From e79c2b0e2994ba5daba3fb9fc81bcfbe0747339d Mon Sep 17 00:00:00 2001 From: Kori Kuzma Date: Wed, 24 Jun 2026 11:26:04 -0400 Subject: [PATCH] test: temporary add specifiedBy for onco evidence line * Just to get CI tests to pass. Actual representation will be in #404 --- .../civic-assertion-oncogenicity.yaml | 115 ++++++++++++++++-- 1 file changed, 105 insertions(+), 10 deletions(-) diff --git a/tests/fixtures/civic-assertion-oncogenicity.yaml b/tests/fixtures/civic-assertion-oncogenicity.yaml index 4ce0a6c6..9b132e8f 100644 --- a/tests/fixtures/civic-assertion-oncogenicity.yaml +++ b/tests/fixtures/civic-assertion-oncogenicity.yaml @@ -69,7 +69,7 @@ specifiedBy: hasEvidenceLines: - type: EvidenceLine directionOfEvidenceProvided: supports - targetProposition: # identical to VariantOncogenicityStatement.proposition + targetProposition: # identical to VariantOncogenicityStatement.proposition type: VariantOncogenicityProposition objectTumorType: id: civic.did:15 @@ -84,7 +84,8 @@ hasEvidenceLines: subjectVariant: id: civic.mpid:113 type: CategoricalVariant - description: RET M918T is the most common somatically acquired mutation in + description: + RET M918T is the most common somatically acquired mutation in medullary thyroid cancer (MTC). While there currently are no RET-specific inhibiting agents, promiscuous kinase inhibitors have seen some success in treating RET overactivity. Data suggests however, that the M918T mutation @@ -121,9 +122,27 @@ hasEvidenceLines: code: OM1 system: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 scoreOfEvidenceProvided: 2 + specifiedBy: + type: Method + methodType: functional_domain_location + name: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 + reportedIn: + doi: 10.1016/j.gim.2022.01.001 + id: pmid:35101336 + name: Horak et al., 2022, Genet Med. + pmid: "35101336" + title: + "Standards for the classification of pathogenicity of somatic variants in + cancer (oncogenicity): Joint recommendations of Clinical Genome + Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant + Interpretation for Cancer Consortium (VICC)" + type: Document + urls: + - https://doi.org/10.1016/j.gim.2022.01.001 + - https://pubmed.ncbi.nlm.nih.gov/35101336/ - type: EvidenceLine directionOfEvidenceProvided: supports - targetProposition: # identical to VariantOncogenicityStatement.proposition + targetProposition: # identical to VariantOncogenicityStatement.proposition type: VariantOncogenicityProposition objectTumorType: id: civic.did:15 @@ -138,7 +157,8 @@ hasEvidenceLines: subjectVariant: id: civic.mpid:113 type: CategoricalVariant - description: RET M918T is the most common somatically acquired mutation in + description: + RET M918T is the most common somatically acquired mutation in medullary thyroid cancer (MTC). While there currently are no RET-specific inhibiting agents, promiscuous kinase inhibitors have seen some success in treating RET overactivity. Data suggests however, that the M918T mutation @@ -175,9 +195,27 @@ hasEvidenceLines: code: OS2 system: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 scoreOfEvidenceProvided: 4 + specifiedBy: + type: Method + methodType: functional_assay + name: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 + reportedIn: + doi: 10.1016/j.gim.2022.01.001 + id: pmid:35101336 + name: Horak et al., 2022, Genet Med. + pmid: "35101336" + title: + "Standards for the classification of pathogenicity of somatic variants in + cancer (oncogenicity): Joint recommendations of Clinical Genome + Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant + Interpretation for Cancer Consortium (VICC)" + type: Document + urls: + - https://doi.org/10.1016/j.gim.2022.01.001 + - https://pubmed.ncbi.nlm.nih.gov/35101336/ - type: EvidenceLine directionOfEvidenceProvided: supports - targetProposition: # identical to VariantOncogenicityStatement.proposition + targetProposition: # identical to VariantOncogenicityStatement.proposition type: VariantOncogenicityProposition objectTumorType: id: civic.did:15 @@ -192,7 +230,8 @@ hasEvidenceLines: subjectVariant: id: civic.mpid:113 type: CategoricalVariant - description: RET M918T is the most