From 09366aa8e38b2d837582d699b19e66556b02285d Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Tue, 31 Oct 2023 22:06:43 -0400 Subject: [PATCH 01/60] General maintenance updates - part 1 Added Diffuse Large B Cell Lymphoma to the controlled vocabulary for disease_term as required for the PRECINCT02 study Changed data type of the physical_exam: assessment_timepoint property to string and added the appropriate property description Modified various properties with the file node: file_description file_size md5sum --- model-desc/icdc-model-props.yml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 691c6f6..caef7c2 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -731,6 +731,7 @@ PropDefinitions: #- http://localhost/terms/domain/disease_term - B Cell Lymphoma - Bladder Cancer + - Diffuse Large B Cell Lymphoma - Fibrolipoma - Glioma - Healthy Control @@ -1027,10 +1028,10 @@ PropDefinitions: Tags: Labeled: File Type file_description: - Desc: An optional description of the file and/or its content, as provided by the data submitter, preferably limited to no more than 60 characters in length. + Desc: A narrative description of the file and/or its content, as provided by the data submitter, preferably limited to no more than 60 characters in length. The file description should clarify the derivation of the file in question, for example, as having been derived from normal tissue versus primary tumor tissue versus metastatic tumor tissue, and do so independently of the file name which may or may not already illustrate file derivation via easily discernable terms. For genomic analysis files, the file description should indicate what rereference genome was used for any alignment of raw sequence data. Src: Data Owner(s) Type: string - Req: Preferred + Req: 'Yes' Tags: Labeled: Description file_format: @@ -1041,14 +1042,14 @@ PropDefinitions: Tags: Labeled: Format file_size: - Desc: The exact size of the file in bytes. + Desc: The exact size of the file quoted in bytes, used to confirm the integrity of files submitted to the ICDC. Although file sizes are re-generated by the ICDC data loader during the downstream processing and validation of all files submitted for ingestion, file sizes calculated by the data submitter immediately prior to file transfer must nonetheless be specified in the File Transfer Manifest as the values for original_file_size.
Submitter-side file sizes are absolutely required for the confirmation of file integrity. Src: Loader-derived - Type: number + Type: integer Req: 'Yes' Tags: Labeled: Size md5sum: - Desc: The 32-character hexadecimal md5 checksum value of the file, used to confirm the integrity of files submitted to the ICDC. + Desc: The 32-character hexadecimal md5 checksum value of the file, used to confirm the integrity of files submitted to the ICDC. Although md5 checksum values are re-generated by the ICDC data loader during the downstream processing and validation of all files submitted for ingestion, md5 checksum values calculated by the data submitter immediately prior to file transfer must nonetheless be specified in the File Transfer Manifest as the values for original_md5sum.
Submitter-side md5 checksum values are absolutely required for the confirmation of file integrity. Src: Loader-derived Type: string Req: 'Yes' @@ -1196,9 +1197,9 @@ PropDefinitions: Type: string # physical_exam props assessment_timepoint: - Desc: Pending + Desc: An indication as to the timing of the visit during which the physical examination was conducted. This could be a visit number indicative of physical examination's chronology, a narrative statement/description of the vist, or a combination of both. Src: Data Owner(s) - Type: integer + Type: string body_system: Desc: Major organ system or physiological characteristic assessed during the examination of the patient/subject/donor during a follow-up visit. Observations are reported independently on each organ system or physiological characteristic. Src: Data Owner(s) From 6f1c73fa4db780fe57b6dd4b12619a046af9d682 Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Wed, 10 Apr 2024 21:03:03 -0400 Subject: [PATCH 02/60] Fix #144 Update model per OSA02 and OSA04 requirements Added values for sample_site Added a new value for specific_sample_pathology Added "Not Determined" as an acceptable value for tumor_grade --- model-desc/icdc-model-props.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index caef7c2..f32d758 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1604,13 +1604,17 @@ PropDefinitions: - Mouth, Maxilla, Mucosa - Muscle - Pancreas + - Phalange - Pleural Effusion - Radius + - Scapula - Skin + - Skin and Muscle - Spleen - Subcutaneous Tissue - Thyroid Gland - Tibia + - Ulna - Unknown - Urethra - Urethra Mid-distal @@ -1674,6 +1678,7 @@ PropDefinitions: - Simple Carcinoma, Invasive, Ductal - Soft Tissue Sarcoma - T Cell Lymphoma + - Telangiectatic Osteosarcoma - Urinary Bladder (organoid) - Undefined - Urothelial Carcinoma @@ -1717,6 +1722,7 @@ PropDefinitions: - Low - Unknown - Not Applicable + - Not Determined Req: Preferred Tags: Labeled: Tumor Grade From 4343c714b10adff7b99bd1dd89fd8a847e964dce Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Mon, 15 Apr 2024 21:45:27 -0400 Subject: [PATCH 03/60] Fix #145 General model maintenance and house-keeping Updated the order in which properties are specified within certain nodes to impose more logical and/or indicate importance in our data loading templates Added guidance as to the correct use of relatively similar acceptable terms within a number of controlled vocabularies to the appropriate property descriptions such that the guidance will be visible to the end user, and removed the corresponding comments where that guidance had previously resided out of sight Trimmed out various other comments --- model-desc/icdc-model-props.yml | 92 ++++++++++++++++----------------- model-desc/icdc-model.yml | 17 +++--- 2 files changed, 53 insertions(+), 56 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index f32d758..b8c4ad1 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -673,19 +673,16 @@ PropDefinitions: Labeled: Weight (kg) # diagnosis props best_response: - Desc: Where applicable, an indication as to the best overall response to therapeutic intervention observed within an individual patient/subject/donor. + Desc: Where applicable, an indication as to the best overall response to therapeutic intervention observed within an individual patient/subject/donor. EXPLAIN HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which response to therapeutic intervention was either deliberately not assessed because no therapeutic intervention was being tested by the study/trial in question, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. Src: Data Owner(s) Enum: - Complete Response - Partial Response - Stable Disease - Progressive Disease - - Not Determined - # included to accommodate situations either where the study in question does not assess the effects of any therapeutic intervention, or where the response to therapeutic intervention could not be determined - - Not Applicable - # included to accommodate situations in which healthy control subjects are included within a study that does assess the effects of a therapeutic intervention - - Unknown - # included to accommodate situations where a value for stage of disease simply isn't available + - Not Determined # included to accommodate situations either where the study in question does not assess the effects of any therapeutic intervention, or where the response to therapeutic intervention could not be determined + - Not Applicable # included to accommodate situations in which healthy control subjects are included within a study that does assess the effects of a therapeutic intervention + - Unknown # included to accommodate situations where a value for stage of disease simply isn't available Req: 'Yes' Tags: Labeled: Response to Treatment @@ -768,10 +765,21 @@ PropDefinitions: Labeled: Follow Up Data Available histological_grade: Desc: The histological grading of the tumor(s) present in the patient/subject/donor, based upon microscopic evaluation(s), and recorded at the subject level; grading of specific tumor samples subject to downstream analysis is recorded at the sample level. - Src: Data Owner(s) - Type: string # temporarily, to facilitate data loading with validation on, until STS is in place + Src: Data Owner(s) EXPLAIN HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which histological grade was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. + #Type: string # temporarily, to facilitate data loading with validation on, until STS is in place #- http://localhost/terms/domain/histological_grade - Req: 'No' + Enum: + - "1" + - "2" + - "3" + - "4" + - High + - Medium + - Low + - Unknown + - Not Applicable + - Not Determined + Req: Preferred Tags: Labeled: Histological Grade histology_cytopathology: @@ -830,7 +838,7 @@ PropDefinitions: Tags: Labeled: Primary Disease Site, Disease Site, Primary Site stage_of_disease: - Desc: The formal assessment of the extent to which the primary cancer with which the patient/subject/donor was diagnosed has progressed, according to the TNM staging or cancer stage grouping criteria. + Desc: The formal assessment of the extent to which the primary cancer with which the patient/subject/donor was diagnosed has progressed, according to the TNM staging or cancer stage grouping criteria. EXPLAIN HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which stage of disease was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. Src: Data Owner(s) Enum: - I @@ -863,12 +871,9 @@ PropDefinitions: - T3N1M1 - T3NXM1 - TXN0M0 - - Not Applicable - # to accommodate situations where the subject is a healthy control - - Not Determined - # to accommodate situations where stage of disease was deliberately not assessed - - Unknown - # to accommodate situations where a value for stage of disease simply isn't available + - Not Applicable # to accommodate situations where the subject is a healthy control + - Not Determined # to accommodate situations where stage of disease was deliberately not assessed + - Unknown # to accommodate situations where a value for stage of disease simply isn't available Req: 'Yes' Tags: Labeled: Stage of Disease @@ -922,7 +927,7 @@ PropDefinitions: value_type: number Req: 'No' measurable_lesion: - Desc: Pending #An indication as to whether any given lesion is large enough for its size to be determined with any accuracy. + Desc: Pending # An indication as to whether any given lesion is large enough for its size to be determined with any accuracy. Src: Data Owner(s) Type: TBD Req: 'No' @@ -999,7 +1004,7 @@ PropDefinitions: # removed residual evaluation props from here # file props file_name: - Desc: The name of the file, maintained exactly as provided by the data submitter. + Desc: The name of the file, inclusive of file extension(s), maintained exactly as provided by the data submitter. Src: Data Owner(s) Type: string Req: 'Yes' @@ -1028,7 +1033,7 @@ PropDefinitions: Tags: Labeled: File Type file_description: - Desc: A narrative description of the file and/or its content, as provided by the data submitter, preferably limited to no more than 60 characters in length. The file description should clarify the derivation of the file in question, for example, as having been derived from normal tissue versus primary tumor tissue versus metastatic tumor tissue, and do so independently of the file name which may or may not already illustrate file derivation via easily discernable terms. For genomic analysis files, the file description should indicate what rereference genome was used for any alignment of raw sequence data. + Desc: A narrative description of the file and/or its content, as provided by the data submitter, preferably limited to no more than 60 characters in length. The file description should clarify the derivation of the file in question, for example, as having been derived from normal tissue versus primary tumor tissue versus metastatic tumor tissue, and do so independently of the file name which may or may not already illustrate file derivation via easily discernable terms.
For genomic analysis files, the file description should indicate what rereference genome was used for any alignment of raw sequence data. Src: Data Owner(s) Type: string Req: 'Yes' @@ -1042,7 +1047,7 @@ PropDefinitions: Tags: Labeled: Format file_size: - Desc: The exact size of the file quoted in bytes, used to confirm the integrity of files submitted to the ICDC. Although file sizes are re-generated by the ICDC data loader during the downstream processing and validation of all files submitted for ingestion, file sizes calculated by the data submitter immediately prior to file transfer must nonetheless be specified in the File Transfer Manifest as the values for original_file_size.
Submitter-side file sizes are absolutely required for the confirmation of file integrity. + Desc: The exact size of the file quoted in bytes, used to confirm the integrity of files submitted to the ICDC. Although file sizes are re-generated by the ICDC data loader during the downstream processing and validation of all files submitted for ingestion, file sizes calculated by the data submitter immediately prior to file transfer must nonetheless be specified in the File Transfer Manifest as the values for original_file_size.
Submitter-side file sizes quoted in bytes and presented in the form of purely numerical strings are absolutely required for the confirmation of file integrity. Src: Loader-derived Type: integer Req: 'Yes' @@ -1441,14 +1446,14 @@ PropDefinitions: Tags: Labeled: Journal digital_object_id: - Desc: Where applicable, the digital object identifier for the cited work, by which it can be permanently identified, and linked to via the internet. + Desc: Where applicable, the digital object identifier for the cited work, by which it can be permanently identified, and linked to via the internet.
Values of this property must contain only the alphanumeric string of the digital object identifier itself, exclusive of any prefix such as "DOI:", such that values can be correctly interpreted and displayed as hyperlinks within the application. Src: Data Owner(s) Type: string Req: Preferred Tags: Labeled: DOI pubmed_id: - Desc: Where applicable, the unique numerical identifier assigned to the cited work by PubMed, by which it can be linked to via the internet. + Desc: Where applicable, the unique numerical identifier assigned to the cited work by PubMed, by which it can be linked to via the internet.
Values of this property must contain only the numeric string of the PubMed ID itself, exclusive of any prefix such as "PMID:", such that values can be correctly interpreted and displayed as hyperlinks within the application. Src: Data Owner(s) Type: number Req: Preferred @@ -1481,7 +1486,7 @@ PropDefinitions: Type: datetime Req: 'No' general_sample_pathology: - Desc: An indication as to whether a sample represents normal tissue versus representing diseased or tumor tissue. + Desc: An indication as to whether a sample represents normal tissue versus representing diseased or tumor tissue. EXPLAIN HERE
For any type of blood sample, the value of this property should be "Not Applicable", unless the patient/subject/donor in question has been diagnosed with any type of hematological malignancy that would render the blood abnormal. Src: Data Owner(s) Enum: - Normal @@ -1507,7 +1512,7 @@ PropDefinitions: Type: string Req: 'No' necropsy_sample: - Desc: An indication as to whether a sample was acquired as a result of a necropsy examination. + Desc: An indication as to whether a sample was acquired as a result of a necropsy examination. EXPLAIN HERE
For cell line samples, the value of this property should be "Not Applicable". Src: Data Owner(s) Enum: - 'Yes' @@ -1518,14 +1523,14 @@ PropDefinitions: Tags: Labeled: Necropsy Sample percentage_tumor: - Desc: The purity of a sample of tumor tissue in terms of the percentage of the sample that is represnted by tumor cells, expressed either as a discrete percentage or as a percentage range. + Desc: The purity of a sample of tumor tissue in terms of the percentage of the sample that is represnted by tumor cells, expressed either as a discrete percentage or as a percentage range. EXPLAIN HERE
The value of this property should be "Not Applicable" for normal samples and blood samples, "Not Determined" for tumor samples in which percentage tumor was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Type: string #changed to string in order to accommodate values being quoted in ranges, as greater or less than, or as Unknown - Req: Preferred + Req: 'Yes' Tags: Labeled: Percentage Tumor sample_chronology: - Desc: An indication as to when a sample was acquired relative to any therapeutic intervention and/or key disease outcome observations. + Desc: An indication as to when a sample was acquired relative to any therapeutic intervention and/or key disease outcome observations. EXPLAIN HERE
The value of this property should be "Not Applicable" for samples acquired via a study/trial that did not asses the effects of any therapeutic intervention, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Enum: - Before Treatment @@ -1540,7 +1545,7 @@ PropDefinitions: Tags: Labeled: Sample Chronology sample_id: - Desc: The globally unique ID by which any given sample can be unambiguously identified and displayed across studies/trials; specifically the preferred value of the sample identifier used by the data submitter, prefixed with the appropriate ICDC study code during data transformation.
This property is used as the key via which child records, e.g. file records, can be associated with the appropriate sample during data loading, and to identify the correct records during data updates. + Desc: The globally unique ID by which any given sample can be unambiguously identified and displayed across studies/trials; specifically the preferred value of the sample identifier used by the data submitter, prefixed with the appropriate ICDC study code.
