From 7dcd40b668041bcd68b58d32538379e05658c75f Mon Sep 17 00:00:00 2001 From: dunnpa <30905520+dunnpa@users.noreply.github.com> Date: Thu, 30 Jan 2025 15:55:02 -0500 Subject: [PATCH 1/4] Update ccdi-model-props.yml --- model-desc/ccdi-model-props.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/model-desc/ccdi-model-props.yml b/model-desc/ccdi-model-props.yml index 14f6eb17..83b5766b 100644 --- a/model-desc/ccdi-model-props.yml +++ b/model-desc/ccdi-model-props.yml @@ -517,7 +517,7 @@ PropDefinitions: - Origin: caDSR Code: '8028962' Value: Biospecimen Preservation Procedure Type - Version: "1.00" + Version: "2.00" Enum: - "-80 degrees C" - "Cytospin Slide" @@ -1158,7 +1158,7 @@ PropDefinitions: - Origin: caDSR Code: '3125302' Value: adverse event - Version: "1.00" + Version: "1.10" Type: value_type: list item_type: @@ -3948,7 +3948,7 @@ PropDefinitions: - Origin: caDSR Code: '11556150' Value: Electronic Data File MD5 Checksum Text - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -3981,7 +3981,7 @@ PropDefinitions: - Origin: caDSR Code: '11556141' Value: Electronic File Pathname Text - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -3992,7 +3992,7 @@ PropDefinitions: - Origin: caDSR Code: '11555664' Value: Electronic Data File Access Level Text - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -4003,7 +4003,7 @@ PropDefinitions: - Origin: caDSR Code: '11555664' Value: Electronic Data File Access Level Text - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -4014,7 +4014,7 @@ PropDefinitions: - Origin: caDSR Code: '11555664' Value: Electronic Data File Access Level Text - Version: "1.00" + Version: "2.00" Enum: - "Controlled" - "Open" @@ -4184,7 +4184,7 @@ PropDefinitions: Desc: A unique sequence of alphanumeric characters used to identify the specimen at it's point of origin. Term: - Origin: caDSR - Code: '6921892' + Code: '15100774' Value: Biospecimen Source Laboratory Identifier Version: "1.00" Type: string @@ -5121,7 +5121,7 @@ PropDefinitions: - Origin: caDSR Code: '11556141' Value: Electronic File Pathname Text - Version: "1.00" + Version: "2.00" Type: string Req: false # 02/22/2022 adeforge, not required? Private: false @@ -5330,7 +5330,7 @@ PropDefinitions: - Origin: caDSR Code: '11524548' Value: Clinical Trial Treatment Arm Text - Version: "1.00" + Version: "2.00" Type: string Req: false Private: false @@ -5352,7 +5352,7 @@ PropDefinitions: - Origin: caDSR Code: '2413202' Value: Clinical Trial Protocol Identifier 64 Character Text - Version: "1.00" + Version: "2.00" Type: string Req: false Private: false @@ -5386,7 +5386,7 @@ PropDefinitions: - Origin: caDSR Code: '2201713' Value: Person Affiliation Role Text Type - Version: "1.00" + Version: "2.00" Enum: - "PI" - "Co-PI" From b26ff32ad221c88979ebe2a7dd9714b1e997beec Mon Sep 17 00:00:00 2001 From: dunnpa <30905520+dunnpa@users.noreply.github.com> Date: Thu, 30 Jan 2025 15:58:47 -0500 Subject: [PATCH 2/4] Update ccdi-model-props.yml --- model-desc/ccdi-model-props.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/model-desc/ccdi-model-props.yml b/model-desc/ccdi-model-props.yml index 83b5766b..518fcd08 100644 --- a/model-desc/ccdi-model-props.yml +++ b/model-desc/ccdi-model-props.yml @@ -3152,7 +3152,7 @@ PropDefinitions: - Origin: caDSR Code: '2690165' Value: Family Member Relationship Type - Version: "1.00" + Version: "2.00" Enum: - "Adopted Daughter" - "Adopted Son" @@ -4964,7 +4964,7 @@ PropDefinitions: - Origin: caDSR Code: '11529031' Value: Genome Assembly NCBI Genetic Reference Sequence Identifier - Version: "1.00" + Version: "2.00" - Origin: NCIt Code: 'C164388' Value: Genetic Reference Sequence @@ -5285,7 +5285,7 @@ PropDefinitions: - Origin: caDSR Code: '11524545' Value: Funding Agency Organization Name Text - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -5296,7 +5296,7 @@ PropDefinitions: - Origin: caDSR Code: '11524546' Value: Funding Agency Program Name Text - Version: "1.00" + Version: "2.00" Type: string Req: false Private: false From 45cdab79fc9bf87accbd700a329045b34c23d178 Mon Sep 17 00:00:00 2001 From: dunnpa <30905520+dunnpa@users.noreply.github.com> Date: Thu, 30 Jan 2025 16:09:34 -0500 Subject: [PATCH 3/4] Update ccdi-model-props.yml --- model-desc/ccdi-model-props.yml | 64 ++++++++++++++------------------- 1 file changed, 26 insertions(+), 38 deletions(-) diff --git a/model-desc/ccdi-model-props.yml b/model-desc/ccdi-model-props.yml index 518fcd08..4cbdbeef 100644 --- a/model-desc/ccdi-model-props.yml +++ b/model-desc/ccdi-model-props.yml @@ -26,7 +26,7 @@ PropDefinitions: - Origin: caDSR Code: '15157224' Value: Subject Diagnosis Year Number - Version: "1.00" + Version: "2.00" Type: string Req: false Private: false @@ -92,7 +92,7 @@ PropDefinitions: - Origin: caDSR Code: '2413274' Value: Equipment Manufacturer Model Name Text - Version: "1.00" + Version: "2.00" Type: string Req: true Key: false @@ -180,7 +180,7 @@ PropDefinitions: - Origin: caDSR Code: '2903393' Value: Image Pixel Spacing Float or Fixed-point Millimeter Number - Version: "1.00" + Version: "2.00" Type: string Req: false Key: false @@ -192,7 +192,7 @@ PropDefinitions: - Origin: caDSR Code: '3113185' Value: Image Plane Slice Thickness Float or Fixed-point Millimeter Number - Version: "1.00" + Version: "2.00" Type: string Req: false Key: false @@ -1096,7 +1096,7 @@ PropDefinitions: - Origin: caDSR Code: '3070936' Value: Study End Point Event Type - Version: "1.00" + Version: "2.00" Enum: - "Progression" - "Relapse" @@ -1115,7 +1115,7 @@ PropDefinitions: - Origin: caDSR Code: '3070936' Value: Study End Point Event Type - Version: "1.00" + Version: "2.00" Enum: - "Censored" - "Not Censored" @@ -1131,7 +1131,7 @@ PropDefinitions: - Origin: caDSR Code: '3229334' Value: Study End Point Event Occurrence Day Count - Version: "1.00" + Version: "1.10" Type: integer Req: false Private: false @@ -2207,7 +2207,7 @@ PropDefinitions: - Origin: caDSR Code: '6142401' Value: Molecular Analysis Test Method Name - Version: "1.00" + Version: "2.00" Enum: - "Comparative Genomic Hybridization" - "Cytogenetics, NOS" @@ -2358,7 +2358,7 @@ PropDefinitions: - Origin: caDSR Code: '2179671' Value: Lab Test Result Unit of Measure Code - Version: "1.00" + Version: "2.00" Type: string Req: false Private: false @@ -2469,7 +2469,7 @@ PropDefinitions: - Origin: caDSR Code: '6142405' Value: Molecular Analysis Cytoband Text - Version: "1.00" + Version: "2.00" Type: string Req: false Private: false @@ -2491,7 +2491,7 @@ PropDefinitions: - Origin: caDSR Code: '6142511' Value: Molecular Analysis Histone Gene Family Category - Version: "1.00" + Version: "2.00" Enum: - "H1" - "H2A" @@ -2667,7 +2667,7 @@ PropDefinitions: Desc: The text term used to describe the type of analyte used for molecular testing. Term: - Origin: caDSR - Code: '6142394' + Code: '15063661' Value: Molecular Analysis Analyte Type Version: "1.00" Enum: @@ -2703,7 +2703,7 @@ PropDefinitions: - Origin: caDSR Code: '6142402' Value: Molecular Analysis Gene Variant Type - Version: "1.00" + Version: "2.00" Type: value_type: list item_type: @@ -2741,7 +2741,7 @@ PropDefinitions: - Origin: caDSR Code: '6142510' Value: Molecular Analysis Genetic Zygosity Type - Version: "1.00" + Version: "2.00" Enum: - "Heterozygous" - "Hemizygous" @@ -2759,7 +2759,7 @@ PropDefinitions: - Origin: caDSR Code: '6142389' Value: Risk Factor - Version: "1.00" + Version: "2.00" Type: value_type: list item_type: @@ -4570,7 +4570,7 @@ PropDefinitions: - Origin: caDSR Code: '14473376' Value: Subject Age At Specimen Collection Day Count - Version: "1.00" + Version: "2.00" Type: integer Req: true Private: false @@ -4663,11 +4663,7 @@ PropDefinitions: Desc: Text description