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Remove duplicate props from icdc-manifest-props.yml #154

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merged 3 commits into from
Jul 26, 2024
Merged

Remove duplicate props from icdc-manifest-props.yml #154

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c09ff4e
Remove duplicate props
Jul 24, 2024
11c2414
add prop display values to manifest YAML
Jul 25, 2024
880a8de
Merge pull request #155 from CBIIT/add-display-vals
erm156 Jul 26, 2024
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166 changes: 107 additions & 59 deletions model-desc/icdc-manifest-props.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,75 +2,123 @@
# Title case names are "reserved" (meaningful to the parser)
# Lower case names are labels for the entities
# The first 4 properties to be listed in the File Manifest are designated in StaticProps. The file node properties are required by the CGC for mapping and the others are designated for context. These will not change and do not need to be read dynamically.

Nodes:
file:
StaticProps:
- file_name
- drs_uri
- property: file_name
display: "name"
- property: drs_uri
display: "drs_uri"
ExportProps:
- file_type
- file_description
- file_format
- file_size
- md5sum
- uuid
- file_location
- property: file_type
display: "File Type"
- property: file_description
display: "File Description"
- property: file_format
display: "File Format"
- property: file_size
display: "File Size"
- property: md5sum
display: "md5sum"
- property: uuid
display: "File UUID"
- property: file_location
display: "File Location"
case:
StaticProps:
- case_id
- property: case_id
display: "Case ID"
study:
StaticProps:
- clinical_study_designation
- property: clinical_study_designation
display: "Study Code"
ExportProps:
- clinical_study_designation
- case_id
- patient_id
- patient_first_name
- cohort_description
- cohort_dose
- cohort_id
- property: patient_id
display: "Patient ID"
- property: patient_first_name
display: "Case Name"
- property: cohort_description
display: "Cohort"
- property: cohort_dose
display: "Cohort Dose"
- property: cohort_id
display: "Cohort ID"
demographic:
ExportProps:
- demographic_id
- breed
- additional_breed_detail
- patient_age_at_enrollment
- date_of_birth
- sex
- weight
- neutered_indicator
- diagnosis_id
- disease_term
- stage_of_disease
- histology_cytopathology
- date_of_histology_confirmation
- histological_grade
- best_response
- pathology_report
- treatment_data
- follow_up_data
- concurrent_disease
- concurrent_disease_type
- property: demographic_id
display: "Demographic ID"
- property: breed
display: "Breed"
- property: additional_breed_detail
display: "Additional Breed Detail"
- property: patient_age_at_enrollment
display: "Age (years)"
- property: date_of_birth
display: "Date of Birth"
- property: sex
display: "Sex"
- property: weight
display: "Weight (kg)"
- property: neutered_indicator
display: "Neutered Status"
- property: diagnosis_id
display: "Diagnosis ID"
- property: disease_term
display: "Disease Term"
- property: stage_of_disease
display: "Stage of Disease"
- property: histology_cytopathology
display: "Histology"
- property: date_of_histology_confirmation
display: "Histology Date"
- property: histological_grade
display: "Histological Grade"
- property: best_response
display: "Best Response"
- property: pathology_report
display: "Pathology Report"
- property: treatment_data
display: "Treatment Data"
- property: follow_up_data
display: "Follow Up Data"
- property: concurrent_disease
display: "Concurrent Disease"
- property: concurrent_disease_type
display: "Concurrent Disease Type"
sample:
ExportProps:
- sample_id
- sample_site
- physical_sample_type
- general_sample_pathology
- tumor_sample_origin
- summarized_sample_type
- molecular_subtype
- specific_sample_pathology
- date_of_sample_collection
- sample_chronology
- necropsy_sample
- tumor_grade
- length_of_tumor
- width_of_tumor
- volume_of_tumor
- percentage_tumor
- sample_preservation



- property: sample_id
display: "Sample ID"
- property: sample_site
display: "Sample Site"
- property: physical_sample_type
display: "Physical Sample Type"
- property: general_sample_pathology
display: "Sample Pathology"
- property: tumor_sample_origin
display: "Tumor Sample Origin"
- property: summarized_sample_type
display: "Sample Type"
- property: molecular_subtype
display: "Molecular Subtype"
- property: specific_sample_pathology
display: "Pathology/Morphology"
- property: date_of_sample_collection
display: "Date of Sample Collection"
- property: sample_chronology
display: "Sample Chronology"
- property: necropsy_sample
display: "Necropsy Sample"
- property: tumor_grade
display: "Tumor Grade"
- property: length_of_tumor
display: "Tumor Length"
- property: width_of_tumor
display: "Tumor Width"
- property: volume_of_tumor
display: "Tumor Volume"
- property: percentage_tumor
display: "Percentage Tumor"
- property: sample_preservation
display: "Sample Preservation"
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