This property is used as the key via which child records, e.g. file records, can be associated with the appropriate sample during data loading, and to identify the correct records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -1548,13 +1553,13 @@ PropDefinitions: Tags: Labeled: Sample ID sample_preservation: - Desc: The method by which a sample was preserved. + Desc: The method by which a sample was preserved. EXPLAIN HERE
The value of this property should be "Not Applicable" for cell line samples not subject to any interim preservation and storage, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Enum: - EDTA - FFPE - RNAlater - - Snap Frozen # list of acceptable values will gradually be expanded as data submission requirements solidify + - Snap Frozen - TRIzol - Not Applicable # included to accommodate cell line samples, which will generally be processed absent interim preservation and storage - Unknown # included to accommodate the inevitable ambiguity about the correct value for a required field @@ -1631,7 +1636,7 @@ PropDefinitions: Enum: - Tissue - Blood - - Cell Line # required for the CCL01 and OSA01 studies + - Cell Line - Organoid - Urine Sediment - Whole Blood @@ -1671,9 +1676,9 @@ PropDefinitions: - Pulmonary Adenocarcinoma - Pulmonary Carcinoma - Simple Carcinoma - - Simple Carcinoma,  Ductular, Vascular Invasive - Simple Carcinoma, Ductal - Simple Carcinoma, Ductular + - Simple Carcinoma, Ductular, Vascular Invasive #removed errant double whitespace and then re-ordered values - Simple Carcinoma, Inflammatory - Simple Carcinoma, Invasive, Ductal - Soft Tissue Sarcoma @@ -1695,9 +1700,6 @@ PropDefinitions: - Normal Cell Line - Normal Tissue - Organoid (ASC-derived) - #- Patient-Derived Organoid - #- Patient-Derived Organoid (urine-derived) - #- PDO - Primary Malignant Tumor Tissue - Urine Sediment - Tumor Cell Line @@ -1710,7 +1712,7 @@ PropDefinitions: Tags: Labeled: Sample Type tumor_grade: - Desc: The grade of the tumor from which the sample was acquired, i.e. the degree of cellular differentiation within the tumor in question, as determined by a pathologist's evaluation. + Desc: The grade of the tumor from which the sample was acquired, i.e. the degree of cellular differentiation within the tumor in question, as determined by a pathologist's evaluation. EXPLAIN HERE
The value of this property should be "Not Applicable" for normal samples and blood samples, "Not Determined" for tumor samples in which grade was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Enum: - "1" @@ -1723,11 +1725,11 @@ PropDefinitions: - Unknown - Not Applicable - Not Determined - Req: Preferred + Req: 'Yes' Tags: Labeled: Tumor Grade tumor_sample_origin: - Desc: An indication as to whether a tumor sample was derived from a primary versus a metastatic tumor. + Desc: An indication as to whether a tumor sample was derived from a primary versus a metastatic tumor. EXPLAIN HERE
The value of this property should be "Not Applicable" for any sample not derived from tumor tissue, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Enum: - Primary @@ -1782,10 +1784,9 @@ PropDefinitions: Tags: Labeled: Study Name clinical_study_type: - Desc: An arbitrary designation of the study/trial to indicate its underlying. - nature, e.g. Clinical Trial, Transcriptomics, Genomics. + Desc: An arbitrary designation of the study/trial to indicate its underlying nature, e.g. Clinical Trial, Transcriptomics, Genomics. Src: Internally-curated - Type: string + Type: string # convert this to a list type property, where multiple values are supported, provided that listed values are all in the associated controlled vocabulary Req: 'Yes' Tags: Labeled: Study Type @@ -1797,7 +1798,7 @@ PropDefinitions: Tags: Labeled: Date of IACUC Approval dates_of_conduct: - Desc: An indication of the general time period during which the study/trial was active, e.g. (from) month and year (to) month and year. + Desc: An indication of the general time period during which the study/trial was active, e.g. "January 2021 to March 2023". Src: Data Owner(s) Type: string Req: Preferred @@ -1820,7 +1821,7 @@ PropDefinitions: Req: 'Yes' # study_arm props arm: - Desc: Where applicable, the nature of each arm into which the study/trial has been divided. For example, in multiple agent clinical trials, the name of the therapeutic agent used in any given study arm. + Desc: Where applicable, the name and/or nature of each arm into which the study/trial has been divided. For example, in multiple agent clinical trials, the name of the therapeutic agent used in any given study arm. Src: Internally-curated Type: string Req: Preferred @@ -1889,12 +1890,11 @@ PropDefinitions: - sq meters value_type: number body_temperature: - Desc: The temperature of the patient/subject/donor at the time of the vital signs evaluation. + Desc: The temperature of the patient/subject/donor at the time of the vital signs evaluation, measured in degrees Fahrenheit. Src: Data Owner(s) Type: units: - degrees F - - degrees C value_type: number date_of_vital_signs: Desc: The date upon which the vital signs evaluation in question was conducted. diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 5c04d78..5f4c417 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -54,12 +54,10 @@ Nodes: Class: secondary Template: 'Yes' Props: - - arm - - ctep_treatment_assignment_code - # arm has no example in the data, putting cohort_description in here - # to help define study_arm + - arm # arm name - arm_description - arm_id # potentially needed to differentiate between arms having the same name, but which actually belong to different studies. Proactively including sooner rather than later. + - ctep_treatment_assignment_code agent: Desc: The Agent node documents the name of each therapeutic agent being administered during a clinical trial. In this way, in clinical trials which assess the efficacy of combination therapies, adverse events observed during the trial can be attributed specifically to one or more of the medications being used. Tags: @@ -80,10 +78,9 @@ Nodes: Class: secondary Template: 'Yes' Props: - - cohort_description - # the intended or protocol dose - - cohort_dose + - cohort_description # cohort name generally inclusive of some detail as to agent and dose - cohort_id # needed to differentiate between cohorts that share values for cohort description, but which actually belong to different studies + - cohort_dose # the intended or protocol dose case: Desc: The Case node contains properties required to unambiguously identify each patient/subject/donor, either based upon the data submitter's original ID, or upon a study-specific Case ID derived from it during data transformation, which prefixes each original ID with a short, study-specific code. Tags: @@ -410,15 +407,15 @@ Nodes: Props: - date_of_vital_signs - body_temperature - - pulse - respiration_rate - respiration_pattern - - systolic_bp + - pulse - pulse_ox + - systolic_bp + - ecg - patient_weight - body_surface_area - modified_ecog - - ecg - assessment_timepoint - phase lab_exam: From b20b901a13696e730f658c748038bb13c2f808b5 Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Tue, 16 Apr 2024 13:06:46 -0400 Subject: [PATCH 04/60] Fix #145 General model maintenance and house-keeping Tidied up markers as to where guidance on use of acceptable terms had been added --- model-desc/icdc-model-props.yml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index b8c4ad1..975bcf5 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -673,7 +673,7 @@ PropDefinitions: Labeled: Weight (kg) # diagnosis props best_response: - Desc: Where applicable, an indication as to the best overall response to therapeutic intervention observed within an individual patient/subject/donor. EXPLAIN HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which response to therapeutic intervention was either deliberately not assessed because no therapeutic intervention was being tested by the study/trial in question, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. + Desc: Where applicable, an indication as to the best overall response to therapeutic intervention observed within an individual patient/subject/donor. GUIDANCE ADDED HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which response to therapeutic intervention was either deliberately not assessed because no therapeutic intervention was being tested by the study/trial in question, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. Src: Data Owner(s) Enum: - Complete Response @@ -765,7 +765,7 @@ PropDefinitions: Labeled: Follow Up Data Available histological_grade: Desc: The histological grading of the tumor(s) present in the patient/subject/donor, based upon microscopic evaluation(s), and recorded at the subject level; grading of specific tumor samples subject to downstream analysis is recorded at the sample level. - Src: Data Owner(s) EXPLAIN HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which histological grade was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. + Src: Data Owner(s) GUIDANCE ADDED HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which histological grade was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. #Type: string # temporarily, to facilitate data loading with validation on, until STS is in place #- http://localhost/terms/domain/histological_grade Enum: @@ -838,7 +838,7 @@ PropDefinitions: Tags: Labeled: Primary Disease Site, Disease Site, Primary Site stage_of_disease: - Desc: The formal assessment of the extent to which the primary cancer with which the patient/subject/donor was diagnosed has progressed, according to the TNM staging or cancer stage grouping criteria. EXPLAIN HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which stage of disease was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. + Desc: The formal assessment of the extent to which the primary cancer with which the patient/subject/donor was diagnosed has progressed, according to the TNM staging or cancer stage grouping criteria. GUIDANCE ADDED HERE
The value of this property should be "Not Applicable" for healthy control patients/subjects/donors, "Not Determined" for patients/subjects/donors in which stage of disease was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for patients/subjects/donors where no other definitive value can be assigned. Src: Data Owner(s) Enum: - I @@ -1486,7 +1486,7 @@ PropDefinitions: Type: datetime Req: 'No' general_sample_pathology: - Desc: An indication as to whether a sample represents normal tissue versus representing diseased or tumor tissue. EXPLAIN HERE
For any type of blood sample, the value of this property should be "Not Applicable", unless the patient/subject/donor in question has been diagnosed with any type of hematological malignancy that would render the blood abnormal. + Desc: An indication as to whether a sample represents normal tissue versus representing diseased or tumor tissue. GUIDANCE ADDED HERE
For any type of blood sample, the value of this property should be "Not Applicable", unless the patient/subject/donor in question has been diagnosed with any type of hematological malignancy that would render the blood abnormal. Src: Data Owner(s) Enum: - Normal @@ -1512,7 +1512,7 @@ PropDefinitions: Type: string Req: 'No' necropsy_sample: - Desc: An indication as to whether a sample was acquired as a result of a necropsy examination. EXPLAIN HERE
For cell line samples, the value of this property should be "Not Applicable". + Desc: An indication as to whether a sample was acquired as a result of a necropsy examination. GUIDANCE ADDED HERE
For cell line samples, the value of this property should be "Not Applicable". Src: Data Owner(s) Enum: - 'Yes' @@ -1523,14 +1523,14 @@ PropDefinitions: Tags: Labeled: Necropsy Sample percentage_tumor: - Desc: The purity of a sample of tumor tissue in terms of the percentage of the sample that is represnted by tumor cells, expressed either as a discrete percentage or as a percentage range. EXPLAIN HERE
The value of this property should be "Not Applicable" for normal samples and blood samples, "Not Determined" for tumor samples in which percentage tumor was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for samples where no other definitive value can be assigned. + Desc: The purity of a sample of tumor tissue in terms of the percentage of the sample that is represnted by tumor cells, expressed either as a discrete percentage or as a percentage range. GUIDANCE ADDED HERE
The value of this property should be "Not Applicable" for normal samples and blood samples, "Not Determined" for tumor samples in which percentage tumor was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Type: string #changed to string in order to accommodate values being quoted in ranges, as greater or less than, or as Unknown Req: 'Yes' Tags: Labeled: Percentage Tumor sample_chronology: - Desc: An indication as to when a sample was acquired relative to any therapeutic intervention and/or key disease outcome observations. EXPLAIN HERE
The value of this property should be "Not Applicable" for samples acquired via a study/trial that did not asses the effects of any therapeutic intervention, and "Unknown" for samples where no other definitive value can be assigned. + Desc: An indication as to when a sample was acquired relative to any therapeutic intervention and/or key disease outcome observations. GUIDANCE ADDED HERE
The value of this property should be "Not Applicable" for samples acquired via a study/trial that did not asses the effects of any therapeutic intervention, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Enum: - Before Treatment @@ -1553,7 +1553,7 @@ PropDefinitions: Tags: Labeled: Sample ID sample_preservation: - Desc: The method by which a sample was preserved. EXPLAIN HERE
The value of this property should be "Not Applicable" for cell line samples not subject to any interim preservation and storage, and "Unknown" for samples where no other definitive value can be assigned. + Desc: The method by which a sample was preserved. GUIDANCE ADDED HERE
The value of this property should be "Not Applicable" for cell line samples not subject to any interim preservation and storage, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Enum: - EDTA @@ -1712,7 +1712,7 @@ PropDefinitions: Tags: Labeled: Sample Type tumor_grade: - Desc: The grade of the tumor from which the sample was acquired, i.e. the degree of cellular differentiation within the tumor in question, as determined by a pathologist's evaluation. EXPLAIN HERE
The value of this property should be "Not Applicable" for normal samples and blood samples, "Not Determined" for tumor samples in which grade was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for samples where no other definitive value can be assigned. + Desc: The grade of the tumor from which the sample was acquired, i.e. the degree of cellular differentiation within the tumor in question, as determined by a pathologist's evaluation. GUIDANCE ADDED HERE
The value of this property should be "Not Applicable" for normal samples and blood samples, "Not Determined" for tumor samples in which grade was either deliberately not assessed, or could not be assessed for any reason, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Enum: - "1" @@ -1729,7 +1729,7 @@ PropDefinitions: Tags: Labeled: Tumor Grade tumor_sample_origin: - Desc: An indication as to whether a tumor sample was derived from a primary versus a metastatic tumor. EXPLAIN HERE
The value of this property should be "Not Applicable" for any sample not derived from tumor tissue, and "Unknown" for samples where no other definitive value can be assigned. + Desc: An indication as to whether a tumor sample was derived from a primary versus a metastatic tumor. GUIDANCE ADDED HERE
The value of this property should be "Not Applicable" for any sample not derived from tumor tissue, and "Unknown" for samples where no other definitive value can be assigned. Src: Data Owner(s) Enum: - Primary From 38913b3de3fadb6ca25402750bfbe28f91a40d9a Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Wed, 1 May 2024 10:35:08 -0500 Subject: [PATCH 05/60] Add new file to support content and content order for download and export of the file manifest --- model-desc/icdc-manifest-props.yml | 82 ++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 model-desc/icdc-manifest-props.yml diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml new file mode 100644 index 0000000..9bc4e08 --- /dev/null +++ b/model-desc/icdc-manifest-props.yml @@ -0,0 +1,82 @@ +# ICDC nodes and props for the file manifest +# Title case names are "reserved" (meaningful to the parser) +# Lower case names are labels for the entities + + +Nodes: +# These properties are required by the CGC + file: + Export: + - file_name + - drs_uri +# This property is ordered for context + study: + Export: + - clinical_study_designation +# This property is ordered for context + case: + Export: + - case_id + file: + Export: + - file_type + - file_description + - file_format + - file_size + - md5sum + - uuid + - file_location + study: + Export: + - clinical_study_designation + - case_id + - patient_id + - patient_first_name + - cohort_description + - cohort_dose + - cohort_id + demographic: + Export: + - 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 + sample: + Export: + - 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 + + + + \ No newline at end of file From d6873c4a98e96cf8805d6de4139f5a0e32338954 Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Tue, 7 May 2024 21:54:32 -0400 Subject: [PATCH 06/60] Fix #144 Update model per OSA02 and OSA04 requirements Changed date_of_iacuc_approval from datetime to string in order to accommodate studies having more than one IACUC approval date, with the OSA02 study being a prime example of that situation --- model-desc/icdc-model-props.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 975bcf5..c73a239 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1793,7 +1793,7 @@ PropDefinitions: date_of_iacuc_approval: Desc: Where applicable, the date upon which the study/trial was approved by the IACUC. Src: Data Owner(s) - Type: datetime + Type: string # changing this from datetime to string in order to accommodate studies having more than one IACUC approval date, with the OSA02 study being a prime example of that situation Req: 'No' Tags: Labeled: Date of IACUC Approval From 817c3a374cfcade6d1eb96fdad16c9febd6bcda4 Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Tue, 14 May 2024 14:42:50 -0500 Subject: [PATCH 07/60] Mitigate duplicate keys in the same object --- model-desc/icdc-manifest-props.yml | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 9bc4e08..e5b2cac 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -3,20 +3,18 @@ # Lower case names are labels for the entities -Nodes: -# These properties are required by the CGC +Static_Props: +# The first 4 properties included in a file manifest will not change and are listed in this block. +# These properties are required by the CGC file: - Export: - - file_name - - drs_uri -# This property is ordered for context - study: - Export: - - clinical_study_designation -# This property is ordered for context + - file_name + - drs_uri +# These properties are ordered for context + study: + - clinical_study_designation case: - Export: - - case_id + - case_id +Nodes: file: Export: - file_type From dfb04b7cf2762dd09b21eb245ec494de30ce542e Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Tue, 14 May 2024 17:05:49 -0500 Subject: [PATCH 08/60] Revise syntax for static props --- model-desc/icdc-manifest-props.yml | 31 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 17 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index e5b2cac..6f56107 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -1,22 +1,14 @@ # ICDC nodes and props for the file manifest # Title case names are "reserved" (meaningful to the parser) # Lower case names are labels for the entities - - -Static_Props: -# The first 4 properties included in a file manifest will not change and are listed in this block. -# These properties are required by the CGC - file: - - file_name - - drs_uri -# These properties are ordered for context - study: - - clinical_study_designation - case: - - case_id +# The first 4 properties listed in the File Manifest are designated in StaticProps. The file properties are required by the CGC and the others are designated for context. These will not change and do not need to be read dynamically. + Nodes: file: - Export: + StaticProps: + - file_name + - drs_uri + ExportProps: - file_type - file_description - file_format @@ -24,7 +16,12 @@ Nodes: - md5sum - uuid - file_location + case: + StaticProps: + - case_id study: + StaticProps: + - clinical_study_designation Export: - clinical_study_designation - case_id @@ -75,6 +72,6 @@ Nodes: - percentage_tumor - sample_preservation - - - \ No newline at end of file + + + \ No newline at end of file From bae05488b2644c0224d004e5d0c2838f31e3ffcd Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Tue, 14 May 2024 17:11:54 -0500 Subject: [PATCH 09/60] Update syntax for props to be exported in the file manifest --- model-desc/icdc-manifest-props.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 6f56107..f9ee855 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -22,7 +22,7 @@ Nodes: study: StaticProps: - clinical_study_designation - Export: + ExportProps: - clinical_study_designation - case_id - patient_id @@ -31,7 +31,7 @@ Nodes: - cohort_dose - cohort_id demographic: - Export: + ExportProps: - demographic_id - breed - additional_breed_detail @@ -53,7 +53,7 @@ Nodes: - concurrent_disease - concurrent_disease_type sample: - Export: + ExportProps: - sample_id - sample_site - physical_sample_type @@ -74,4 +74,3 @@ Nodes: - \ No newline at end of file From c332dc109c1903dbee08ff159f0e98b1ff62de2f Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 14 May 2024 17:17:25 -0500 Subject: [PATCH 10/60] update comments --- model-desc/icdc-manifest-props.