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 diff --git a/model-desc/icdc-manifest-props.yml b/model-desc/icdc-manifest-props.yml new file mode 100644 index 0000000..21aac36 --- /dev/null +++ b/model-desc/icdc-manifest-props.yml @@ -0,0 +1,106 @@ +# 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 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: + - property: file_name + 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" + case: + StaticProps: + - property: case_id + display: "Case ID" + study: + StaticProps: + - property: clinical_study_designation + display: "Study Code" + ExportProps: + - property: patient_id + display: "Patient ID" + - property: patient_first_name + display: "Case Name" + cohort: + ExportProps: + - property: cohort_description + display: "Cohort" + - property: cohort_dose + display: "Cohort Dose" + - property: cohort_id + display: "Cohort ID" + demographic: + ExportProps: + - demographic_record_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: + 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" diff --git a/model-desc/icdc-model-props.yml b/model-desc/icdc-model-props.yml index 691c6f6..fe77499 100644 --- a/model-desc/icdc-model-props.yml +++ b/model-desc/icdc-model-props.yml @@ -1,5 +1,18 @@ PropDefinitions: + + # crdc_id + crdc_id: + Desc: The crdc_id is a unique identifier that is generated by the CRDC Submission Portal. + Type: string + Tags: + Template: 'No' # adverse_event props + 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 + 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) @@ -143,7 +156,7 @@ 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) @@ -152,102 +165,103 @@ 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 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: @@ -265,9 +279,10 @@ 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' @@ -303,13 +318,19 @@ 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: Internally-curated + Src: Data Owner(s) Type: string Req: 'Yes' Key: true # cycle props + 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' + 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) @@ -625,8 +646,8 @@ PropDefinitions: Src: Data Owner(s) 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. + 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 Req: 'Yes' @@ -673,19 +694,16 @@ 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. 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 - 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 @@ -718,7 +736,7 @@ 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 @@ -731,6 +749,7 @@ PropDefinitions: #- http://localhost/terms/domain/disease_term - B Cell Lymphoma - Bladder Cancer + - Diffuse Large B Cell Lymphoma - Fibrolipoma - Glioma - Healthy Control @@ -767,10 +786,21 @@ 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) 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 - Req: 'No' + Enum: + - "1" + - "2" + - "3" + - "4" + - High + - Medium + - Low + - Unknown + - Not Applicable + - Not Determined + Req: Preferred Tags: Labeled: Histological Grade histology_cytopathology: @@ -795,7 +825,9 @@ PropDefinitions: Src: Data Owner(s) Enum: #- http://localhost/terms/domain/primary_disease_site + - Abdomen - Bladder + - Urethra - Bladder, Prostate - Bladder, Urethra - Bladder, Urethra, Prostate @@ -807,18 +839,35 @@ 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 @@ -829,7 +878,7 @@ 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. 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 @@ -862,12 +911,9 @@ 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 @@ -881,7 +927,55 @@ 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 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 (2-3 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' + 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' + 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' + 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_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 + 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' + Key: true date_of_evaluation: Desc: The date upon which the extent of disease evaluation was conducted. Src: Data Owner(s) @@ -895,7 +989,7 @@ 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. @@ -905,7 +999,7 @@ 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. @@ -921,7 +1015,7 @@ 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' @@ -964,7 +1058,7 @@ 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 @@ -998,7 +1092,7 @@ 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' @@ -1008,29 +1102,32 @@ 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 + - 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 - - Data Analysis Whitepaper # for any document detailing a data analysis pipeline and/or methodology - - Affymetrix GeneChip Analysis File + - Whole Exome Sequence File + - Whole Genome Sequence File Req: 'Yes' 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 +1138,14 @@ 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 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: 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' @@ -1071,134 +1168,144 @@ PropDefinitions: - validated - submitted - released - # let's talk about this one /maj - Req: 'Yes' + Req: 'No' + 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' 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. Src: Loader-derived Type: string - Req: 'Yes' - # 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 + Req: 'No' + Tags: + Template: 'No' + # # 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_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' + Key: true 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) @@ -1236,6 +1343,12 @@ PropDefinitions: Src: Data Owner(s) Type: TBD # principal_investigator props + 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. + 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) @@ -1258,11 +1371,17 @@ PropDefinitions: Tags: Labeled: Principal Investigators # prior_surgery props + 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' + Key: true 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. @@ -1272,8 +1391,8 @@ 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 @@ -1290,6 +1409,12 @@ PropDefinitions: Type: TBD Req: 'No' # prior_therapy props + 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' + Key: true agent_name: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: @@ -1379,7 +1504,7 @@ 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' @@ -1413,11 +1538,10 @@ 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) @@ -1440,14 +1564,15 @@ 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.