common somatically acquired mutation in + description: + RET M918T is the most common somatically acquired mutation in medullary thyroid cancer (MTC). While there currently are no RET-specific inhibiting agents, promiscuous kinase inhibitors have seen some success in treating RET overactivity. Data suggests however, that the M918T mutation @@ -229,9 +268,27 @@ hasEvidenceLines: code: OP4 system: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 scoreOfEvidenceProvided: 1 + specifiedBy: + type: Method + methodType: population_frequency + name: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 + reportedIn: + doi: 10.1016/j.gim.2022.01.001 + id: pmid:35101336 + name: Horak et al., 2022, Genet Med. + pmid: "35101336" + title: + "Standards for the classification of pathogenicity of somatic variants in + cancer (oncogenicity): Joint recommendations of Clinical Genome + Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant + Interpretation for Cancer Consortium (VICC)" + type: Document + urls: + - https://doi.org/10.1016/j.gim.2022.01.001 + - https://pubmed.ncbi.nlm.nih.gov/35101336/ - type: EvidenceLine directionOfEvidenceProvided: supports - targetProposition: # identical to VariantOncogenicityStatement.proposition + targetProposition: # identical to VariantOncogenicityStatement.proposition type: VariantOncogenicityProposition objectTumorType: id: civic.did:15 @@ -246,7 +303,8 @@ hasEvidenceLines: subjectVariant: id: civic.mpid:113 type: CategoricalVariant - description: RET M918T is the most common somatically acquired mutation in + description: + RET M918T is the most common somatically acquired mutation in medullary thyroid cancer (MTC). While there currently are no RET-specific inhibiting agents, promiscuous kinase inhibitors have seen some success in treating RET overactivity. Data suggests however, that the M918T mutation @@ -283,9 +341,27 @@ hasEvidenceLines: code: OP1 system: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 scoreOfEvidenceProvided: 1 + specifiedBy: + type: Method + methodType: computational_prediction + name: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 + reportedIn: + doi: 10.1016/j.gim.2022.01.001 + id: pmid:35101336 + name: Horak et al., 2022, Genet Med. + pmid: "35101336" + title: + "Standards for the classification of pathogenicity of somatic variants in + cancer (oncogenicity): Joint recommendations of Clinical Genome + Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant + Interpretation for Cancer Consortium (VICC)" + type: Document + urls: + - https://doi.org/10.1016/j.gim.2022.01.001 + - https://pubmed.ncbi.nlm.nih.gov/35101336/ - type: EvidenceLine directionOfEvidenceProvided: supports - targetProposition: # identical to VariantOncogenicityStatement.proposition + targetProposition: # identical to VariantOncogenicityStatement.proposition type: VariantOncogenicityProposition objectTumorType: id: civic.did:15 @@ -300,7 +376,8 @@ hasEvidenceLines: subjectVariant: id: civic.mpid:113 type: CategoricalVariant - description: RET M918T is the most common somatically acquired mutation in + description: + RET M918T is the most common somatically acquired mutation in medullary thyroid cancer (MTC). While there currently are no RET-specific inhibiting agents, promiscuous kinase inhibitors have seen some success in treating RET overactivity. Data suggests however, that the M918T mutation @@ -337,3 +414,21 @@ hasEvidenceLines: code: OP3 system: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 scoreOfEvidenceProvided: 1 + specifiedBy: + type: Method + methodType: somatic_hotspot_recurrence + name: ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022 + reportedIn: + doi: 10.1016/j.gim.2022.01.001 + id: pmid:35101336 + name: Horak et al., 2022, Genet Med. + pmid: "35101336" + title: + "Standards for the classification of pathogenicity of somatic variants in + cancer (oncogenicity): Joint recommendations of Clinical Genome + Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant + Interpretation for Cancer Consortium (VICC)" + type: Document + urls: + - https://doi.org/10.1016/j.gim.2022.01.001 + - https://pubmed.ncbi.nlm.nih.gov/35101336/