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index f9ee855..452df44 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -1,7 +1,7 @@ # ICDC nodes and props for the file manifest # Title case names are "reserved" (meaningful to the parser) # Lower case names are labels for the entities -# The first 4 properties listed in the File Manifest are designated in StaticProps. The file properties are required by the CGC and the others are designated for context. These will not change and do not need to be read dynamically. +# 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: From bff91ea3ba271ba3333940b3dc248e6c8946c47d Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Wed, 3 Jul 2024 15:02:37 -0500 Subject: [PATCH 11/60] CRDCDH-1308 --- model-desc/icdc-model-props.yml | 13 ++++++++---- model-desc/icdc-model.yml | 35 +++++++++++++++++++++++++++++++-- 2 files changed, 42 insertions(+), 6 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index c73a239..2cc7dca 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1,4 +1,10 @@ PropDefinitions: + # crdc_id + crdc_id: + Desc: The crdc_id is a unique identifier that is generated by Data Hub + Type: string + Tags: + Template: 'No' # adverse_event props day_in_cycle: Desc: Numerically, the day in the treatment cycle upon which any given adverse event was first observed, where Day 1 is the first day of the treatment cycle within which the adverse event was observed. Some patients/subjects may undergo multiple treatment cycles, such that two or more adverse events may be observed on the same day in cycle, but actually be observed on different dates, because they occur in different treatment cycles. @@ -1077,13 +1083,12 @@ PropDefinitions: - validated - submitted - released - # let's talk about this one /maj - Req: 'Yes' + Req: 'No' uuid: Desc: The universally unique alpha-numeric identifier assigned to each file. Src: Loader-derived Type: string - Req: 'Yes' + Req: 'No' Key: true Tags: Labeled: File UUID, File ID @@ -1091,7 +1096,7 @@ PropDefinitions: Desc: The specific location within the ICDC S3 storage bucket at which the file is stored, expressed in terms of a unique url. Src: Loader-derived Type: string - Req: 'Yes' + Req: 'No' # follow_up props contact_type: Desc: need vocab diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 5f4c417..52a5c28 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -2,7 +2,8 @@ # Title case names are "reserved" (meaningful to the parser) # Lower case names are labels for the entities # document number - really a property of properties (where did this question appear) - +Handle: ICDC +Version: v1.0.0 Nodes: program: Desc: Within the Integrated Canine Data Commons, studies are grouped into discrete programs, based upon the origins and/or scientific nature of each study/trial. These programs may or may not directly relate to any official, e.g. NCI, funding program. The Program node contains the properties required to appropriately characterize any given ICDC program. @@ -18,6 +19,7 @@ Nodes: - program_full_description - program_external_url - program_sort_order + - crdc_id study: Desc: The Study node contains properties required to characterize each study/trial in terms of a title, how and why the study/trial was conducted, and the results that were generated. Tags: @@ -35,6 +37,7 @@ Nodes: - dates_of_conduct - accession_id - study_disposition + - crdc_id study_site: Desc: The Study Site node contains properties which identify the various sites at which any given study/trial was conducted, either in terms of where clinical trial patients were assessed and treated, or in terms of the geographical sites at which biospecimens were acquired from patients/subjects/donors for subsequent analysis. Tags: @@ -46,6 +49,7 @@ Nodes: - site_short_name - veterinary_medical_center - registering_institution + - crdc_id study_arm: Desc: The Study Arm node contains properties required to describe the arms into which any given study/trial was divided. Division of a study/trial into multiple arms is optional and is at the discretion of the data owners, based upon the way in which the study/trial in question was structured, and how best that structure can be represented within the ICDC. Where applicable, the appropriate study arms are defined during the study on-boarding process and then created via a specific data loading file. Tags: @@ -58,6 +62,7 @@ Nodes: - arm_description - arm_id # potentially needed to differentiate between arms having the same name, but which actually belong to different studies. Proactively including sooner rather than later. - ctep_treatment_assignment_code + - crdc_id agent: Desc: The Agent node documents the name of each therapeutic agent being administered during a clinical trial. In this way, in clinical trials which assess the efficacy of combination therapies, adverse events observed during the trial can be attributed specifically to one or more of the medications being used. Tags: @@ -70,6 +75,7 @@ Nodes: - medication # d/n from STUDY_MED_ADMIN/SDAD/1 - document_number + - crdc_id cohort: Desc: The Cohort node contains properties required to describe the cohorts into which any given study/trial was divided. Division of a study/trial into multiple cohorts is optional and is at the discretion of the data owners, based upon the way in which the study/trial in question was structured, and how best that structure can be represented within the ICDC. Where applicable, the appropriate cohorts are defined during the study on-boarding process and then created via a specific data loading file. Tags: @@ -81,6 +87,7 @@ Nodes: - cohort_description # cohort name generally inclusive of some detail as to agent and dose - cohort_id # needed to differentiate between cohorts that share values for cohort description, but which actually belong to different studies - cohort_dose # the intended or protocol dose + - crdc_id case: Desc: The Case node contains properties required to unambiguously identify each patient/subject/donor, either based upon the data submitter's original ID, or upon a study-specific Case ID derived from it during data transformation, which prefixes each original ID with a short, study-specific code. Tags: @@ -92,6 +99,7 @@ Nodes: - case_id - patient_id - patient_first_name + - crdc_id registration: Desc: The Registration node functions to capture multiple IDs that may be associated with any single patient/subject/donor. Specifically, it captures multiple IDs in the form of Key:Value pairs, which represent each alternate ID and the specific source from which that alternate ID originates. These registrations can then be used to identify multi-study participants, i.e. canine individuals enrolled in two or more ICDC studies as study-specific cases, but which nonetheless represent the same underlying patient/subject/donor. Tags: @@ -102,7 +110,8 @@ Nodes: Props: - registration_origin - registration_id - #- is_primary_id + - crdc_id + # - is_primary_id biospecimen_source: Desc: The Biospecimen Source node functions essentially as a look-up table used by the front-end of the application to convert the names of biobanks and tissue repositories represented in the form of acronyms into human-readable, full text names. Tags: @@ -113,6 +122,7 @@ Nodes: Props: - biospecimen_repository_acronym - biospecimen_repository_full_name + - crdc_id canine_individual: Desc: The Canine Individual node contains only a single property, i.e. canine_individual_id, a loader-generated ID which identifies each underlying canine subject represented by two or more study-specific ICDC cases. This ID functions to map data sets ultimately derived from the same underlying patient/subject/donor, but generated from discrete cases in separate studies, to the underlying canine individual, such that all data sets derived from any given canine individual can be identified within the application’s user interface and combined. Tags: @@ -122,6 +132,7 @@ Nodes: Template: 'No' Props: - canine_individual_id + - crdc_id demographic: Desc: The Demographic node is comprised of properties which describe the key characteristics of each patient/subject/donor, such as breed, sex and neutered status. Tags: @@ -138,6 +149,7 @@ Nodes: - sex - weight - neutered_indicator + - crdc_id cycle: Desc: In clinical trials where therapeutic agents are administered in multiple discrete treatment cycles, the properties within the Cycle node serve to capture the dates upon which each cycle started and ended, providing a detailed timeframe for the therapeutic intervention(s) in question. Adverse events can then be associated with the correct cycle based upon when they were observed. Tags: @@ -150,6 +162,7 @@ Nodes: - cycle_number - date_of_cycle_start - date_of_cycle_end + - crdc_id visit: Desc: Clinical trials typically require the patient to make multiple visits to the study site for clinical evaluation and/or the administration of additional medication(s). Properties within the Visit node serve to capture the date upon which each visit occurs. Adverse events and various clinical assessments can then be associated with the correct visit based upon date. Tags: @@ -162,6 +175,7 @@ Nodes: - visit_date - visit_number - visit_id + - crdc_id principal_investigator: Desc: The Principal Investigator node contains properties which identify the principal investigator(s) responsible for any given study/trial. A study/trial may have one or more principal investigators, and any given individual may be listed as a principal investigator on more than one study/trial. Tags: @@ -173,6 +187,7 @@ Nodes: - pi_first_name - pi_last_name - pi_middle_initial + - crdc_id diagnosis: Desc: The Diagnosis node contains numerous properties which fully characterize the type of cancer with which any given patient/subject/donor was diagnosed, inclusive of stage. This node also contains properties pertaining to comorbidities, and the availability of pathology reports, treatment data and follow-up data. Tags: @@ -196,6 +211,7 @@ Nodes: - follow_up_data - concurrent_disease - concurrent_disease_type + - crdc_id enrollment: Desc: The Enrollment node is comprised of properties which document when and where a patient/subject/donor was enrolled onto a study/trial. Tags: @@ -213,6 +229,7 @@ Nodes: - veterinary_medical_center #- cohort_description - patient_subgroup + - crdc_id prior_therapy: Desc: Properties within the Prior Therapy node detail therapies received by the patient/subject/donor prior to being enrolled in the study/trial in question. Clinical trials will typically capture more of this information than will cross-sectional and/or mechanistic studies. Tags: @@ -248,6 +265,7 @@ Nodes: - date_of_last_dose_any_therapy - treatment_performed_at_site - treatment_performed_in_minimal_residual + - crdc_id prior_surgery: Desc: Properties within the Prior Surgery node detail surgical procedures that the patient/subject/donor underwent prior to being enrolled in the study/trial in question. Clinical trials will typically capture more of this information than will cross-sectional and/or mechanistic studies. Tags: @@ -263,6 +281,7 @@ Nodes: - surgical_finding - residual_disease - therapeutic_indicator + - crdc_id agent_administration: Desc: Properties within the Agent Administration node detail the dosing of the therapeutic agent(s) being studied, alongside the specifics of how and when such agents were administered. Tags: @@ -294,6 +313,7 @@ Nodes: - missed_dose_units_of_measure - medication_course_number - comment + - crdc_id sample: Desc: The Sample node contains numerous properties which provide an in-depth characterization of the types of samples which were collected from any given patient/subject/donor and subsequently analyzed. Many of these sample annotations are required. Tags: @@ -320,6 +340,7 @@ Nodes: - percentage_tumor - sample_preservation - comment + - crdc_id assay: Desc: The Assay node does not yet have any properties associated with it and is not currently used. Tags: @@ -345,6 +366,7 @@ Nodes: - file_status - uuid - file_location + - crdc_id image: Desc: The Image node does not yet have any properties associated with it and is not currently used. Tags: @@ -366,6 +388,7 @@ Nodes: - image_collection_url - repository_name - collection_access + - crdc_id physical_exam: Desc: Properties within the Physical Exam node detail observations around the status of multiple body systems as of a patient enrolled in a clinical trial, as of that patient being examined by a veterinarian during a scheduled visit to the appropriate study site. Tags: @@ -382,6 +405,7 @@ Nodes: - pe_comment - phase_pe - assessment_timepoint + - crdc_id publication: Desc: The Publication node is comprised of properties which describe publications that are directly associated with any given study/trial of interest, inclusive of the location(s) at which publications can be viewed in electronic form. Tags: @@ -396,6 +420,7 @@ Nodes: - journal_citation - digital_object_id - pubmed_id + - crdc_id vital_signs: Desc: Properties within the Vital Signs node detail observations around the key indicators of the bodily functions of a patient enrolled in a clinical trial, as of that patient being examined by a veterinarian during a scheduled visit to the appropriate study site. Tags: @@ -418,6 +443,7 @@ Nodes: - modified_ecog - assessment_timepoint - phase + - crdc_id lab_exam: Desc: The Lab Exam node does not yet have any properties associated with it and is not currently used. Tags: @@ -456,6 +482,7 @@ Nodes: - other_attribution_description - dose_limiting_toxicity - unexpected_adverse_event + - crdc_id disease_extent: Desc: Properties within the Disease Extent node detail the extent to which the disease for which the patient is being treated has either responded to treatment or progressed, based upon observations of one or more specific lesions. Tags: @@ -477,6 +504,7 @@ Nodes: - longest_measurement - evaluation_number - evaluation_code + - crdc_id follow_up: Desc: The Follow-up node is comprised of properties which document when a follow-up evaluation was performed, and what observations were made at each follow-up evaluation. Tags: @@ -495,6 +523,7 @@ Nodes: - treatment_since_last_contact - physical_exam_performed - physical_exam_changes + - crdc_id off_study: # off_study, off_treatment -- how related? should be a dependency and normalize properties? Desc: Properties within the Off Study node detail when a patient was removed from a clinical trial relative to other key dates, and the reason(s) for the patient being removed. @@ -515,6 +544,7 @@ Nodes: - date_last_medication_administration - best_resp_vet_tx_tp_best_response - date_of_best_response + - crdc_id off_treatment: Desc: Properties within the Off Treatment node detail when a clinical trial patient's treatment was curtailed relative to other key dates. Properties also detail the best response to treatment observed to that point, and the reason(s) for treatment being curtailed. Tags: @@ -533,6 +563,7 @@ Nodes: - date_last_medication_administration - best_resp_vet_tx_tp_best_response - date_of_best_response + - crdc_id Relationships: member_of: Mul: many_to_one From 0dfbc2ce82928906da0942f284330b6838201b0d Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Wed, 3 Jul 2024 15:14:31 -0500 Subject: [PATCH 12/60] Add file_id --- model-desc/icdc-model-props.yml | 2 ++ model-desc/icdc-model.yml | 1 + 2 files changed, 3 insertions(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 2cc7dca..d1e5739 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1009,6 +1009,8 @@ PropDefinitions: # Type: string # removed residual evaluation props from here # file props + file_id: + Desc: DCF GUID (including "dg.4DFC/" prefix)supplied by the CRDC Data Hub. file_name: Desc: The name of the file, inclusive of file extension(s), maintained exactly as provided by the data submitter. Src: Data Owner(s) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 52a5c28..02668ad 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -367,6 +367,7 @@ Nodes: - uuid - file_location - crdc_id + - file_id image: Desc: The Image node does not yet have any properties associated with it and is not currently used. Tags: From d33eee6d109310c889a2b51a80ff39e9504af481 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Wed, 3 Jul 2024 15:44:38 -0500 Subject: [PATCH 13/60] Remove quotes causing validation error. --- model-desc/icdc-model-props.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index d1e5739..088887a 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1010,7 +1010,7 @@ PropDefinitions: # removed residual evaluation props from here # file props file_id: - Desc: DCF GUID (including "dg.4DFC/" prefix)supplied by the CRDC Data Hub. + Desc: DCF GUID (including dg.4DFC/ prefix)supplied by the CRDC Data Hub. file_name: Desc: The name of the file, inclusive of file extension(s), maintained exactly as provided by the data submitter. Src: Data Owner(s) From 1211087dbc1f06fe6cf3e4a6f87f6a2bb806ecd1 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Wed, 3 Jul 2024 15:50:28 -0500 Subject: [PATCH 14/60] Update icdc-model-props.yml --- model-desc/icdc-model-props.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 088887a..85e6a74 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1011,6 +1011,9 @@ PropDefinitions: # file props file_id: Desc: DCF GUID (including dg.4DFC/ prefix)supplied by the CRDC Data Hub. + Src: Data Hub Loader + Type: string + Req: 'No' file_name: Desc: The name of the file, inclusive of file extension(s), maintained exactly as provided by the data submitter. Src: Data Owner(s) From da78c2ed85c02dded13ca3852642df6aef96618f Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Tue, 9 Jul 2024 18:15:02 -0500 Subject: [PATCH 15/60] Changes requested by Data Hub --- model-desc/icdc-model-props.yml | 7 +------ model-desc/icdc-model.yml | 1 - 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 85e6a74..c0b2e7d 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1009,11 +1009,6 @@ PropDefinitions: # Type: string # removed residual evaluation props from here # file props - file_id: - Desc: DCF GUID (including dg.4DFC/ prefix)supplied by the CRDC Data Hub. - Src: Data Hub Loader - Type: string - Req: 'No' file_name: Desc: The name of the file, inclusive of file extension(s), maintained exactly as provided by the data submitter. Src: Data Owner(s) @@ -1093,7 +1088,7 @@ PropDefinitions: Desc: The universally unique alpha-numeric identifier assigned to each file. Src: Loader-derived Type: string - Req: 'No' + Req: 'Yes' Key: true Tags: Labeled: File UUID, File ID diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 02668ad..52a5c28 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -367,7 +367,6 @@ Nodes: - uuid - file_location - crdc_id - - file_id image: Desc: The Image node does not yet have any properties associated with it and is not currently used. Tags: From b378bd31b230238475bbc8fc3981896356566f47 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 9 Jul 2024 18:19:10 -0500 Subject: [PATCH 16/60] Update icdc-model-props.yml --- model-desc/icdc-model-props.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index c0b2e7d..708a5cc 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1091,6 +1091,7 @@ PropDefinitions: Req: 'Yes' Key: true Tags: + Template: 'No' Labeled: File UUID, File ID file_location: Desc: The specific location within the ICDC S3 storage bucket at which the file is stored, expressed in terms of a unique url. From b0bd63be597ad7fe0cfc28ed0fb59aa77e654698 Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Thu, 11 Jul 2024 17:05:54 -0500 Subject: [PATCH 17/60] additional updates requested --- model-desc/icdc-model-props.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 708a5cc..ed65620 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1084,6 +1084,8 @@ PropDefinitions: - submitted - released Req: 'No' + Tags: + Template: 'No' uuid: Desc: The universally unique alpha-numeric identifier assigned to each file. Src: Loader-derived @@ -1098,6 +1100,8 @@ PropDefinitions: Src: Loader-derived Type: string Req: 'No' + Tags: + Template: 'No' # follow_up props contact_type: Desc: need vocab From 18e8d5718f831b7021c796cca0a616d38611ce77 Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Thu, 11 Jul 2024 17:09:16 -0500 Subject: [PATCH 18/60] Revert "additional updates requested" This reverts commit b0bd63be597ad7fe0cfc28ed0fb59aa77e654698. --- model-desc/icdc-model-props.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index ed65620..708a5cc 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1084,8 +1084,6 @@ PropDefinitions: - submitted - released Req: 'No' - Tags: - Template: 'No' uuid: Desc: The universally unique alpha-numeric identifier assigned to each file. Src: Loader-derived @@ -1100,8 +1098,6 @@ PropDefinitions: Src: Loader-derived Type: string Req: 'No' - Tags: - Template: 'No' # follow_up props contact_type: Desc: need vocab From 1e91a18322ab268dc6e150fedffe259cf51edf1e Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Thu, 11 Jul 2024 17:17:12 -0500 Subject: [PATCH 19/60] additional changes requested --- model-desc/icdc-model-props.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 708a5cc..ed65620 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1084,6 +1084,8 @@ PropDefinitions: - submitted - released Req: 'No' + Tags: + Template: 'No' uuid: Desc: The universally unique alpha-numeric identifier assigned to each file. Src: Loader-derived @@ -1098,6 +1100,8 @@ PropDefinitions: Src: Loader-derived Type: string Req: 'No' + Tags: + Template: 'No' # follow_up props contact_type: Desc: need vocab From 712371943a36a410a665af85b5a56ea189f10870 Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Mon, 22 Jul 2024 16:12:04 -0500 Subject: [PATCH 20/60] Data model updates requested by the CRDC Data Hub --- model-desc/icdc-model-props.yml | 475 +++++++++++++++++++------------- model-desc/icdc-model.yml | 177 ++++++------ 2 files changed, 367 insertions(+), 285 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index ed65620..dbb17df 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -6,6 +6,12 @@ PropDefinitions: Tags: Template: 'No' # adverse_event props + adverse_event_id: + Desc: A globally unique identifier via which adverse event records can be differentiated from one another across studies/trials. Specifically the value of case_id concatenated with the value of adverse_event_term.