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: - 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 @@ -1459,11 +1584,12 @@ PropDefinitions: Src: Data Owner(s) Type: string Req: 'Yes' - registration_id: - Desc: Any ID used by a data submitter to identify a patient/subject/donor, either locally or globally. + 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 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: @@ -1480,7 +1606,7 @@ 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. 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 @@ -1506,7 +1632,7 @@ 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. GUIDANCE ADDED HERE
For cell line samples, the value of this property should be "Not Applicable". Src: Data Owner(s) Enum: - 'Yes' @@ -1517,14 +1643,14 @@ 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. 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: 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. 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 @@ -1539,7 +1665,7 @@ 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 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' @@ -1547,13 +1673,13 @@ 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. 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 - 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 @@ -1565,6 +1691,7 @@ 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 @@ -1579,13 +1706,21 @@ 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 @@ -1595,21 +1730,33 @@ 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 - Unknown - Urethra - Urethra Mid-distal @@ -1626,7 +1773,8 @@ PropDefinitions: Enum: - Tissue - Blood - - Cell Line # required for the CCL01 and OSA01 studies + - Cell Line + - Fractionated Blood (PBMNC) - Organoid - Urine Sediment - Whole Blood @@ -1646,6 +1794,7 @@ PropDefinitions: - Complex Carcinoma - Endometrium (organoid) - Fibroblastic Osteosarcoma + - Fibrosarcoma - Giant Cell Osteosarcoma - Hemangiosarcoma - Histiocytic Sarcoma @@ -1662,19 +1811,22 @@ PropDefinitions: - Osteosarcoma - Osteosarcoma; Combined Type - Pancreas (organoid) + - Peripheral Nerve Sheath Tumor - Primitive T-Cell Leukemia - 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 - T Cell Lymphoma + - 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 @@ -1689,9 +1841,7 @@ PropDefinitions: - Normal Cell Line - Normal Tissue - Organoid (ASC-derived) - #- Patient-Derived Organoid - #- Patient-Derived Organoid (urine-derived) - #- PDO + - Peripheral Blood Mononuclear Cells - Primary Malignant Tumor Tissue - Urine Sediment - Tumor Cell Line @@ -1704,7 +1854,7 @@ 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. 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" @@ -1716,11 +1866,12 @@ PropDefinitions: - Low - Unknown - Not Applicable - Req: Preferred + - Not Determined + 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. 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 @@ -1775,22 +1926,21 @@ 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 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 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 @@ -1813,7 +1963,7 @@ 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 @@ -1843,10 +1993,11 @@ 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: @@ -1860,20 +2011,26 @@ 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. - Src: Data-derived + 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' Key: true 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 # Type: integer + 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 + 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) @@ -1882,12 +2039,11 @@ 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. @@ -1900,8 +2056,8 @@ 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) @@ -1930,8 +2086,8 @@ 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) @@ -1946,3 +2102,32 @@ 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_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' + 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_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' + 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 5c04d78..f1ed7a4 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 +37,22 @@ Nodes: - dates_of_conduct - 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 and metastasis), 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_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: @@ -46,6 +64,7 @@ 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: @@ -54,24 +73,25 @@ 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. - 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 + - ctep_treatment_assignment_code + - 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: @@ -80,10 +100,10 @@ Nodes: Class: secondary Template: 'Yes' Props: - - cohort_description - # the intended or protocol dose - - cohort_dose - - cohort_id # needed to differentiate