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Normalizes cancer_grade for Bloodpac and capitalizes GDC, PDC commons name #8294

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merged 1 commit into from
Jan 23, 2025
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Normalizes cancer_grade for Bloodpac and capitalizes GDC, PDC commons name #8294

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74 changes: 44 additions & 30 deletions prometheus.data-commons.org/metadata/aggregate_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@
"study_description": "path:name",
"full_name": "",
"short_name": "",
"commons": "gdc",
"commons": "GDC",
"study_url": "",
"_subjects_count": {
"path": "summary.case_count",
Expand All @@ -152,7 +152,7 @@
"keep_original_fields": false,
"field_mappings": {
"authz": "/VA",
"commons": "pdc",
"commons": "PDC",
"tags": [
{
"name": "path:disease_type",
Expand Down Expand Up @@ -213,7 +213,21 @@
"subject_ethnicity": "path:ethnicity",
"subject_metastasis": "path:metastasis",
"subject_cancer_type": "path:cancer_type",
"subject_cancer_grade": "path:cancer_grade",
"subject_cancer_grade": {
"path": "cancer_grade",
"filters": [
"normalize_value"
],
"filterParams": {
"normalize_value": {
"Grade 1": "Grade I",
"Grade 2": "Grade II",
"Grade 3": "Grade III",
"Grade 4": "Grade IV"
}
},
"default": ""
},
"subject_cancer_stage": "path:cancer_stage",
"subject_year_of_birth": "path:year_of_birth",
"subject_primary_disease": "path:primary_disease",
Expand All @@ -234,7 +248,7 @@
"tags": {
"path": "tags",
"filters": [
"normalize_tags"
"normalize_tags"
],
"filterParams": {
"normalize_tags": {
Expand Down Expand Up @@ -284,14 +298,14 @@
],
"filterParams": {
"normalize_value": {
"M": "Male",
"F": "Female",
"male": "Male",
"female": "Female",
"not reported": "Not Reported"
"M": "Male",
"F": "Female",
"male": "Male",
"female": "Female",
"not reported": "Not Reported"
}
},
"default": ""
"default": ""
},
"subject_ethnicity": {
"path": "ethnicity",
Expand All @@ -300,10 +314,10 @@
],
"filterParams": {
"normalize_value": {
"NOT HISPANIC OR LATINO": "Not Hispanic or Latino",
"not reported": "Not Reported",
"DECLINED TO ANSWER": "Declined to Answer",
"HISPANIC OR LATINO": "Hispanic or Latino"
"NOT HISPANIC OR LATINO": "Not Hispanic or Latino",
"not reported": "Not Reported",
"DECLINED TO ANSWER": "Declined to Answer",
"HISPANIC OR LATINO": "Hispanic or Latino"
}
},
"default": ""
Expand All @@ -323,14 +337,14 @@
],
"filterParams": {
"normalize_value": {
"Grade 1": "Grade I",
"G1": "Grade I",
"Grade 2": "Grade II",
"G2": "Grade II",
"Grade 3": "Grade III",
"G3": "Grade III",
"Grade 4": "Grade IV",
"G4": "Grade IV"
"Grade 1": "Grade I",
"G1": "Grade I",
"Grade 2": "Grade II",
"G2": "Grade II",
"Grade 3": "Grade III",
"G3": "Grade III",
"Grade 4": "Grade IV",
"G4": "Grade IV"
}
},
"default": ""
Expand Down Expand Up @@ -403,7 +417,7 @@
}
],
"_unique_id": "path:id",
"commons": "gdc",
"commons": "GDC",
"disease_type": "path:disease_type",
"primary_site": "path:primary_site",
"subject_id": "path:submitter_id",
Expand All @@ -412,7 +426,7 @@
"subject_gender": {
"path": "demographic.gender",
"filters": [
"normalize_value"
"normalize_value"
],
"filterParams": {
"normalize_value": {
Expand All @@ -428,7 +442,7 @@
"subject_ethnicity": {
"path": "demographic.ethnicity",
"filters": [
"normalize_value"
"normalize_value"
],
"filterParams": {
"normalize_value": {
Expand All @@ -445,7 +459,7 @@
"subject_cancer_grade": {
"path": "diagnoses[*].tumor_grade",
"filters": [
"normalize_value"
"normalize_value"
],
"filterParams": {
"normalize_value": {
Expand Down Expand Up @@ -487,7 +501,7 @@
}
],
"_unique_id": "path:case_submitter_id",
"commons": "pdc",
"commons": "GDC",
"disease_type": "path:disease_type",
"primary_site": "path:primary_site",
"subject_id": "path:case_submitter_id",
Expand All @@ -496,7 +510,7 @@
"subject_gender": {
"path": "demographic.gender",
"filters": [
"normalize_value"
"normalize_value"
],
"filterParams": {
"normalize_value": {
Expand All @@ -512,7 +526,7 @@
"subject_ethnicity": {
"path": "demographic.ethnicity",
"filters": [
"normalize_value"
"normalize_value"
],
"filterParams": {
"normalize_value": {
Expand All @@ -529,7 +543,7 @@
"subject_cancer_grade": {
"path": "diagnoses[*].tumor_grade",
"filters": [
"normalize_value"
"normalize_value"
],
"filterParams": {
"normalize_value": {
Expand Down
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