This property is used as the key to identify the correct adverse event records during data upates. + Src: Data Owner(s) + Type: string + Req: true + Key: true day_in_cycle: Desc: Numerically, the day in the treatment cycle upon which any given adverse event was first observed, where Day 1 is the first day of the treatment cycle within which the adverse event was observed. Some patients/subjects may undergo multiple treatment cycles, such that two or more adverse events may be observed on the same day in cycle, but actually be observed on different dates, because they occur in different treatment cycles. Src: Data Owner(s) @@ -158,102 +164,103 @@ PropDefinitions: - 'No' - Undefined # accommodates situations where there is any ambiguity in terms of an adverse event being expected or not Req: 'Yes' - # agent props - document_number: - Desc: S/N of the executed CRF - Src: ALL - Type: - pattern: "^R[0-9]+$\n" - medication: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: - - http://localhost/terms/domain/medication - # agent_administration props - comment: - Desc: generic comment - Type: string - date_of_missed_dose: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: datetime + # # agent props **proposing deprecation or removal of all props in this node as it contains no data across ingested studies as of 7/16/24 + # document_number: + # Desc: S/N of the executed CRF + # Src: ALL + # Type: + # pattern: "^R[0-9]+$\n" + # medication: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: + # - http://localhost/terms/domain/medication + # agent_administration props **proposing deprecation or removal of all props in this node as it contains no data across ingested studies as of 7/16/24 + # comment: + # Desc: generic comment + # Type: string + # date_of_missed_dose: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: datetime # document_number also included in agent_administration - dose_level: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: - units: - - mg/kg - value_type: number - dose_units_of_measure: - Deprecated: true - Src: STUDY_MED_ADMIN/SDAD/1 - Type: string + # dose_level: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: + # units: + # - mg/kg + # value_type: number + # dose_units_of_measure: + # Deprecated: true + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: string # medication also included in agent_administration - medication_actual_dose: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: - units: - - mg/kg - value_type: number - medication_actual_units_of_measure: - Deprecated: true - Src: STUDY_MED_ADMIN/SDAD/1 - Type: string - medication_course_number: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: string - medication_duration: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: - units: - - days - - hr - - min - value_type: number - medication_lot_number: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: string - medication_missed_dose: - Desc: Q.- form has "medication" - Src: STUDY_MED_ADMIN/SDAD/1 - Type: - - http://localhost/terms/domain/agent_name - medication_units_of_measure: - Deprecated: true - Src: STUDY_MED_ADMIN/SDAD/1 - Type: string - medication_vial_id: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: string - missed_dose_amount: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: - units: - - mg/kg - value_type: number - missed_dose_units_of_measure: - Deprecated: true - Desc: Q.- form has "dose uom_ful" - Src: STUDY_MED_ADMIN/SDAD/1 - Type: string - phase: - Desc: Where should this live?/What is? - Src: COURSE INIT/CINIT/1 - Type: TBD - route_of_administration: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: - - http://localhost/terms/domain/route_of_administration - start_time: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: datetime - stop_time: - Src: STUDY_MED_ADMIN/SDAD/1 - Type: datetime + # medication_actual_dose: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: + # units: + # - mg/kg + # value_type: number + # medication_actual_units_of_measure: + # Deprecated: true + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: string + # medication_course_number: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: string + # medication_duration: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: + # units: + # - days + # - hr + # - min + # value_type: number + # medication_lot_number: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: string + # medication_missed_dose: + # Desc: Q.- form has "medication" + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: + # - http://localhost/terms/domain/agent_name + # medication_units_of_measure: + # Deprecated: true + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: string + # medication_vial_id: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: string + # missed_dose_amount: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: + # units: + # - mg/kg + # value_type: number + # missed_dose_units_of_measure: + # Deprecated: true + # Desc: Q.- form has "dose uom_ful" + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: string + # phase: + # Desc: Where should this live?/What is? + # Src: COURSE INIT/CINIT/1 + # Type: TBD + # route_of_administration: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: + # - http://localhost/terms/domain/route_of_administration + # start_time: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: datetime + # stop_time: + # Src: STUDY_MED_ADMIN/SDAD/1 + # Type: datetime # biospecimen_source props biospecimen_repository_acronym: - Desc: The name of the biobank or tissue repository from which or to which samples for any given patient/subject/donor were acquired or submitted, expressed in the form of an acronym. + Desc: The name of the biobank or tissue repository from which or to which samples for any given patient/subject/donor were acquired or submitted, expressed in the form of an acronym.
This property is used as the key v to identify the correct biospecimen repository records during data updates. Src: Internally-curated Type: string Req: 'Yes' + Key: true Tags: Labeled: Biobank biospecimen_repository_full_name: @@ -311,11 +318,17 @@ PropDefinitions: Labeled: Cohorts cohort_id: Desc: A unique identifier via which cohorts can be differentiated from one another across studies/trials.
This property is used as the key via which cases can be associated with the appropriate cohort during data loading, and to identify the correct records during data updates. - Src: Internally-curated + Src: Data Owner(s) Type: string Req: 'Yes' Key: true # cycle props + cycle_id: + Desc: A globally unique identifier for each therapy cycle administered to a patient/subject; specifically the value of case_id concatenated with the value of cycle_number.
This property is used as the key via which child records, e.g. visit records, can be associated with the appropriate cycle during data loading, and to identify the correct cycle records during data upates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true cycle_number: Desc: For a patient/subject/donor enrolled in a clinical trial evaluating the effects of therapy administered in multiple cycles, the number of the treatment cycle during which visits occurred such that therapy could be administered and/or clinical observations could be made, with cycles numbered according to their chronological order. Src: Data Owner(s) @@ -632,7 +645,7 @@ PropDefinitions: Type: datetime Req: 'No' demographic_id: - Desc: A unique identifier of each demographic record, used to identify the correct demographic records during data updates. The value of this property will generally be the same as the value of the case_id property. + Desc: A unique identifier of each demographic record, used to identify the correct demographic records during data updates.
The value of this property will generally be the same as the value of the case_id property.
This property is used as the key to identify the correct demographic records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -894,6 +907,12 @@ PropDefinitions: Tags: Labeled: Treatment Data Available # disease_extent props + disease_extent_id: + Desc: A globally unique identifier of each evaluation of disease extent for a subject/patient/donor; specifically the value of case_id concatenated with the value of evaluation_code.
This property is used as the key to identify the correct disease extent records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true date_of_evaluation: Desc: The date upon which the extent of disease evaluation was conducted. Src: Data Owner(s) @@ -918,7 +937,8 @@ PropDefinitions: Desc: An arbitrary numerical designation for each lesion subject to evaluation, by which that lesion can be unambiguously identified. Src: Data Owner(s) Type: Integer - Req: 'No' + Req: 'Yes' + Key: true lesion_site: Desc: The overall anatomical location of the lesion being assessed in terms of the organ or organ system in which it is located. For example, lung, lymph node, etc. Src: Data Owner(s) @@ -1087,7 +1107,7 @@ PropDefinitions: Tags: Template: 'No' uuid: - Desc: The universally unique alpha-numeric identifier assigned to each file. + Desc: The universally unique alpha-numeric identifier assigned to each file.
This property is used as the key to identify the correct file records during data updates. Src: Loader-derived Type: string Req: 'Yes' @@ -1102,115 +1122,121 @@ PropDefinitions: Req: 'No' Tags: Template: 'No' - # follow_up props - contact_type: - Desc: need vocab - Src: FOLLOW_UP/FLWU/1 - Type: string - date_of_last_contact: - Src: FOLLOW_UP/FLWU/1 - Type: datetime + # # follow_up props proposing deprecation or removal of props as this node does not contain any data values as of 7/16/24. + # contact_type: + # Desc: need vocab + # Src: FOLLOW_UP/FLWU/1 + # Type: string + # date_of_last_contact: + # Src: FOLLOW_UP/FLWU/1 + # Type: datetime # document_number: also included in follow_up node, defined elsewhere in this document # Desc: S/N of the executed CRF # Src: ALL # Type: # pattern: "^R[0-9]+$\n" - explain_unknown_status: - Desc: free text? - Src: FOLLOW_UP/FLWU/1 - Type: string - patient_status: - Desc: need vocab - Src: FOLLOW_UP/FLWU/1 - Type: string - physical_exam_changes: - Desc: How described? Relative to data already stored in "physical_exam" node? - Src: FOLLOW_UP/FLWU/1 - Type: TBD - physical_exam_performed: - Desc: y/n - Src: FOLLOW_UP/FLWU/1 - Type: boolean - treatment_since_last_contact: - Desc: y/n - Src: FOLLOW_UP/FLWU/1 - Type: boolean - # image collection props - image_collection_name: - Desc: The name of the image collection exactly as it appears at the location where the collection can be viewed and/or accessed. - Src: Internally-curated - Type: string - Req: 'Yes' - Tags: - Labeled: Collection - image_type_included: - Desc: A list of the image types included in the image collection, drawn from a list of acceptable values. - Src: Internally-curated - Type: - value_type: list - Enum: - - CT - - Histopathology - - MRI - - PET - - X-ray - - Optical - - Ultrasound - Req: 'Yes' - Tags: - Labeled: Image Types - image_collection_url: - Desc: The external url via which the image collection can be viewed and/or accessed. - Src: Internally-curated - Type: string - Req: 'Yes' - repository_name: - Desc: The name of the image repository within which the image collection can be found, stated in the form of the appropriate acronym. - Src: Internally-curated - Type: string - Req: 'Yes' - collection_access: - Desc: Indicator as to whether the image collection can be accessed via download versus being accessible only via the cloud. - Src: Internally-curated - Enum: - - Download - - Cloud - Req: 'Yes' + # explain_unknown_status: + # Desc: free text? + # Src: FOLLOW_UP/FLWU/1 + # Type: string + # patient_status: + # Desc: need vocab + # Src: FOLLOW_UP/FLWU/1 + # Type: string + # physical_exam_changes: + # Desc: How described? Relative to data already stored in "physical_exam" node? + # Src: FOLLOW_UP/FLWU/1 + # Type: TBD + # physical_exam_performed: + # Desc: y/n + # Src: FOLLOW_UP/FLWU/1 + # Type: boolean + # treatment_since_last_contact: + # Desc: y/n + # Src: FOLLOW_UP/FLWU/1 + # Type: boolean + # suggesting deprecation or removal of image collection props as all imgaing data will be stored and fetched through the IDC & TCIA API. + # image_collection_name: + # Desc: The name of the image collection exactly as it appears at the location where the collection can be viewed and/or accessed. + # Src: Internally-curated + # Type: string + # Req: 'Yes' + # Tags: + # Labeled: Collection + # image_type_included: + # Desc: A list of the image types included in the image collection, drawn from a list of acceptable values. + # Src: Internally-curated + # Type: + # value_type: list + # Enum: + # - CT + # - Histopathology + # - MRI + # - PET + # - X-ray + # - Optical + # - Ultrasound + # Req: 'Yes' + # Tags: + # Labeled: Image Types + # image_collection_url: + # Desc: The external url via which the image collection can be viewed and/or accessed. + # Src: Internally-curated + # Type: string + # Req: 'Yes' + # repository_name: + # Desc: The name of the image repository within which the image collection can be found, stated in the form of the appropriate acronym. + # Src: Internally-curated + # Type: string + # Req: 'Yes' + # collection_access: + # Desc: Indicator as to whether the image collection can be accessed via download versus being accessible only via the cloud. + # Src: Internally-curated + # Enum: + # - Download + # - Cloud + # Req: 'Yes' # off_study props and - # off_treatment props - best_resp_vet_tx_tp_best_response: - Src: OFF_STUDY/OSSM/1 - Type: TBD - best_resp_vet_tx_tp_secondary_response: - Src: OFF_STUDY/OSSM/1 - Type: TBD - date_last_medication_administration: - Src: OFF_STUDY/OSSM/1 - Type: datetime - date_of_best_response: - Src: OFF_STUDY/OSSM/1 - Type: datetime - date_of_disease_progression: - Src: OFF_STUDY/OSSM/1 - Type: datetime - date_off_study: - Src: OFF_STUDY/OSSM/1 - Type: datetime - date_off_treatment: - Src: OFF_STUDY/OSSM/1 - Type: datetime + # off_treatment props proposing deprecation or removal as these nodes do not contain any data values across all ingested studies as of 7/16/24 + # best_resp_vet_tx_tp_best_response: + # Src: OFF_STUDY/OSSM/1 + # Type: TBD + # best_resp_vet_tx_tp_secondary_response: + # Src: OFF_STUDY/OSSM/1 + # Type: TBD + # date_last_medication_administration: + # Src: OFF_STUDY/OSSM/1 + # Type: datetime + # date_of_best_response: + # Src: OFF_STUDY/OSSM/1 + # Type: datetime + # date_of_disease_progression: + # Src: OFF_STUDY/OSSM/1 + # Type: datetime + # date_off_study: + # Src: OFF_STUDY/OSSM/1 + # Type: datetime + # date_off_treatment: + # Src: OFF_STUDY/OSSM/1 + # Type: datetime # document_number: also included in off_study node, defined elsewhere in this document # Desc: S/N of the executed CRF # Src: ALL # Type: # pattern: "^R[0-9]+$\n" - reason_off_study: - Src: OFF_STUDY/OSSM/1 - Type: string - reason_off_treatment: - Src: OFF_STUDY/OSSM/1 - Type: string + # reason_off_study: + # Src: OFF_STUDY/OSSM/1 + # Type: string + # reason_off_treatment: + # Src: OFF_STUDY/OSSM/1 + # Type: string # physical_exam props + physical_exam_id: + Desc: A globally unique identifier of each physical exam record; specifically the value of case_id concatenated with the value of date_of_examination, the date upon which the physical exam was conducted.
This property is used as the key to identify the correct physical exam records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true assessment_timepoint: Desc: An indication as to the timing of the visit during which the physical examination was conducted. This could be a visit number indicative of physical examination's chronology, a narrative statement/description of the vist, or a combination of both. Src: Data Owner(s) @@ -1252,6 +1278,8 @@ PropDefinitions: Src: Data Owner(s) Type: TBD # principal_investigator props + pi_id: + Desc: A globally unique identifier via which principle investigator can be differentiated across studies; specifically the value of study_id concatenated with the value of pi_last_name,
This property is used as the key via which child records, e.g. cohort records, can be associated with the appropriate principle investigator, and to identify the correct principle investigator records during data updates. pi_first_name: Desc: The first or given name of each principal investigator of the study/trial. Src: Data Owner(s) @@ -1274,6 +1302,12 @@ PropDefinitions: Tags: Labeled: Principal Investigators # prior_surgery props + prior_surgery_id: + Desc: A globally unique identifier of each prior surgery record;
This property is used as the key to identify the correct prior surgery records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true anatomical_site_of_surgery: Desc: The anatomical location at which the prior surgery in question occurred. Src: Data Owner(s) @@ -1306,6 +1340,12 @@ PropDefinitions: Type: TBD Req: 'No' # prior_therapy props + prior_therapy_id: + Desc: A globally unique identifier of each prior therapy record;
This property is used as the key to identify the correct prior therapy records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true agent_name: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: @@ -1395,7 +1435,7 @@ PropDefinitions: Type: TBD # program props program_acronym: - Desc: The name of the program under which related studies will be grouped, expressed in the form of the acronym by which it will identified within the UI.
This property is used as the key via which study records can be associated with the appropriate program during data loading, and to identify the correct records during data updates. + Desc: The name of the program under which related studies will be grouped, expressed in the form of the acronym by which it will identified within the UI.
This property is used as the key via which child records, e.g. study records can be associated with the appropriate program during data loading, and to identify the correct records during data updates. Src: Internally-curated Type: string Req: 'Yes' @@ -1429,11 +1469,10 @@ PropDefinitions: Req: 'No' # publication props publication_title: - Desc: The full title of the publication stated exactly as it appears on the published work.
This property is used as the key via which to identify the correct records during data updates. + Desc: The full title of the publication stated exactly as it appears on the published work. Src: Data Owner(s) Type: string Req: 'Yes' - Key: true authorship: Desc: A list of authors for the cited work. More specifically, for publications with no more than three authors, authorship quoted in full; for publications with more than three authors, authorship abbreviated to first author et al. Src: Data Owner(s) @@ -1456,10 +1495,11 @@ PropDefinitions: Tags: Labeled: Journal digital_object_id: - Desc: Where applicable, the digital object identifier for the cited work, by which it can be permanently identified, and linked to via the internet.
Values of this property must contain only the alphanumeric string of the digital object identifier itself, exclusive of any prefix such as "DOI:", such that values can be correctly interpreted and displayed as hyperlinks within the application. + Desc: Where applicable, the digital object identifier for the cited work, by which it can be permanently identified, and linked to via the internet.
Values of this property must contain only the alphanumeric string of the digital object identifier itself, exclusive of any prefix such as "DOI:", such that values can be correctly interpreted and displayed as hyperlinks within the application.
This property is used as the key via which to identify the correct publication records during data updates. Src: Data Owner(s) Type: string - Req: Preferred + Req: 'Yes' + Key: true Tags: Labeled: DOI pubmed_id: @@ -1476,10 +1516,11 @@ PropDefinitions: Type: string Req: 'Yes' registration_id: - Desc: Any ID used by a data submitter to identify a patient/subject/donor, either locally or globally. + Desc: A globally unique identifier to describe a patient/donor/subject; specifically the value of case_id.