between cohorts that share values for cohort description, but which actually belong to different studies + - cohort_description # cohort name generally inclusive of some detail as to agent and dose + - 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: 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: @@ -92,9 +112,10 @@ Nodes: Class: primary Template: 'Yes' Props: - - case_id + - case_record_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: @@ -104,8 +125,9 @@ Nodes: Template: 'Yes' Props: - registration_origin - - registration_id - #- is_primary_id + - registration_record_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: @@ -116,6 +138,7 @@ 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: @@ -125,6 +148,7 @@ 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: @@ -133,7 +157,7 @@ Nodes: Class: primary Template: 'Yes' Props: - - demographic_id + - demographic_record_id - breed - additional_breed_detail - patient_age_at_enrollment @@ -141,6 +165,7 @@ 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: @@ -150,9 +175,11 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - cycle_record_id - 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: @@ -164,7 +191,8 @@ 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. Tags: @@ -173,9 +201,11 @@ Nodes: Class: primary Template: 'Yes' Props: + - person_record_id - 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: @@ -185,7 +215,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'No' Props: - - diagnosis_id + - diagnosis_record_id - disease_term - primary_disease_site - stage_of_disease @@ -199,6 +229,7 @@ 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: @@ -207,15 +238,15 @@ Nodes: Class: primary Template: 'Yes' Props: - - enrollment_id + - enrollment_record_id - date_of_registration - registering_institution - initials - date_of_informed_consent - - site_short_name - 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: @@ -225,6 +256,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - prior_therapy_record_id - date_of_first_dose - date_of_last_dose - agent_name @@ -251,6 +283,7 @@ 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: @@ -260,43 +293,46 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - prior_surgery_record_id - date_of_surgery - procedure - anatomical_site_of_surgery - surgical_finding - residual_disease - therapeutic_indicator - 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: @@ -323,6 +359,7 @@ 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: @@ -330,7 +367,8 @@ 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: @@ -348,27 +386,30 @@ Nodes: - file_status - uuid - file_location - 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 + - crdc_id + # 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 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 + 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: @@ -378,6 +419,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - physical_exam_record_id - date_of_examination - day_in_cycle - body_system @@ -385,6 +427,7 @@ 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: @@ -399,6 +442,7 @@ 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: @@ -408,19 +452,21 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - vital_signs_record_id - 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 + - crdc_id lab_exam: Desc: The Lab Exam node does not yet have any properties associated with it and is not currently used. Tags: @@ -429,7 +475,8 @@ 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. @@ -440,6 +487,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - adverse_event_record_id - day_in_cycle - date_of_onset - existing_adverse_event @@ -459,6 +507,7 @@ 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: @@ -468,6 +517,7 @@ Nodes: Template: 'Yes' Clinical_Data_Export: 'Yes' Props: + - disease_extent_record_id - lesion_number - lesion_site - lesion_description @@ -480,62 +530,69 @@ Nodes: - longest_measurement - evaluation_number - evaluation_code - 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 - 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 - 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 @@ -566,10 +623,9 @@ 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 - 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. @@ -589,8 +645,6 @@ Relationships: of_study_arm: Mul: many_to_many Ends: - - Src: agent - Dst: study_arm - Src: case Dst: study_arm Mul: many_to_one @@ -598,6 +652,9 @@ 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 @@ -612,14 +669,6 @@ 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: @@ -645,8 +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 @@ -673,8 +722,8 @@ Relationships: Ends: - Src: file Dst: assay - - Src: image - Dst: assay + # - Src: image + # Dst: assay Props: null from_diagnosis: Mul: many_to_one @@ -682,18 +731,6 @@ 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: