod": "clinical testing" - } - ], - "variantSet": { - "variant": [ - { - "hgvs": "c.2040G>A", - "gene": [ - { - "symbol": "PCCA" - } - ] - } - ] - }, - "recordStatus": "novel" - }, - { - "clinicalSignificance": { - "clinicalSignificanceDescription": "Pathogenic", - "dateLastEvaluated": "2021-03-12", - "modeOfInheritance": "Autosomal recessive inheritance" - }, - "conditionSet": { - "condition": [ - { - "db": "OMIM", - "id": "250100" - } - ] - }, - "localID": "e1bdbf66cd8df98d0d6874a9c4a0d7bc", - "localKey": "e1bdbf66cd8df98d0d6874a9c4a0d7bc", - "observedIn": [ - { - "affectedStatus": "yes", - "alleleOrigin": "germline", - "collectionMethod": "clinical testing" - } - ], - "variantSet": { - "variant": [ - { - "hgvs": "c.465+1G>A", - "gene": [ - { - "symbol": "ARSA" - } - ] - } - ] - }, - "recordStatus": "novel" - }, - { - "clinicalSignificance": { - "clinicalSignificanceDescription": "Pathogenic", - "dateLastEvaluated": "2021-03-12", - "modeOfInheritance": "Autosomal recessive inheritance" - }, - "conditionSet": { - "condition": [ - { - "db": "OMIM", - "id": "251000" - } - ] - }, - "localID": "ace28c419a620040c49be5ec9cb7ba37", - "localKey": "ace28c419a620040c49be5ec9cb7ba37", - "observedIn": [ - { - "affectedStatus": "yes", - "alleleOrigin": "germline", - "collectionMethod": "clinical testing" - }, - { - "affectedStatus": "yes", - "alleleOrigin": "germline", - "collectionMethod": "clinical testing" - } - ], - "variantSet": { - "variant": [ - { - "hgvs": "c.278G>A", - "gene": [ - { - "symbol": "MMUT" - } - ] - } - ] - }, - "recordStatus": "novel" - } - ], - "submissionName": "SUB1234", - "clinvarSubmissionReleaseStatus": "public" -}