This property is used as the key to identify the registration records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' + Key: true #is_primary_id: #Desc: Indicator as to whether the ID in question was also independently captured as patient_id and therefore used to create case_id; for each study/trial participant subject, one, and only one, registration ID must be flagged as being a primary ID #Type: @@ -1861,10 +1902,11 @@ PropDefinitions: Type: string Req: 'No' site_short_name: - Desc: The widely-accepted acronym for the institution at which the patient/subject/donor was enrolled into the study/trial, and then treated under the appropriate veterinary medicine program. + Desc: The widely-accepted acronym for the institution at which the patient/subject/donor was enrolled into the study/trial, and then treated under the appropriate veterinary medicine program.
This property is used as the key to identify the correct records during data updates. Src: Data Owner(s) Type: string - Req: 'No' + Req: 'Yes' + Key: true Tags: Labeled: Study Site veterinary_medical_center: @@ -1880,7 +1922,7 @@ PropDefinitions: Req: 'No' visit_id: Desc: A globally unique identifier of each visit record; specifically the value of case_id concatenated with the value of visit_date, the date upon which the visit occurred.
This property is used as the key via which child records, e.g. physical examination records, can be associated with the appropriate visit, and to identify the correct visit records during data updates. - Src: Data-derived + Src: Data Owner(s) Type: string Req: 'Yes' Key: true @@ -1892,6 +1934,12 @@ PropDefinitions: # assessment_timepoint: also included in vital_signs node, defined elsewhere # Src: PHYSICAL_EXAM/PE/1 # Type: integer + vital_signs_id: + Desc: A globally unique identifier of each vital signs record collected during a scheduled visit; specifically the value of case_id concatenated with the value of date_of_vital_signs, the date upon which the vital signs evaluation in question was conducted.
This property is used as the key to identify the correct vital signs records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true body_surface_area: Desc: The body surface area of the patient/subject/donor at the time of the vital signs evaluation, expressed in square meters. Src: Data Owner(s) @@ -1963,3 +2011,32 @@ PropDefinitions: units: - mm Hg value_type: integer + # lab_exam props + lab_exam: + Desc: Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting. Tests can help determine a diagnosis, plan treatment, check to see if treatment is working, or monitor the disease over time. + Src: Data Owner(s) + Type: string + Req: 'Yes' + lab_exam_id: + Desc: A globally unique identifier of each lab exam record; specifically the value of case_id concatenated with the value of lab_exam_date, the date upon which the lab exam occurred.
This property is used as the key to identify the correct lab exam records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true + lab_exam_date: + Desc: The date upon which the lab exam occurred. + Src: Data Owner(s) + Type: datetime + Req: 'Yes' + # assay props + assay_id: + Desc: A globally unique identifier of each assay record; specifically the value of case_id concatenated with the value of assay type.
This property is used as the key to identify the correct physical exam records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true + assay_type: + Desc: The type of assay being conducted. + Src: Data Owner(s) + Type: string + Req: 'Yes' diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 52a5c28..51a1e2b 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -63,19 +63,20 @@ Nodes: - arm_id # potentially needed to differentiate between arms having the same name, but which actually belong to different studies. Proactively including sooner rather than later. - ctep_treatment_assignment_code - crdc_id - agent: - Desc: The Agent node documents the name of each therapeutic agent being administered during a clinical trial. In this way, in clinical trials which assess the efficacy of combination therapies, adverse events observed during the trial can be attributed specifically to one or more of the medications being used. - Tags: - Category: clinical_trial - Assignment: extended - Class: secondary - Template: 'No' - Clinical_Data_Export: 'Yes' - Props: - - medication - # d/n from STUDY_MED_ADMIN/SDAD/1 - - document_number - - crdc_id + # proposing deprecation or removal of the agent node as it contains no data across ingested studies as of 7/16/24. + # agent: + # Desc: The Agent node documents the name of each therapeutic agent being administered during a clinical trial. In this way, in clinical trials which assess the efficacy of combination therapies, adverse events observed during the trial can be attributed specifically to one or more of the medications being used. + # Tags: + # Category: clinical_trial + # Assignment: extended + # Class: secondary + # Template: 'No' + # Clinical_Data_Export: 'Yes' + # Props: + # - medication + # # d/n from STUDY_MED_ADMIN/SDAD/1 + # - document_number + # - crdc_id cohort: Desc: The Cohort node contains properties required to describe the cohorts into which any given study/trial was divided. Division of a study/trial into multiple cohorts is optional and is at the discretion of the data owners, based upon the way in which the study/trial in question was structured, and how best that structure can be represented within the ICDC. Where applicable, the appropriate cohorts are defined during the study on-boarding process and then created via a specific data loading file. Tags: @@ -375,20 +376,21 @@ Nodes: Class: secondary Template: 'No' Props: null - image_collection: - Desc: The Image Collection node is comprised of properties which describe collections of images that are associated with any given study/trial. These properties characterize such image collections in terms of the types of images they contain, where the collections are hosted, and how they can be accessed. - Tags: - Category: study - Assignment: core - Class: secondary - Template: 'Yes' - Props: - - image_collection_name - - image_type_included - - image_collection_url - - repository_name - - collection_access - - crdc_id + # proposing deprecation or removal the image_collection node as it contains no data across ingested studies as of 7/16/24 + # image_collection: + # Desc: The Image Collection node is comprised of properties which describe collections of images that are associated with any given study/trial. These properties characterize such image collections in terms of the types of images they contain, where the collections are hosted, and how they can be accessed. + # Tags: + # Category: study + # Assignment: core + # Class: secondary + # Template: 'Yes' + # Props: + # - image_collection_name + # - image_type_included + # - image_collection_url + # - repository_name + # - collection_access + # - crdc_id physical_exam: Desc: Properties within the Physical Exam node detail observations around the status of multiple body systems as of a patient enrolled in a clinical trial, as of that patient being examined by a veterinarian during a scheduled visit to the appropriate study site. Tags: @@ -505,65 +507,68 @@ Nodes: - evaluation_number - evaluation_code - crdc_id - follow_up: - Desc: The Follow-up node is comprised of properties which document when a follow-up evaluation was performed, and what observations were made at each follow-up evaluation. - Tags: - Category: clinical_trial - Assignment: extended - Class: secondary - Template: 'Yes' - Clinical_Data_Export: 'Yes' - Props: - # d/n from FOLLOW_UP/FLWU/1 - - document_number - - date_of_last_contact - - patient_status - - explain_unknown_status - - contact_type - - treatment_since_last_contact - - physical_exam_performed - - physical_exam_changes - - crdc_id - off_study: - # off_study, off_treatment -- how related? should be a dependency and normalize properties? - Desc: Properties within the Off Study node detail when a patient was removed from a clinical trial relative to other key dates, and the reason(s) for the patient being removed. - Tags: - Category: clinical_trial - Assignment: extended - Class: secondary - Template: 'Yes' - Clinical_Data_Export: 'Yes' - Props: - # d/n from OFF_STUDY/OSSM/1 - - document_number - - date_off_study - - reason_off_study - - date_of_disease_progression - - date_off_treatment - - best_resp_vet_tx_tp_secondary_response - - date_last_medication_administration - - best_resp_vet_tx_tp_best_response - - date_of_best_response - - crdc_id - off_treatment: - Desc: Properties within the Off Treatment node detail when a clinical trial patient's treatment was curtailed relative to other key dates. Properties also detail the best response to treatment observed to that point, and the reason(s) for treatment being curtailed. - Tags: - Category: clinical_trial - Assignment: extended - Class: secondary - Template: 'Yes' - Clinical_Data_Export: 'Yes' - Props: - # d/n from OFF_TREATMENT/OTSM/1 - - document_number - - date_off_treatment - - reason_off_treatment - - date_of_disease_progression - - best_resp_vet_tx_tp_secondary_response - - date_last_medication_administration - - best_resp_vet_tx_tp_best_response - - date_of_best_response - - crdc_id + # proposing deprecation or removal of the follow-up node as it contains no data across ingested studies as of 7/16/24. + # follow_up: + # Desc: The Follow-up node is comprised of properties which document when a follow-up evaluation was performed, and what observations were made at each follow-up evaluation. + # Tags: + # Category: clinical_trial + # Assignment: extended + # Class: secondary + # Template: 'Yes' + # Clinical_Data_Export: 'Yes' + # Props: + # # d/n from FOLLOW_UP/FLWU/1 + # - document_number + # - date_of_last_contact + # - patient_status + # - explain_unknown_status + # - contact_type + # - treatment_since_last_contact + # - physical_exam_performed + # - physical_exam_changes + # - crdc_id + # proposing deprecation or removal off_study node as it contains no data across ingested studies as of 7/16/24. + # off_study: + # # off_study, off_treatment -- how related? should be a dependency and normalize properties? + # Desc: Properties within the Off Study node detail when a patient was removed from a clinical trial relative to other key dates, and the reason(s) for the patient being removed. + # Tags: + # Category: clinical_trial + # Assignment: extended + # Class: secondary + # Template: 'Yes' + # Clinical_Data_Export: 'Yes' + # Props: + # # d/n from OFF_STUDY/OSSM/1 + # - document_number + # - date_off_study + # - reason_off_study + # - date_of_disease_progression + # - date_off_treatment + # - best_resp_vet_tx_tp_secondary_response + # - date_last_medication_administration + # - best_resp_vet_tx_tp_best_response + # - date_of_best_response + # - crdc_id + # proposing deprecation or removal of the off_treatment node as it contains no data across ingested studies as of 7/16/24. + # off_treatment: + # Desc: Properties within the Off Treatment node detail when a clinical trial patient's treatment was curtailed relative to other key dates. Properties also detail the best response to treatment observed to that point, and the reason(s) for treatment being curtailed. + # Tags: + # Category: clinical_trial + # Assignment: extended + # Class: secondary + # Template: 'Yes' + # Clinical_Data_Export: 'Yes' + # Props: + # # d/n from OFF_TREATMENT/OTSM/1 + # - document_number + # - date_off_treatment + # - reason_off_treatment + # - date_of_disease_progression + # - best_resp_vet_tx_tp_secondary_response + # - date_last_medication_administration + # - best_resp_vet_tx_tp_best_response + # - date_of_best_response + # - crdc_id Relationships: member_of: Mul: many_to_one From d7b38c79335f96d22643f3a0c70589393756c718 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Mon, 22 Jul 2024 16:22:22 -0500 Subject: [PATCH 21/60] Update icdc-model-props.yml added missing fields for pi_id --- model-desc/icdc-model-props.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index dbb17df..6aaf12d 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1280,6 +1280,10 @@ PropDefinitions: # principal_investigator props pi_id: Desc: A globally unique identifier via which principle investigator can be differentiated across studies; specifically the value of study_id concatenated with the value of pi_last_name,
This property is used as the key via which child records, e.g. cohort records, can be associated with the appropriate principle investigator, and to identify the correct principle investigator records during data updates. + Src: Data Onwer(s) + Type: string + Req: 'Yes' + Key: true pi_first_name: Desc: The first or given name of each principal investigator of the study/trial. Src: Data Owner(s) From c09ff4e2159db0e6156fb68161557459c5cab9bd Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Wed, 24 Jul 2024 12:36:25 -0500 Subject: [PATCH 22/60] Remove duplicate props --- model-desc/icdc-manifest-props.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 452df44..2961031 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -23,8 +23,6 @@ Nodes: StaticProps: - clinical_study_designation ExportProps: - - clinical_study_designation - - case_id - patient_id - patient_first_name - cohort_description From 11c2414f00ef39c20fea27f5460470a80c79e431 Mon Sep 17 00:00:00 2001 From: Eric Miller Date: Thu, 25 Jul 2024 14:41:37 -0400 Subject: [PATCH 23/60] add prop display values to manifest YAML --- model-desc/icdc-manifest-props.yml | 164 +++++++++++++++++++---------- 1 file changed, 107 insertions(+), 57 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 2961031..13a1b04 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -2,73 +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: - - 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" From e2ae0bf5a23d0991c4fe75680a5eccf893bb8ba5 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 30 Jul 2024 10:54:30 -0500 Subject: [PATCH 24/60] Comment out agent_administration --- model-desc/icdc-model.yml | 64 +++++++++++++++++++-------------------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 51a1e2b..c759bf8 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -283,38 +283,38 @@ Nodes: - residual_disease - therapeutic_indicator - crdc_id - agent_administration: - Desc: Properties within the Agent Administration node detail the dosing of the therapeutic agent(s) being studied, alongside the specifics of how and when such agents were administered. - Tags: - Category: clinical_trial - Assignment: extended - Class: secondary - Template: 'Yes' - Clinical_Data_Export: 'Yes' - Props: - # d/n from STUDY_MED_ADMIN/SDAD/1 - - document_number - - medication - - route_of_administration - - medication_lot_number - - medication_vial_id - - medication_actual_units_of_measure - - medication_duration - - medication_units_of_measure - - medication_actual_dose - # what is phase? - - phase - - start_time - - stop_time - - dose_level - - dose_units_of_measure - - date_of_missed_dose - - medication_missed_dose - - missed_dose_amount - - missed_dose_units_of_measure - - medication_course_number - - comment - - crdc_id + # agent_administration: + # Desc: Properties within the Agent Administration node detail the dosing of the therapeutic agent(s) being studied, alongside the specifics of how and when such agents were administered. + # Tags: + # Category: clinical_trial + # Assignment: extended + # Class: secondary + # Template: 'Yes' + # Clinical_Data_Export: 'Yes' + # Props: + # # d/n from STUDY_MED_ADMIN/SDAD/1 + # - document_number + # - medication + # - route_of_administration + # - medication_lot_number + # - medication_vial_id + # - medication_actual_units_of_measure + # - medication_duration + # - medication_units_of_measure + # - medication_actual_dose + # # what is phase? + # - phase + # - start_time + # - stop_time + # - dose_level + # - dose_units_of_measure + # - date_of_missed_dose + # - medication_missed_dose + # - missed_dose_amount + # - missed_dose_units_of_measure + # - medication_course_number + # - comment + # - crdc_id sample: Desc: The Sample node contains numerous properties which provide an in-depth characterization of the types of samples which were collected from any given patient/subject/donor and subsequently analyzed. Many of these sample annotations are required. Tags: From 863140c4e72f784ca787b0bb19ec950f58ab26cf Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Tue, 13 Aug 2024 13:47:06 -0500 Subject: [PATCH 25/60] Update key prop names --- model-desc/icdc-manifest-props.yml | 2 +- model-desc/icdc-model-props.yml | 61 ++++++++-------- model-desc/icdc-model.yml | 109 ++++++++++++++++------------- 3 files changed, 92 insertions(+), 80 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 452df44..d7776ee 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -32,7 +32,7 @@ Nodes: - cohort_id demographic: ExportProps: - - demographic_id + - demographic_record_id - breed - additional_breed_detail - patient_age_at_enrollment diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index dbb17df..370da4c 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -6,8 +6,8 @@ PropDefinitions: Tags: Template: 'No' # adverse_event props - adverse_event_id: - Desc: A globally unique identifier via which adverse event records can be differentiated from one another across studies/trials. Specifically the value of case_id concatenated with the value of adverse_event_term.
This property is used as the key to identify the correct adverse event records during data upates. + adverse_event_record_id: + Desc: A unique identifier via which adverse event records can be differentiated from one another across studies/trials. Specifically the value of case_id concatenated with the value of adverse_event_term.
This property is used as the key to identify the correct adverse event records during data upates. Src: Data Owner(s) Type: string Req: true @@ -256,7 +256,7 @@ PropDefinitions: # Type: datetime # biospecimen_source props biospecimen_repository_acronym: - Desc: The name of the biobank or tissue repository from which or to which samples for any given patient/subject/donor were acquired or submitted, expressed in the form of an acronym.
This property is used as the key v to identify the correct biospecimen repository records during data updates. + Desc: The name of the biobank or tissue repository from which or to which samples for any given patient/subject/donor were acquired or submitted, expressed in the form of an acronym.
This property is used as the key to identify the correct biospecimen repository records during data updates. Src: Internally-curated Type: string Req: 'Yes' @@ -278,9 +278,10 @@ PropDefinitions: Key: true Tags: Labeled: Canine ID + Template: 'No' # case props - case_id: - Desc: The globally unique ID by which any given patient/subject/donor can be unambiguously identified and displayed across studies/trials; specifically the value of patient_id as supplied by the data submitter, prefixed with the appropriate ICDC study code during data alignment and/or transformation.
This property is used as the key via which child records, e.g. sample records, can be associated with the appropriate case during data loading, and to identify the correct records during data updates. + case_record_id: + Desc: The unique ID by which any given patient/subject/donor can be unambiguously identified and displayed across studies/trials; specifically the value of patient_id as supplied by the data submitter, prefixed with the appropriate ICDC study code during data alignment and/or transformation.
This property is used as the key via which child records, e.g. sample records, can be associated with the appropriate case during data loading, and to identify the correct records during data updates. Src: Internally-generated Type: string Req: 'Yes' @@ -316,15 +317,15 @@ PropDefinitions: Req: 'No' Tags: Labeled: Cohorts - cohort_id: + cohort_record_id: Desc: A unique identifier via which cohorts can be differentiated from one another across studies/trials.
This property is used as the key via which cases can be associated with the appropriate cohort during data loading, and to identify the correct records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' Key: true # cycle props - cycle_id: - Desc: A globally unique identifier for each therapy cycle administered to a patient/subject; specifically the value of case_id concatenated with the value of cycle_number.