of a sample or specimen. Term: - Origin: caDSR - Code: '2003907' - Value: Sample Description Text - Version: "1.00" - - Origin: caDSR - Code: '5432687' + Code: '14688604' Value: Tissue Sample Description Version: "1.00" Type: string @@ -4723,7 +4719,7 @@ PropDefinitions: - Origin: caDSR Code: '6273393' Value: Sequencing Library Technique Type - Version: "1.00" + Version: "2.00" Enum: - "AMPLICON" - "Archer Fusion" @@ -4990,11 +4986,7 @@ PropDefinitions: - Origin: caDSR Code: '11529072' Value: Nucleotide Sequence Alignment Software Name Text - Version: "1.00" - - Origin: NCIt - Code: 'C175896' - Value: Sequence Alignment Software Name - Version: "1.00" + Version: "2.00" Type: string Req: false Private: false @@ -5005,7 +4997,7 @@ PropDefinitions: - Origin: caDSR Code: '6347743' Value: Sequencing Library Creation Method Type - Version: "1.00" + Version: "2.00" Enum: - "5-Methylcytidine Antibody" - "Affinity Enrichment" @@ -5088,7 +5080,7 @@ PropDefinitions: - Origin: caDSR Code: '11459810' Value: Study Name Text - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -5099,7 +5091,7 @@ PropDefinitions: - Origin: caDSR Code: '11459812' Value: Study Short Name Text - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -5110,7 +5102,7 @@ PropDefinitions: - Origin: caDSR Code: '3444002' Value: Study Research Identification Descriptive Text - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -5132,7 +5124,7 @@ PropDefinitions: - Origin: caDSR Code: '12373576' Value: Research Activity Experimental Method Type - Version: "1.00" + Version: "2.00" Type: value_type: list item_type: @@ -5175,10 +5167,6 @@ PropDefinitions: size_of_data_being_uploaded: Desc: The measure (in bytes) of how much space a data file takes up on a storage medium. Term: - - Origin: caDSR - Code: '12373576' - Value: Data File Size Value - Version: "1.00" - Origin: NCIt Code: 'C171192' Value: Electronic Data File Size Integer @@ -5307,7 +5295,7 @@ PropDefinitions: - Origin: caDSR Code: '3434057' Value: Grant Funding Identifier Number - Version: "1.00" + Version: "2.00" Type: string Req: true Private: false @@ -5424,7 +5412,7 @@ PropDefinitions: - Origin: caDSR Code: '10624734' Value: Person ORCID Text - Version: "2.00" + Version: "3.00" Type: string Req: true Private: false From 9ecb086e09f1b3ff31ba11c0c6ba18416f6dfa84 Mon Sep 17 00:00:00 2001 From: dunnpa <30905520+dunnpa@users.noreply.github.com> Date: Thu, 30 Jan 2025 16:12:23 -0500 Subject: [PATCH 4/4] Update ccdi-model-props.yml --- model-desc/ccdi-model-props.yml | 18 +----------------- 1 file changed, 1 insertion(+), 17 deletions(-) diff --git a/model-desc/ccdi-model-props.yml b/model-desc/ccdi-model-props.yml index 4cbdbeef..a558fe4c 100644 --- a/model-desc/ccdi-model-props.yml +++ b/model-desc/ccdi-model-props.yml @@ -3378,10 +3378,6 @@ PropDefinitions: Code: '14616474' Value: PDX Tumor Preparation Text Version: "1.00" - - Origin: PubMedCentral - Code: 'PMC5738926' - Value: PDX-MI Minimal Information for Patient-Derived Tumor Xenograft Models - Version: "1.00" Type: string Req: true Private: false @@ -4645,19 +4641,7 @@ PropDefinitions: - 'Not Applicable' Req: true Strict: false - Private: false -# biosample_accession: -# Desc: An alphanumeric identifier (SAMN accession number) assigned to a set of descriptive information for biological materials used to generate data that has been or will be submitted to archives provided by the National Center for Biotechnology Information (NCBI). The alphanumeric identifier assigned to the specimen to uniquely identify it. -# Term: -# - Origin: caDSR -# Code: '2230047' -# Value: Specimen Accession Number -# - Origin: NCIt -# Code: 'C175889' -# Value: BioSample Accession Number -# Type: string -# Req: false -# Private: false + Private: false #sample sample_description: Desc: Text description of a sample or specimen.