This property is used as the key via which child records, e.g. visit records, can be associated with the appropriate cycle during data loading, and to identify the correct cycle records during data upates. + cycle_record_id: + Desc: A unique identifier for each therapy cycle administered to a patient/subject; specifically the value of case_id concatenated with the value of cycle_number.
This property is used as the key via which child records, e.g. visit records, can be associated with the appropriate cycle during data loading, and to identify the correct cycle records during data upates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -644,7 +645,7 @@ PropDefinitions: Src: Data Owner(s) Type: datetime Req: 'No' - demographic_id: + demographic_record_id: Desc: A unique identifier of each demographic record, used to identify the correct demographic records during data updates.
The value of this property will generally be the same as the value of the case_id property.
This property is used as the key to identify the correct demographic records during data updates. Src: Data Owner(s) Type: string @@ -734,7 +735,7 @@ PropDefinitions: Src: Data Owner(s) Type: datetime Req: 'No' - diagnosis_id: + diagnosis_record_id: Desc: A unique identifier of each diagnosis record, used to associate child records, e.g. pathology reports, with the appropriate parent, and to identify the correct diagnosis records during data updates. The value of this property will generally be the same as the value of the case_id property. Src: Data Owner(s) Type: string @@ -907,8 +908,8 @@ PropDefinitions: Tags: Labeled: Treatment Data Available # disease_extent props - disease_extent_id: - Desc: A globally unique identifier of each evaluation of disease extent for a subject/patient/donor; specifically the value of case_id concatenated with the value of evaluation_code.
This property is used as the key to identify the correct disease extent records during data updates. + disease_extent_record_id: + Desc: A unique identifier of each evaluation of disease extent for a subject/patient/donor; specifically the value of case_id concatenated with the value of evaluation_code.
This property is used as the key to identify the correct disease extent records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -996,7 +997,7 @@ PropDefinitions: Req: 'No' Tags: Labeled: Date of Registration - enrollment_id: + enrollment_record_id: Desc: A unique identifier of each enrollment record, used to associate child records, e.g. prior surgery records, with the appropriate parent, and to identify the correct enrollment records during data updates. The value of this property will generally be the same as the value of the case_id property. Src: Data Owner(s) Type: string @@ -1231,8 +1232,8 @@ PropDefinitions: # Src: OFF_STUDY/OSSM/1 # Type: string # physical_exam props - physical_exam_id: - Desc: A globally unique identifier of each physical exam record; specifically the value of case_id concatenated with the value of date_of_examination, the date upon which the physical exam was conducted.
This property is used as the key to identify the correct physical exam records during data updates. + physical_exam_record_id: + Desc: A unique identifier of each physical exam record; specifically the value of case_id concatenated with the value of date_of_examination, the date upon which the physical exam was conducted.
This property is used as the key to identify the correct physical exam records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -1278,8 +1279,8 @@ PropDefinitions: Src: Data Owner(s) Type: TBD # principal_investigator props - pi_id: - Desc: A globally unique identifier via which principle investigator can be differentiated across studies; specifically the value of study_id concatenated with the value of pi_last_name,
This property is used as the key via which child records, e.g. cohort records, can be associated with the appropriate principle investigator, and to identify the correct principle investigator records during data updates. + person_record_id: + Desc: A unique identifier via which a principle investigator can be differentiated across studies; specifically the value of study_id concatenated with the value of pi_last_name,
This property is used as the key via which child records, e.g. cohort records, can be associated with the appropriate principle investigator, and to identify the correct principle investigator records during data updates. pi_first_name: Desc: The first or given name of each principal investigator of the study/trial. Src: Data Owner(s) @@ -1302,8 +1303,8 @@ PropDefinitions: Tags: Labeled: Principal Investigators # prior_surgery props - prior_surgery_id: - Desc: A globally unique identifier of each prior surgery record;
This property is used as the key to identify the correct prior surgery records during data updates. + prior_surgery_record_id: + Desc: A unique identifier of each prior surgery record;
This property is used as the key to identify the correct prior surgery records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -1340,8 +1341,8 @@ PropDefinitions: Type: TBD Req: 'No' # prior_therapy props - prior_therapy_id: - Desc: A globally unique identifier of each prior therapy record;
This property is used as the key to identify the correct prior therapy records during data updates. + prior_therapy_record_id: + Desc: A unique identifier of each prior therapy record;
This property is used as the key to identify the correct prior therapy records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -1515,7 +1516,7 @@ PropDefinitions: Src: Data Owner(s) Type: string Req: 'Yes' - registration_id: + registration_record_id: Desc: A globally unique identifier to describe a patient/donor/subject; specifically the value of case_id.
This property is used as the key to identify the registration records during data updates. Src: Data Owner(s) Type: string @@ -1596,7 +1597,7 @@ PropDefinitions: Tags: Labeled: Sample Chronology sample_id: - Desc: The globally unique ID by which any given sample can be unambiguously identified and displayed across studies/trials; specifically the preferred value of the sample identifier used by the data submitter, prefixed with the appropriate ICDC study code.
This property is used as the key via which child records, e.g. file records, can be associated with the appropriate sample during data loading, and to identify the correct records during data updates. + Desc: The unique ID by which any given sample can be unambiguously identified and displayed across studies/trials; specifically the preferred value of the sample identifier used by the data submitter, prefixed with the appropriate ICDC study code.
This property is used as the key via which child records, e.g. file records, can be associated with the appropriate sample during data loading, and to identify the correct records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -1920,8 +1921,8 @@ PropDefinitions: Src: Data-derived Type: datetime Req: 'No' - visit_id: - Desc: A globally unique identifier of each visit record; specifically the value of case_id concatenated with the value of visit_date, the date upon which the visit occurred.
This property is used as the key via which child records, e.g. physical examination records, can be associated with the appropriate visit, and to identify the correct visit records during data updates. + visit_record_id: + Desc: A unique identifier of each visit record; specifically the value of case_id concatenated with the value of visit_date, the date upon which the visit occurred.
This property is used as the key via which child records, e.g. physical examination records, can be associated with the appropriate visit, and to identify the correct visit records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -1934,7 +1935,7 @@ PropDefinitions: # assessment_timepoint: also included in vital_signs node, defined elsewhere # Src: PHYSICAL_EXAM/PE/1 # Type: integer - vital_signs_id: + vital_signs_record_id: Desc: A globally unique identifier of each vital signs record collected during a scheduled visit; specifically the value of case_id concatenated with the value of date_of_vital_signs, the date upon which the vital signs evaluation in question was conducted.
This property is used as the key to identify the correct vital signs records during data updates. Src: Data Owner(s) Type: string @@ -2017,8 +2018,8 @@ PropDefinitions: Src: Data Owner(s) Type: string Req: 'Yes' - lab_exam_id: - Desc: A globally unique identifier of each lab exam record; specifically the value of case_id concatenated with the value of lab_exam_date, the date upon which the lab exam occurred.
This property is used as the key to identify the correct lab exam records during data updates. + lab_exam_record_id: + Desc: A unique identifier of each lab exam record; specifically the value of case_id concatenated with the value of lab_exam_date, the date upon which the lab exam occurred.
This property is used as the key to identify the correct lab exam records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' @@ -2029,8 +2030,8 @@ PropDefinitions: Type: datetime Req: 'Yes' # assay props - assay_id: - Desc: A globally unique identifier of each assay record; specifically the value of case_id concatenated with the value of assay type.
This property is used as the key to identify the correct physical exam records during data updates. + assay_record_id: + Desc: A unique identifier of each assay record; specifically the value of case_id concatenated with the value of assay type.
This property is used as the key to identify the correct physical exam records during data updates. Src: Data Owner(s) Type: string Req: 'Yes' diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 51a1e2b..66b494f 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -86,7 +86,7 @@ Nodes: Template: 'Yes' Props: - cohort_description # cohort name generally inclusive of some detail as to agent and dose - - cohort_id # needed to differentiate between cohorts that share values for cohort description, but which actually belong to different studies + - cohort_record_id # needed to differentiate between cohorts that share values for cohort description, but which actually belong to different studies - cohort_dose # the intended or protocol dose - crdc_id case: @@ -97,7 +97,7 @@ Nodes: Class: primary Template: 'Yes' Props: - - case_id + - case_record_id - patient_id - patient_first_name - crdc_id @@ -110,7 +110,7 @@ Nodes: Template: 'Yes' Props: - registration_origin - - registration_id + - registration_record_id - crdc_id # - is_primary_id biospecimen_source: @@ -142,7 +142,7 @@ Nodes: Class: primary Template: 'Yes' Props: - - demographic_id + - demographic_record_id - breed - additional_breed_detail - patient_age_at_enrollment @@ -160,6 +160,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - cycle_record_id - cycle_number - date_of_cycle_start - date_of_cycle_end @@ -175,7 +176,7 @@ Nodes: Props: - visit_date - visit_number - - visit_id + - visit_record_id - crdc_id principal_investigator: Desc: The Principal Investigator node contains properties which identify the principal investigator(s) responsible for any given study/trial. A study/trial may have one or more principal investigators, and any given individual may be listed as a principal investigator on more than one study/trial. @@ -185,6 +186,7 @@ Nodes: Class: primary Template: 'Yes' Props: + - person_record_id - pi_first_name - pi_last_name - pi_middle_initial @@ -198,7 +200,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'No' Props: - - diagnosis_id + - diagnosis_record_id - disease_term - primary_disease_site - stage_of_disease @@ -221,7 +223,7 @@ Nodes: Class: primary Template: 'Yes' Props: - - enrollment_id + - enrollment_record_id - date_of_registration - registering_institution - initials @@ -240,6 +242,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - prior_therapy_record_id - date_of_first_dose - date_of_last_dose - agent_name @@ -276,6 +279,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - prior_surgery_record_id - date_of_surgery - procedure - anatomical_site_of_surgery @@ -283,38 +287,38 @@ Nodes: - residual_disease - therapeutic_indicator - crdc_id - agent_administration: - Desc: Properties within the Agent Administration node detail the dosing of the therapeutic agent(s) being studied, alongside the specifics of how and when such agents were administered. - Tags: - Category: clinical_trial - Assignment: extended - Class: secondary - Template: 'Yes' - Clinical_Data_Export: 'Yes' - Props: - # d/n from STUDY_MED_ADMIN/SDAD/1 - - document_number - - medication - - route_of_administration - - medication_lot_number - - medication_vial_id - - medication_actual_units_of_measure - - medication_duration - - medication_units_of_measure - - medication_actual_dose - # what is phase? - - phase - - start_time - - stop_time - - dose_level - - dose_units_of_measure - - date_of_missed_dose - - medication_missed_dose - - missed_dose_amount - - missed_dose_units_of_measure - - medication_course_number - - comment - - crdc_id + # agent_administration:proposing deprecation of this node. + # Desc: Properties within the Agent Administration node detail the dosing of the therapeutic agent(s) being studied, alongside the specifics of how and when such agents were administered. + # Tags: + # Category: clinical_trial + # Assignment: extended + # Class: secondary + # Template: 'Yes' + # Clinical_Data_Export: 'Yes' + # Props: + # # d/n from STUDY_MED_ADMIN/SDAD/1 + # - document_number + # - medication + # - route_of_administration + # - medication_lot_number + # - medication_vial_id + # - medication_actual_units_of_measure + # - medication_duration + # - medication_units_of_measure + # - medication_actual_dose + # # what is phase? + # - phase + # - start_time + # - stop_time + # - dose_level + # - dose_units_of_measure + # - date_of_missed_dose + # - medication_missed_dose + # - missed_dose_amount + # - missed_dose_units_of_measure + # - medication_course_number + # - comment + # - crdc_id sample: Desc: The Sample node contains numerous properties which provide an in-depth characterization of the types of samples which were collected from any given patient/subject/donor and subsequently analyzed. Many of these sample annotations are required. Tags: @@ -349,7 +353,8 @@ Nodes: Assignment: extended Class: secondary Template: 'No' - Props: null + Props: + - assay_record_id file: Desc: Files can be associated with ICDC study, case, diagnosis and sample records, but are not themselves stored within the application. Instead, the application stores records as to the existence and nature of such files. The File node is comprised of properties which characterize these files in terms of their size, format and content, such that they can be appropriately represented within the application’s UI, and in terms of their storage location, such that they can be retrieved for analysis. Tags: @@ -368,14 +373,15 @@ Nodes: - uuid - file_location - crdc_id - image: - Desc: The Image node does not yet have any properties associated with it and is not currently used. - Tags: - Category: data_file - Assignment: core - Class: secondary - Template: 'No' - Props: null + # proposing deprecation or removal of the image node. + # image: + # Desc: The Image node does not yet have any properties associated with it and is not currently used. + # Tags: + # Category: data_file + # Assignment: core + # Class: secondary + # Template: 'No' + # Props: null # proposing deprecation or removal the image_collection node as it contains no data across ingested studies as of 7/16/24 # image_collection: # Desc: The Image Collection node is comprised of properties which describe collections of images that are associated with any given study/trial. These properties characterize such image collections in terms of the types of images they contain, where the collections are hosted, and how they can be accessed. @@ -400,6 +406,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - physical_exam_record_id - date_of_examination - day_in_cycle - body_system @@ -432,6 +439,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - vital_signs_record_id - date_of_vital_signs - body_temperature - respiration_rate @@ -454,7 +462,8 @@ Nodes: Class: secondary Template: 'No' Clinical_Data_Export: 'Yes' - Props: null + Props: + - lab_exam_record_id adverse_event: # how to link? To case and agent? Also to visit/followup? Desc: Properties within the Adverse Event node detail unexpected medical, physical and behavioral problems occurring during therapy, in terms of what issues are observed, their severity, and what is considered to be their root cause. @@ -465,6 +474,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - adverse_event_record_id - day_in_cycle - date_of_onset - existing_adverse_event @@ -494,6 +504,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - disease_extent_record_id - lesion_number - lesion_site - lesion_description From 18396041d75cb1fdb6651a996963f96a6e7d805c Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:39:01 -0500 Subject: [PATCH 26/60] resolve merge conflict Removed pi_id to resolve merge conflict. --- model-desc/icdc-model-props.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index ab4bddf..c778f27 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1279,17 +1279,12 @@ PropDefinitions: Src: Data Owner(s) Type: TBD # principal_investigator props -<<<<<<< HEAD person_record_id: Desc: A unique identifier via which a principle investigator can be differentiated across studies; specifically the value of study_id concatenated with the value of pi_last_name,
This property is used as the key via which child records, e.g. cohort records, can be associated with the appropriate principle investigator, and to identify the correct principle investigator records during data updates. -======= - pi_id: - Desc: A globally unique identifier via which principle investigator can be differentiated across studies; specifically the value of study_id concatenated with the value of pi_last_name,
This property is used as the key via which child records, e.g. cohort records, can be associated with the appropriate principle investigator, and to identify the correct principle investigator records during data updates. Src: Data Onwer(s) Type: string Req: 'Yes' Key: true ->>>>>>> e2ae0bf5a23d0991c4fe75680a5eccf893bb8ba5 pi_first_name: Desc: The first or given name of each principal investigator of the study/trial. Src: Data Owner(s) From 43dd4a3335249a3230bfbb441b36262c6a49697f Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Wed, 14 Aug 2024 09:43:41 -0500 Subject: [PATCH 27/60] remove relationships involving agent node --- model-desc/icdc-model.yml | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 66b494f..a38aeb2 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -633,8 +633,6 @@ Relationships: of_study_arm: Mul: many_to_many Ends: - - Src: agent - Dst: study_arm - Src: case Dst: study_arm Mul: many_to_one @@ -656,14 +654,6 @@ Relationships: Dst: study Mul: many_to_one Props: null - of_agent: - Mul: many_to_one - Ends: - - Src: agent_administration - Dst: agent - - Src: adverse_event - Dst: agent - Props: null had_adverse_event: Mul: many_to_one Ends: @@ -726,18 +716,6 @@ Relationships: - Src: file Dst: diagnosis Props: null - went_off_study: - Mul: one_to_one - Ends: - - Src: case - Dst: off_study - Props: null - went_off_treatment: - Mul: one_to_one - Ends: - - Src: case - Dst: off_treatment - Props: null next: Mul: one_to_one Ends: From 5283ba6b258df9a26ccc50affc6991ede956541b Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Wed, 14 Aug 2024 17:27:25 -0500 Subject: [PATCH 28/60] Update icdc-model.yml --- model-desc/icdc-model.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index a38aeb2..818d13f 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -228,7 +228,6 @@ Nodes: - registering_institution - initials - date_of_informed_consent - - site_short_name - veterinary_medical_center #- cohort_description - patient_subgroup From 3eb03b4fd159409dab0db4b36e9d26ed1f8d1d50 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Fri, 16 Aug 2024 11:45:11 -0500 Subject: [PATCH 29/60] Add urethra as permissible value --- model-desc/icdc-model-props.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index c778f27..0a7014d 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -825,6 +825,7 @@ PropDefinitions: Enum: #- http://localhost/terms/domain/primary_disease_site - Bladder + - Urethra - Bladder, Prostate - Bladder, Urethra - Bladder, Urethra, Prostate From 76b42b09414e26d59cf777dd3a02dc3022711e89 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Mon, 19 Aug 2024 15:31:21 -0500 Subject: [PATCH 30/60] remove multiple key from extent of disease node --- model-desc/icdc-model-props.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 0a7014d..debaadd 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -940,7 +940,6 @@ PropDefinitions: Src: Data Owner(s) Type: Integer Req: 'Yes' - Key: true lesion_site: Desc: The overall anatomical location of the lesion being assessed in terms of the organ or organ system in which it is located. For example, lung, lymph node, etc. Src: Data Owner(s) From bdd66b2ba9f38ff1724cc2537cd820f90157cb9a Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 20 Aug 2024 12:38:22 -0500 Subject: [PATCH 31/60] add type string to respiration_pattern prop --- model-desc/icdc-model-props.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index debaadd..323db57 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -2000,8 +2000,8 @@ PropDefinitions: respiration_pattern: Desc: An indication as to the normality of the breathing pattern of the patient/subject/donor at the time of the vital signs evaluation. Src: Data Owner(s) - Type: - - http://localhost/terms/domain/respiration_pattern + Type: string + # - http://localhost/terms/domain/respiration_pattern respiration_rate: Desc: The rate of respiration of the patient/subject/donor at the time of the vital signs evaluation, measured in the number of breaths taken per minute. Src: Data Owner(s) From 5723bcdbeb879fad83e496e303013ed7baa20869 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 20 Aug 2024 12:42:48 -0500 Subject: [PATCH 32/60] update anatomical_site_of_surgery to type string --- model-desc/icdc-model-props.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 323db57..3c80f5c 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1316,8 +1316,8 @@ PropDefinitions: anatomical_site_of_surgery: Desc: The anatomical location at which the prior surgery in question occurred. Src: Data Owner(s) - Type: - - https://localhost/term/domain/anatomical_site + Type: string + # - https://localhost/term/domain/anatomical_site Req: 'Yes' date_of_surgery: Desc: The date upon which the prior surgery in question occurred. From 7a6c373b4ceddc41456633d437b517aded590d76 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 20 Aug 2024 12:44:14 -0500 Subject: [PATCH 33/60] update procedure prop to type string --- model-desc/icdc-model-props.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 3c80f5c..b537c87 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1327,8 +1327,8 @@ PropDefinitions: procedure: Desc: The type of procedure performed during the prior surgery in question. Src: Data Owner(s) - Type: - - https://localhost/term/domain/procedure + Type: string + # - https://localhost/term/domain/procedure Req: 'Yes' residual_disease: Desc: TBD From 38202db031199490ebcb8a350d04a7887d38bd64 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 20 Aug 2024 13:16:58 -0500 Subject: [PATCH 34/60] update modified_ecog prop to type string --- model-desc/icdc-model-props.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index b537c87..7c964a5 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1970,8 +1970,8 @@ PropDefinitions: modified_ecog: Desc: The Eastern Cooperative Oncology Group (ECOG) performance status of the patient/subject/donor at the time of the vital signs evaluation. The value of this metric indicates the overall function of the patient/subject/donor and his/her ability to tolerate therapy. Src: Data Owner(s) - Type: - - http://localhost/terms/domain/modified_ecog + Type: string + # - http://localhost/terms/domain/modified_ecog patient_weight: Desc: The weight of the patient/subject/donor at the time of the vital signs evaluation, measured in kilograms. Src: Data Owner(s) From ea7ba4f92dbfccc7fb26d4483db8095bc1a92e1a Mon Sep 17 00:00:00 2001 From: Eric Miller Date: Wed, 21 Aug 2024 13:16:15 -0400 Subject: [PATCH 35/60] remove manifest props to demo dynamic update (TO BE REVERTED) --- model-desc/icdc-manifest-props.yml | 152 ++++++++++++++--------------- 1 file changed, 76 insertions(+), 76 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 13a1b04..a647e9c 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -36,89 +36,89 @@ Nodes: ExportProps: - 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" + # - 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: - 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" + # - 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: - 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" + # - 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" From b70acdc2d065304376887d38aadc529ae3555e3a Mon Sep 17 00:00:00 2001 From: Eric Miller <51423770+erm156@users.noreply.github.com> Date: Wed, 21 Aug 2024 13:23:26 -0400 Subject: [PATCH 36/60] Revert "remove manifest props to demo dynamic update (TO BE REVERTED)" --- model-desc/icdc-manifest-props.yml | 152 ++++++++++++++--------------- 1 file changed, 76 insertions(+), 76 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index a647e9c..13a1b04 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -36,89 +36,89 @@ Nodes: ExportProps: - 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" + - 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: - 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" + - 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: - 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" + - 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" From f1bba3b68c5fe394ee09c0a7610b38914e4f6933 Mon Sep 17 00:00:00 2001 From: Eric Miller Date: Wed, 21 Aug 2024 13:42:49 -0400 Subject: [PATCH 37/60] remove properties from manifest YAML to demo dynamic update (TO BE REVERTED) --- model-desc/icdc-manifest-props.yml | 136 ++++++++++++++--------------- 1 file changed, 68 insertions(+), 68 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 13a1b04..c41f2ca 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -50,75 +50,75 @@ Nodes: 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" + # - 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: - 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" + # - 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" From 5766372bd7fc773cfff078c20423c49b742300be Mon Sep 17 00:00:00 2001 From: Eric Miller <51423770+erm156@users.noreply.github.com> Date: Wed, 21 Aug 2024 14:29:23 -0400 Subject: [PATCH 38/60] =?UTF-8?q?Revert=20"remove=20properties=20from=20ma?= =?UTF-8?q?nifest=20YAML=20to=20demo=20dynamic=20update=20(TO=20BE=20RE?= =?UTF-8?q?=E2=80=A6"?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- model-desc/icdc-manifest-props.yml | 136 ++++++++++++++--------------- 1 file changed, 68 insertions(+), 68 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index c41f2ca..13a1b04 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -50,75 +50,75 @@ Nodes: 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" + - 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: - 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" + - 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" From 715653cbddece51664fa38af9825a19306a3e028 Mon Sep 17 00:00:00 2001 From: Eric Miller Date: Mon, 26 Aug 2024 14:38:29 -0400 Subject: [PATCH 39/60] remove all non-static props for QA test (to be reverted) --- model-desc/icdc-manifest-props.yml | 208 ++++++++++++++--------------- 1 file changed, 104 insertions(+), 104 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 13a1b04..7bfe4d7 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -10,21 +10,21 @@ Nodes: display: "name" - property: drs_uri display: "drs_uri" - ExportProps: - - 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" + # ExportProps: + # - 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: - property: case_id @@ -33,92 +33,92 @@ Nodes: StaticProps: - property: clinical_study_designation display: "Study Code" - ExportProps: - - 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: - - 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: - - 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" + # ExportProps: + # - 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: + # - 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: + # - 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" From 73562f1f0bec5b0ca61bf1da6250968f7c5a5bc2 Mon Sep 17 00:00:00 2001 From: Eric Miller <51423770+erm156@users.noreply.github.com> Date: Mon, 26 Aug 2024 14:57:48 -0400 Subject: [PATCH 40/60] Revert "remove all non-static props for QA test (to be reverted)" --- model-desc/icdc-manifest-props.yml | 208 ++++++++++++++--------------- 1 file changed, 104 insertions(+), 104 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 7bfe4d7..13a1b04 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -10,21 +10,21 @@ Nodes: display: "name" - property: drs_uri display: "drs_uri" - # ExportProps: - # - 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" + ExportProps: + - 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: - property: case_id @@ -33,92 +33,92 @@ Nodes: StaticProps: - property: clinical_study_designation display: "Study Code" - # ExportProps: - # - 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: - # - 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: - # - 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" + ExportProps: + - 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: + - 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: + - 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" From 6989839e76dc097a72de8ca0c35e0e20951fc110 Mon Sep 17 00:00:00 2001 From: Eric Miller Date: Mon, 26 Aug 2024 15:02:17 -0400 Subject: [PATCH 41/60] remove all non-static file props --- model-desc/icdc-manifest-props.yml | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 13a1b04..31ae9fa 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -10,21 +10,21 @@ Nodes: display: "name" - property: drs_uri display: "drs_uri" - ExportProps: - - 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" + # ExportProps: + # - 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: - property: case_id From aa296c5af65de138bdab3364a8f1f538467431f4 Mon Sep 17 00:00:00 2001 From: Eric Miller <51423770+erm156@users.noreply.github.com> Date: Mon, 26 Aug 2024 15:16:00 -0400 Subject: [PATCH 42/60] Revert "remove all non-static file props (to be reverted)" --- model-desc/icdc-manifest-props.yml | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 31ae9fa..13a1b04 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -10,21 +10,21 @@ Nodes: display: "name" - property: drs_uri display: "drs_uri" - # ExportProps: - # - 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" + ExportProps: + - 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: - property: case_id From 093ce90042b6a931461520b247f8eb80dc0a9682 Mon Sep 17 00:00:00 2001 From: Eric Miller Date: Mon, 26 Aug 2024 15:23:40 -0400 Subject: [PATCH 43/60] add test property --- model-desc/icdc-manifest-props.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 13a1b04..d60fc75 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -86,6 +86,8 @@ Nodes: display: "Concurrent Disease" - property: concurrent_disease_type display: "Concurrent Disease Type" + - property: test_property + display: "Test Property" sample: ExportProps: - property: sample_id From cbdf8b8958c8de4eeeaf19dceb6cf46112f8798f Mon Sep 17 00:00:00 2001 From: Eric Miller <51423770+erm156@users.noreply.github.com> Date: Mon, 26 Aug 2024 15:40:11 -0400 Subject: [PATCH 44/60] Revert "add test property (to be reverted)" --- model-desc/icdc-manifest-props.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index d60fc75..13a1b04 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -86,8 +86,6 @@ Nodes: display: "Concurrent Disease" - property: concurrent_disease_type display: "Concurrent Disease Type" - - property: test_property - display: "Test Property" sample: ExportProps: - property: sample_id From 6c591fa6f2d3516f15659214f289b40b8111335a Mon Sep 17 00:00:00 2001 From: Eric Miller Date: Tue, 27 Aug 2024 17:24:30 -0400 Subject: [PATCH 45/60] add cohort node and move props --- model-desc/icdc-manifest-props.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml index 13a1b04..e728024 100644 --- a/model-desc/icdc-manifest-props.yml +++ b/model-desc/icdc-manifest-props.yml @@ -38,6 +38,8 @@ Nodes: display: "Patient ID" - property: patient_first_name display: "Case Name" + cohort: + ExportProps: - property: cohort_description display: "Cohort" - property: cohort_dose From 89cb083b14147073db7cc1bb7bf0c51682f2106b Mon Sep 17 00:00:00 2001 From: "Mark A. Jensen" Date: Tue, 12 Nov 2024 15:41:58 -0500 Subject: [PATCH 46/60] fix(validataion) - change 'Integer' to 'integer' in Types to comply with the spec --- model-desc/icdc-model-props.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index ed65620..49b645a 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -907,7 +907,7 @@ PropDefinitions: evaluation_number: Desc: The number of the evaluation durinhg which any given lesion was examined, with evaluations numbered according to their chronological order. Src: Data Owner(s) - Type: Integer + Type: integer Req: 'No' lesion_description: Desc: Additional detail as to the specific location of the lesion subject to evaluation. For example, in the case of a lymph node lesion, the specific lymph node in which the lesion is located. @@ -917,7 +917,7 @@ PropDefinitions: lesion_number: Desc: An arbitrary numerical designation for each lesion subject to evaluation, by which that lesion can be unambiguously identified. Src: Data Owner(s) - Type: Integer + Type: integer Req: 'No' lesion_site: Desc: The overall anatomical location of the lesion being assessed in terms of the organ or organ system in which it is located. For example, lung, lymph node, etc. @@ -1887,7 +1887,7 @@ PropDefinitions: visit_number: Desc: The number of the visit during which therapy was administered and/or clinical observations were made, with visits numbered according to their chronological order. Src: Data-deived - Type: Integer + Type: integer # vital_signs props # assessment_timepoint: also included in vital_signs node, defined elsewhere # Src: PHYSICAL_EXAM/PE/1 From 51b000911b26db6fedf68fcdc76d31c3011d76a2 Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Tue, 19 Nov 2024 12:01:27 -0600 Subject: [PATCH 47/60] CRDCDH-1684 --- model-desc/icdc-model-props.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 7c964a5..75e37c3 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1,7 +1,7 @@ PropDefinitions: # crdc_id crdc_id: - Desc: The crdc_id is a unique identifier that is generated by Data Hub + Desc: The crdc_id is a unique identifier that is generated by the CRDC Submission Portal. Type: string Tags: Template: 'No' From c607cd881d2a1ad49e2d94bb030a6eacdaaf8e6f Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Wed, 19 Feb 2025 13:39:23 -0500 Subject: [PATCH 48/60] Fix #168 Update model per STS01 and OSA04 requirements Expanded controlled vocabularies for the following properties: primary_disease_site sample_site physical_sample_type summarized_sample_type specific_sample_pathology file_type --- model-desc/icdc-model-props.yml | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index ed65620..09a7e0a 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -810,6 +810,7 @@ PropDefinitions: Src: Data Owner(s) Enum: #- http://localhost/terms/domain/primary_disease_site + - Abdomen - Bladder - Bladder, Prostate - Bladder, Urethra @@ -822,18 +823,35 @@ PropDefinitions: - Brain - Carpus - Chest Wall + - Cranial Sternum - Distal Urethra + - Elbow Joint + - Femur + - Flank + - Hip + - Hock + - Humerus + - Inguinal Region - Kidney + - Knee Region + - Lip - Lung - Lymph Node - Mammary Gland + - Mandible + - Maxilla - Mouth + - Neck - Not Applicable - Pleural Cavity + - Rib Region - Shoulder - Skin - Spleen - Subcutis + - Tarsus + - Thigh + - Thorax - Thyroid Gland - Unknown - Urethra, Prostate @@ -1035,6 +1053,9 @@ PropDefinitions: - Variant Report # for reports detailing validated variants - Data Analysis Whitepaper # for any document detailing a data analysis pipeline and/or methodology - Affymetrix GeneChip Analysis File + - scATAC Sequence File # required for the OSA04 study + - scH5 Matrix File # required for the OSA04 study + - scRNA Sequence File # required for the OSA04 study Req: 'Yes' Tags: Labeled: File Type @@ -1581,6 +1602,7 @@ PropDefinitions: Src: Data Owner(s) Enum: #string # temporarily, to facilitate data loading with validation on, until STS is in place #- http://localhost/terms/domain/anatomical_location + - Abdomen - Bladder - Bladder Apex - Bladder Apex-Mid @@ -1595,13 +1617,21 @@ PropDefinitions: - Brain - Carpus - Cerebellar + - Cranial Sternum - Cutis - Distal Urethra + - Elbow Joint - Femur + - Flank - Genitourinary Tract - Hemispheric + - Hip + - Hock - Humerus + - Inguinal Region - Kidney + - Knee Region + - Lip - Liver - Liver, Spleen, Heart - Lung @@ -1611,22 +1641,30 @@ PropDefinitions: - Lymph Node - Lymph Node, Popliteal - Mammary Gland + - Mandible - Mandible, Mucosa + - Maxilla - Midline - Mouth - Mouth, Lingual - Mouth, Mandible, Mucosa - Mouth, Maxilla, Mucosa - Muscle + - Neck - Pancreas - Phalange - Pleural Effusion - Radius + - Rib Region - Scapula + - Skeletal Muscle - Skin - Skin and Muscle - Spleen - Subcutaneous Tissue + - Tarsus + - Thigh + - Thorax - Thyroid Gland - Tibia - Ulna @@ -1647,6 +1685,7 @@ PropDefinitions: - Tissue - Blood - Cell Line + - Fractionated Blood (PBMNC) - Organoid - Urine Sediment - Whole Blood @@ -1666,6 +1705,7 @@ PropDefinitions: - Complex Carcinoma - Endometrium (organoid) - Fibroblastic Osteosarcoma + - Fibrosarcoma - Giant Cell Osteosarcoma - Hemangiosarcoma - Histiocytic Sarcoma @@ -1682,6 +1722,7 @@ PropDefinitions: - Osteosarcoma - Osteosarcoma; Combined Type - Pancreas (organoid) + - Peripheral Nerve Sheath Tumor - Primitive T-Cell Leukemia - Pulmonary Adenocarcinoma - Pulmonary Carcinoma @@ -1696,6 +1737,7 @@ PropDefinitions: - Telangiectatic Osteosarcoma - Urinary Bladder (organoid) - Undefined + - Undifferentiated Pleiomorphic Sarcoma - Urothelial Carcinoma - Urothelial Carcinoma (organoid) # these represent the de facto acceptable values, i.e. the values that our data submitters have used thus far @@ -1710,6 +1752,7 @@ PropDefinitions: - Normal Cell Line - Normal Tissue - Organoid (ASC-derived) + - Peripheral Blood Mononuclear Cells - Primary Malignant Tumor Tissue - Urine Sediment - Tumor Cell Line From 7b5adaa53f2372c6b7090fc575306444c020b82e Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Wed, 19 Feb 2025 15:08:18 -0500 Subject: [PATCH 49/60] Fix #168 Update Model per STS01 and OSA04 requirements - fix "Integer" Changed datatype of "Integer" to "integer" on the following three properties: disease_extent: evalutaion_number disease_extent: lesion_number visit: visit_number This brings in the same changes that were PR'ed by Mark Jensen as of 11-12-2024, but which never got merged in. --- model-desc/icdc-model-props.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 09a7e0a..00c553a 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -925,7 +925,7 @@ PropDefinitions: evaluation_number: Desc: The number of the evaluation durinhg which any given lesion was examined, with evaluations numbered according to their chronological order. Src: Data Owner(s) - Type: Integer + Type: integer Req: 'No' lesion_description: Desc: Additional detail as to the specific location of the lesion subject to evaluation. For example, in the case of a lymph node lesion, the specific lymph node in which the lesion is located. @@ -935,7 +935,7 @@ PropDefinitions: lesion_number: Desc: An arbitrary numerical designation for each lesion subject to evaluation, by which that lesion can be unambiguously identified. Src: Data Owner(s) - Type: Integer + Type: integer Req: 'No' lesion_site: Desc: The overall anatomical location of the lesion being assessed in terms of the organ or organ system in which it is located. For example, lung, lymph node, etc. @@ -1930,7 +1930,7 @@ PropDefinitions: visit_number: Desc: The number of the visit during which therapy was administered and/or clinical observations were made, with visits numbered according to their chronological order. Src: Data-deived - Type: Integer + Type: integer # vital_signs props # assessment_timepoint: also included in vital_signs node, defined elsewhere # Src: PHYSICAL_EXAM/PE/1 From ad9b13943224e72d1de5de22850e88b4c563ee5f Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Mon, 24 Feb 2025 17:11:19 -0500 Subject: [PATCH 50/60] Fix #168 Update Model per STS01 and OSA04 requirements - polish Updated the controlled vocabulary for the file_type property putting acceptable terms into alphabetical order; existing order was entirely arbitrary and was being propagated as is into the Data Model Navigator, where it really should be presented in a logical order. --- model-desc/icdc-model-props.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 00c553a..6866b26 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1038,24 +1038,24 @@ PropDefinitions: Desc: An indication as to the nature of the file in terms of its content, i.e. what type of information the file contains, as opposed to the file's format. Src: Data Owner(s) Enum: - - Study Protocol - - Supplemental Data File - - Pathology Report - - Image File - - RNA Sequence File - - Whole Genome Sequence File - - Whole Exome Sequence File + - Affymetrix GeneChip Analysis File + - Array CGH Analysis File # required for the MGT01 study + - Data Analysis Whitepaper # for any document detailing a data analysis pipeline and/or methodology - DNA Methylation Analysis File + - Image File - Index File - - Array CGH Analysis File # required for the MGT01 study - - Variant Call File # for raw .vcf files - Mutation Annotation File # for annotated .maf files - - Variant Report # for reports detailing validated variants - - Data Analysis Whitepaper # for any document detailing a data analysis pipeline and/or methodology - - Affymetrix GeneChip Analysis File + - Pathology Report + - RNA Sequence File - scATAC Sequence File # required for the OSA04 study - scH5 Matrix File # required for the OSA04 study - scRNA Sequence File # required for the OSA04 study + - Study Protocol + - Supplemental Data File + - Variant Call File # for raw .vcf files + - Variant Report # for reports detailing validated variants + - Whole Exome Sequence File + - Whole Genome Sequence File Req: 'Yes' Tags: Labeled: File Type From 20dd783924159a9c83b8ca92020ede223098f025 Mon Sep 17 00:00:00 2001 From: Philip Musk Date: Tue, 18 Mar 2025 21:28:13 -0400 Subject: [PATCH 51/60] Fix #168 - additional minor updates Unrelated to either the STS01 or the OSA04 studies: Changed cardinality of the relationship between diagnosis and case from many_to_one to one_to_one Updated the dose_limiting_toxicity and unexpected_adverse_event properties with the adverse_event node from Required to Preferred, in order to accommodate the blanks values we're seeing in the data generated by the PRECINCT01 and PRECINCT02 studies --- model-desc/icdc-model-props.yml | 4 ++-- model-desc/icdc-model.yml | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 6866b26..79c9610 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -149,7 +149,7 @@ PropDefinitions: - 'Yes' - 'No' - Not Applicable # accommodates situations where an adverse event is not attributed to any therapeutic agent and cannot therefore be limiting in terms of dosage - Req: 'Yes' + Req: Preferred # preferred instead of required accommodates siutations where the source data simply doesn't have any values, but if values are available, they must be compliant with the controlled vocabulary defined above unexpected_adverse_event: Desc: An indication as to whether any given adverse event observed during the clinical trial is completely unanticipated and therefore considered novel. Src: Data Owner(s) @@ -157,7 +157,7 @@ PropDefinitions: - 'Yes' - 'No' - Undefined # accommodates situations where there is any ambiguity in terms of an adverse event being expected or not - Req: 'Yes' + Req: Preferred # preferred instead of required accommodates siutations where the source data simply doesn't have any values, but if values are available, they must be compliant with the controlled vocabulary defined above # agent props document_number: Desc: S/N of the executed CRF diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 52a5c28..79e548d 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -594,6 +594,7 @@ Relationships: Mul: one_to_one - Src: diagnosis Dst: case + Mul: one_to_one # changed form many_to_one to one_to_one given that thus far, we've only ever needed to define a single primary diagnosis, and as elegant as supporting multiple diagnoses might appear, it is becoming more trouble than it's worth - Src: cycle Dst: case - Src: follow_up From 18b4b4a80e56cd0b2779e1375dac91e082a57a7b Mon Sep 17 00:00:00 2001 From: PhilipMusk <46568331+PhilipMusk@users.noreply.github.com> Date: Wed, 19 Mar 2025 12:40:28 -0400 Subject: [PATCH 52/60] Update model-test-and-deploy.yml - update yml version Changed: uses: CBIIT/bento-workflows/.github/workflows/model-test-and-deploy.yml@v.. from uses: CBIIT/bento-workflows/.github/workflows/model-test-and-deploy.yml@v2.1.7 to uses: CBIIT/bento-workflows/.github/workflows/model-test-and-deploy.yml@v2.3.12 --- .github/workflows/model-test-and-deploy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/model-test-and-deploy.yml b/.github/workflows/model-test-and-deploy.yml index 0edbed6..30ae57d 100644 --- a/.github/workflows/model-test-and-deploy.yml +++ b/.github/workflows/model-test-and-deploy.yml @@ -13,7 +13,7 @@ jobs: permissions: packages: read contents: write - uses: CBIIT/bento-workflows/.github/workflows/model-test-and-deploy.yml@v2.1.7 + uses: CBIIT/bento-workflows/.github/workflows/model-test-and-deploy.yml@v2.3.12 with: model_files: | icdc-model.yml icdc-model-props.yml From 33386b503637dbf6d38a2e86f4b88f4ed3eb1bde Mon Sep 17 00:00:00 2001 From: "Mark A. Jensen" Date: Fri, 21 Mar 2025 18:15:27 -0400 Subject: [PATCH 53/60] bump cicd --- model-desc/icdc-model-props.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 79c9610..3f160d9 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1,4 +1,5 @@ PropDefinitions: + # crdc_id crdc_id: Desc: The crdc_id is a unique identifier that is generated by Data Hub From 54b9d90edc35740aeff6f8adc40548f42ef75360 Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Tue, 15 Apr 2025 17:46:10 -0400 Subject: [PATCH 54/60] Add human relevance node and props --- model-desc/icdc-model-props.yml | 38 +++++++++++++++++++++++++++++++++ model-desc/icdc-model.yml | 17 +++++++++++++++ 2 files changed, 55 insertions(+) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 3f160d9..dc37bff 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -912,6 +912,44 @@ PropDefinitions: Req: Preferred Tags: Labeled: Treatment Data Available + # human_relevance props + human_relevance_record_id: + Desc: A unique identifier via which human relevance records can be differentiated from one another across studies/trials. Specifically, this value should be equivalent to study_code.
This property is used as the key to identify the correct human relevance records during data updates. + Src: Internally-curated + Type: string + Req: 'Yes' + Key: true + human_relevance_statement: + Desc: A brief (2 sentences and high-level statement of a study's relevance to human cancer research using words that are understandable to the lay public. + Src: Data Owner(s) + Type: string + Req: 'Yes' + applicable_human_cancer: + Desc: The applicable human cancer relevant to the canine study. + Src: Data Owner(s) + Type: + value_type: list + item_type: string + Req: 'No' + experimental_therapy: + Desc: The experimental therapy or therapies relevant to the canine study if applicable. + Type: + value_type: list + item_type: string + Req: 'No' + experimental_treatment: + Desc: The experimental treatment or treatments relevant to the canine study if applicable. + Type: + value_type: list + item_type: string + Req: 'No' + + relevant_human_genes: + Desc: The human genes relevant to the canine study if applicable. + Type: + value_type: list + item_type: string + Req: 'No' # disease_extent props date_of_evaluation: Desc: The date upon which the extent of disease evaluation was conducted. diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 79e548d..f026003 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -38,6 +38,20 @@ Nodes: - accession_id - study_disposition - crdc_id + human_relevance: + Desc: The Human Relevance node contains properties required to demonstrate how each study/trial offers unique opportunities for the cancer research community to gain significant insights into understanding human cancer biology (including initiation, progression, metastases), developing new treatments, mitigating toxicities, and improving outcomes for both canines and humans. + Tags: + Category: study + Assignment: core + Class: primary + Template: 'Yes' + Props: + - human_relevance_record_id + - human_relevance_statement + - applicable_human_cancer + - experimental_therapy + - experimental_treatment + - relevant_human_genes study_site: Desc: The Study Site node contains properties which identify the various sites at which any given study/trial was conducted, either in terms of where clinical trial patients were assessed and treated, or in terms of the geographical sites at which biospecimens were acquired from patients/subjects/donors for subsequent analysis. Tags: @@ -627,6 +641,9 @@ Relationships: of_study: Mul: many_to_many Ends: + - Src: human_relevance + Dst: study + Mul: one_to_one - Src: study_site Dst: study - Src: principal_investigator From f9145de87494c9f5a45678792d7c40aa88e5aeeb Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Wed, 16 Apr 2025 16:33:12 -0400 Subject: [PATCH 55/60] Updates per reviewer comments --- model-desc/icdc-model-props.yml | 26 +++++++++++++++----------- model-desc/icdc-model.yml | 7 ++++--- 2 files changed, 19 insertions(+), 14 deletions(-) diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index dc37bff..28a20cc 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -914,42 +914,46 @@ PropDefinitions: Labeled: Treatment Data Available # human_relevance props human_relevance_record_id: - Desc: A unique identifier via which human relevance records can be differentiated from one another across studies/trials. Specifically, this value should be equivalent to study_code.
This property is used as the key to identify the correct human relevance records during data updates. + Desc: A unique identifier via which human relevance records can be differentiated from one another across studies/trials. Specifically, this value should be the same as the study's Study Code, i.e. the value of the clinical_study_designation property.
This property is used as the key to identify the correct human relevance records during data updates. Src: Internally-curated Type: string Req: 'Yes' Key: true human_relevance_statement: - Desc: A brief (2 sentences and high-level statement of a study's relevance to human cancer research using words that are understandable to the lay public. + Desc: A brief (2-3 sentence) and high-level statement of a study's relevance to human cancer research, using words that are understandable to the lay public. Src: Data Owner(s) Type: string Req: 'Yes' - applicable_human_cancer: - Desc: The applicable human cancer relevant to the canine study. + relevant_human_cancer: + Desc: The human cancer or cancers to which the canine study directly relates. Src: Data Owner(s) Type: value_type: list item_type: string Req: 'No' - experimental_therapy: - Desc: The experimental therapy or therapies relevant to the canine study if applicable. + relevant_experimental_therapeutic_intervention: + Desc: Where applicable, the experimental therapeutic intervention or interventions being investigated in canine subjects, but which are nonetheless relevant to human therapeutic interventions. Type: value_type: list item_type: string Req: 'No' - experimental_treatment: - Desc: The experimental treatment or treatments relevant to the canine study if applicable. + relevant_human_genes: + Desc: Where applicable, the human genes corresponding to the canine genes being examined as potential disease drivers and/or biomarkers and/or novel therapeutic targets. Type: value_type: list item_type: string Req: 'No' - - relevant_human_genes: - Desc: The human genes relevant to the canine study if applicable. + relevant_human_pathways: + Desc: Where applicable, the human pathway or pathways corresponding to the canine pathways being examined and/or elucidated as potential disease drivers and/or novel therapeutic targets. Type: value_type: list item_type: string Req: 'No' + nci_link_to_relevant_human_cancer: + Desc: A link to general information about the relevant cancer type from the NCI. For example, https://www.cancer.gov/types/bladder + Src: Internally-curated + Type: string + Req: 'No' # disease_extent props date_of_evaluation: Desc: The date upon which the extent of disease evaluation was conducted. diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index f026003..9453d6d 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -39,7 +39,7 @@ Nodes: - study_disposition - crdc_id human_relevance: - Desc: The Human Relevance node contains properties required to demonstrate how each study/trial offers unique opportunities for the cancer research community to gain significant insights into understanding human cancer biology (including initiation, progression, metastases), developing new treatments, mitigating toxicities, and improving outcomes for both canines and humans. + Desc: The Human Relevance node contains properties required to demonstrate how each study/trial offers unique opportunities for the cancer research community to gain significant insights into understanding human cancer biology (including initiation, progression and metastases), developing new treatments, mitigating toxicities, and improving outcomes for both canines and humans. Tags: Category: study Assignment: core @@ -49,9 +49,10 @@ Nodes: - human_relevance_record_id - human_relevance_statement - applicable_human_cancer - - experimental_therapy - - experimental_treatment + - experimental_therapeutic_intervention - relevant_human_genes + - relevant_human_pathways + - nci_link_to_relevant_human_cancer study_site: Desc: The Study Site node contains properties which identify the various sites at which any given study/trial was conducted, either in terms of where clinical trial patients were assessed and treated, or in terms of the geographical sites at which biospecimens were acquired from patients/subjects/donors for subsequent analysis. Tags: From cb941051d499a65baf8689e97bc13f629106f927 Mon Sep 17 00:00:00 2001 From: kuffelgr Date: Thu, 17 Apr 2025 12:09:45 -0400 Subject: [PATCH 56/60] Fix spelling error --- model-desc/icdc-model.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 9453d6d..19801bf 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -39,7 +39,7 @@ Nodes: - study_disposition - crdc_id human_relevance: - Desc: The Human Relevance node contains properties required to demonstrate how each study/trial offers unique opportunities for the cancer research community to gain significant insights into understanding human cancer biology (including initiation, progression and metastases), developing new treatments, mitigating toxicities, and improving outcomes for both canines and humans. + Desc: The Human Relevance node contains properties required to demonstrate how each study/trial offers unique opportunities for the cancer research community to gain significant insights into understanding human cancer biology (including initiation, progression and metastasis), developing new treatments, mitigating toxicities, and improving outcomes for both canines and humans. Tags: Category: study Assignment: core From af0a02b1479acf5d46a9d477307413fe957d5896 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 5 Aug 2025 16:46:29 -0500 Subject: [PATCH 57/60] remove follow_up relationship --- model-desc/icdc-model.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index 1458579..b63f323 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -627,8 +627,6 @@ Relationships: Mul: one_to_one # changed form many_to_one to one_to_one given that thus far, we've only ever needed to define a single primary diagnosis, and as elegant as supporting multiple diagnoses might appear, it is becoming more trouble than it's worth - Src: cycle Dst: case - - Src: follow_up - Dst: case - Src: sample Dst: case # to accommodate a Sample being directly associated with a Case, rather than being only indirectly associated with a Case through a Visit, etc. From d8e4dc3c6ea8b2cb63b5b1f5ac50532de16606e1 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 5 Aug 2025 16:49:10 -0500 Subject: [PATCH 58/60] restore image_collection --- model-desc/icdc-model.yml | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index b63f323..ff67ee2 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -396,21 +396,20 @@ Nodes: # Class: secondary # Template: 'No' # Props: null - # proposing deprecation or removal the image_collection node as it contains no data across ingested studies as of 7/16/24 - # image_collection: - # Desc: The Image Collection node is comprised of properties which describe collections of images that are associated with any given study/trial. These properties characterize such image collections in terms of the types of images they contain, where the collections are hosted, and how they can be accessed. - # Tags: - # Category: study - # Assignment: core - # Class: secondary - # Template: 'Yes' - # Props: - # - image_collection_name - # - image_type_included - # - image_collection_url - # - repository_name - # - collection_access - # - crdc_id + image_collection: + Desc: The Image Collection node is comprised of properties which describe collections of images that are associated with any given study/trial. These properties characterize such image collections in terms of the types of images they contain, where the collections are hosted, and how they can be accessed. + Tags: + Category: study + Assignment: core + Class: secondary + Template: 'Yes' + Props: + - image_collection_name + - image_type_included + - image_collection_url + - repository_name + - collection_access + - crdc_id physical_exam: Desc: Properties within the Physical Exam node detail observations around the status of multiple body systems as of a patient enrolled in a clinical trial, as of that patient being examined by a veterinarian during a scheduled visit to the appropriate study site. Tags: From f3d26ea1382ab4cca3cdb2c6912edcde4f100518 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 5 Aug 2025 16:50:59 -0500 Subject: [PATCH 59/60] remove agent_administration relationship --- model-desc/icdc-model.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index ff67ee2..c6ba69f 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -694,8 +694,8 @@ Relationships: on_visit: Mul: many_to_one Ends: - - Src: agent_administration - Dst: visit + # - Src: agent_administration + # Dst: visit - Src: sample Dst: visit - Src: physical_exam From 7808001fed358199d07e0f9a8f2800977e109c55 Mon Sep 17 00:00:00 2001 From: Gina Kuffel <86427262+kuffelgr@users.noreply.github.com> Date: Tue, 5 Aug 2025 16:53:14 -0500 Subject: [PATCH 60/60] remove image relationship --- model-desc/icdc-model.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model-desc/icdc-model.yml b/model-desc/icdc-model.yml index c6ba69f..f1ed7a4 100644 --- a/model-desc/icdc-model.yml +++ b/model-desc/icdc-model.yml @@ -722,8 +722,8 @@ Relationships: Ends: - Src: file Dst: assay - - Src: image - Dst: assay + # - Src: image + # Dst: assay Props: null from_diagnosis: Mul: many_to_one