From 807e7bc3614ca5c05086fc0d5bec00bb57a30e31 Mon Sep 17 00:00:00 2001 From: github-actions Date: Fri, 22 Nov 2024 18:35:07 +0000 Subject: [PATCH] deploy artifacts to github page --- docs/README.md | 1352 +++++++++++++-------------- docs/model-desc/cds-model-props.yml | 5 +- docs/model-desc/cds-model.svg | 1352 +++++++++++++-------------- docs/model-desc/cds-model.txt | 19 +- docs/model-desc/cds-model.yml | 2 +- 5 files changed, 1366 insertions(+), 1364 deletions(-) diff --git a/docs/README.md b/docs/README.md index 2633d66..a61cddb 100644 --- a/docs/README.md +++ b/docs/README.md @@ -26,672 +26,710 @@ Zoom to Node: - - -treatment - -treatment - - - -crdc_id - -days_to_treatment - -response - -therapeutic_agents - -treatment_id - -treatment_type - - - - + -treatment->participant - - -of_participant +file->study + + +of_study - - -NonDICOMpathologyImages - -NonDICOMpathologyImages - - - -NonDICOMpathologyImages_id - -acquisition_method_type - -embedding_medium - -immersion - -lens_numerical_aperture - -nominal_magnification - -objective - -staining_method - -tissue_fixative - -tumor_tissue_type - - + + +file->participant + + +of_participant - - -NonDICOMpathologyImages->image - - -of_image + + +file->sample + + +from_sample + + + +file->file + + +associated_with diff --git a/docs/model-desc/cds-model-props.yml b/docs/model-desc/cds-model-props.yml index a5878e5..71cb9e3 100644 --- a/docs/model-desc/cds-model-props.yml +++ b/docs/model-desc/cds-model-props.yml @@ -5134,6 +5134,7 @@ PropDefinitions: Enum: - 'Yes' - 'No' + - Censored - Unknown - Not Reported - Not Allowed To Collect @@ -5142,7 +5143,7 @@ PropDefinitions: Original Source: DSS Code: "13529783" Value: Disease Progression Or Recurrence Indicator - Version: '1.00' + Version: '2.00' # study role_or_affiliation: Desc: The text that describes the distinguishable characteristics of the action or activity assigned to or required or expected of a person in a formal association with a group or organization. @@ -10947,4 +10948,4 @@ PropDefinitions: Req: true description: Desc: Any additional information about the dataset that might be relevant formatted as a short sentence or paragraph - Type: string \ No newline at end of file + Type: string diff --git a/docs/model-desc/cds-model.svg b/docs/model-desc/cds-model.svg index f0572ea..2d45f71 100644 --- a/docs/model-desc/cds-model.svg +++ b/docs/model-desc/cds-model.svg @@ -3,672 +3,710 @@ Perl - + -image - -image - - - -citation_or_DOI - -de_identification_method_description - -de_identification_method_type - -de_identification_software - -image_modality - -imaging_equipment_manufacturer - -imaging_equipment_model - -imaging_protocol - -imaging_software - -license - -longitudinal_temporal_event_offset - -longitudinal_temporal_event_type - -organ_or_tissue - -performed_imaging_study_typeCode - -species - -study_link_id - - - - - -file - -file - - - -checksum_algorithm - -checksum_value - -crdc_id - -experimental_strategy_and_data_subtypes - -file_description - -file_id - -file_mapping_level - -file_name - -file_size - -file_type - -file_url_in_cds - -md5sum - -submission_version - - - - - -image->file - - -of_file - - - -diagnosis - -diagnosis - - - -age_at_diagnosis - -crdc_id - -days_to_last_followup - -days_to_last_known_disease_status - -days_to_last_known_status - -days_to_recurrence - -diagnosis_id - -disease_type - -incidence_type - -last_known_disease_status - -morphology - -primary_diagnosis - -primary_site - -progression_or_recurrence - -site_of_resection_or_biopsy - -study_diagnosis_id - -tissue_or_organ_of_origin - -tumor_grade - -tumor_stage_clinical_m - -tumor_stage_clinical_n - -tumor_stage_clinical_t - -vital_status - - +NonDICOMpathologyImages + +NonDICOMpathologyImages + + + +NonDICOMpathologyImages_id + +acquisition_method_type + +embedding_medium + +immersion + +lens_numerical_aperture + +nominal_magnification + +objective + +staining_method + +tissue_fixative + +tumor_tissue_type + + - - -participant - -participant - - - -crdc_id - -dbGaP_subject_id - -ethnicity - -gender - -participant_id - -race - -sex - -study_participant_id - - + + +image + +image + + + +citation_or_DOI + +de_identification_method_description + +de_identification_method_type + +de_identification_software + +image_modality + +imaging_equipment_manufacturer + +imaging_equipment_model + +imaging_protocol + +imaging_software + +license + +longitudinal_temporal_event_offset + +longitudinal_temporal_event_type + +organ_or_tissue + +performed_imaging_study_typeCode + +species + +study_link_id + + - - -diagnosis->participant - - -of_participant + + +NonDICOMpathologyImages->image + + +of_image - + proteomic - -proteomic - - - -aliquot_id - -analytical_fractions - -instrument_make - -proteomic_design_description - -proteomic_instrument_model - - + +proteomic + + + +aliquot_id + +analytical_fractions + +instrument_make + +proteomic_design_description + +proteomic_instrument_model + + + + + +file + +file + + + +checksum_algorithm + +checksum_value + +crdc_id + +experimental_strategy_and_data_subtypes + +file_description + +file_id + +file_mapping_level + +file_name + +file_size + +file_type + +file_url_in_cds + +md5sum + +submission_version + + - + proteomic->file - - -of_file - - - -NonDICOMCTimages - -NonDICOMCTimages - - - -CTAquisitionProtocolElement_ctdiPhantomTypeCode - -CTAquisitionProtocolElement_ctdiVol - -CTAquisitionProtocolElement_exposureModulationType_Code - -CTAquisitionProtocolElement_gantryDetectorTilt - -CTAquisitionProtocolElement_kVp - -CTAquisitionProtocolElement_singleCollimationWidth - -CTAquisitionProtocolElement_spiralPitchFactor - -CTAquisitionProtocolElement_totalCollimationWidth - -CTImageReconstructionProtocolElement_convolutionKernel - -CTImageReconstructionProtocolElement_convolutionKernelGroupCode - -NonDICOMCTimages_id - - + + +of_file - - -NonDICOMCTimages->image - - -of_image + + +treatment + +treatment + + + +crdc_id + +days_to_treatment + +response + +therapeutic_agents + +treatment_id + +treatment_type + + - - -NonDICOMradiologyAllModalities - -NonDICOMradiologyAllModalities - - - -NonDICOMradiologyAllModalities_id - -performed_imaging_study_acquisitionTypeCode - -performed_imaging_study_admittingDiagnosisCode - -performed_imaging_study_algorithmCode - -performed_imaging_study_bodyPositionCode - -performed_imaging_study_cardiacSynchronizationTechniqueCode - -performed_imaging_study_dataCollectionDiameter - -performed_imaging_study_description - -performed_imaging_study_lossyImageCompressionIndicator - -performed_imaging_study_nonAcquisitionModalitiesInStudyCode - -performed_imaging_study_primaryAnatomicSiteCode - -performed_imaging_study_reconstructionDiameter - -performed_imaging_study_reconstructionFieldOfViewHeight - -performed_imaging_study_reconstructionFieldOfViewWidth - -performed_imaging_study_reconstructionInterval - -performed_imaging_study_respiratoryMotionTechniqueCode - -performed_imaging_study_sliceThickness - -performed_imaging_study_summary - - + + +participant + +participant + + + +crdc_id + +dbGaP_subject_id + +ethnicity + +gender + +participant_id + +race + +sex + +study_participant_id + + - + -NonDICOMradiologyAllModalities->image - - -of_image +treatment->participant + + +of_participant - + study - -study - - - -acl - -adult_or_childhood_study - -authz - -bioproject_accession - -cds_primary_bucket - -cds_requestor - -cds_secondary_bucket - -cds_tertiary_bucket - -clinical_trial_arm - -clinical_trial_identifier - -clinical_trial_repository - -clinical_trial_system - -co_investigator_email - -co_investigator_name - -crdc_id - -data_access_level - -data_types - -email - -file_types - -file_types_and_format - -first_name - -funding_agency - -funding_source_program_name - -grant_id - -index_date - -+ 20 properties - - + +study + + + +acl + +adult_or_childhood_study + +authz + +bioproject_accession + +cds_primary_bucket + +cds_requestor + +cds_secondary_bucket + +cds_tertiary_bucket + +clinical_trial_arm + +clinical_trial_identifier + +clinical_trial_repository + +clinical_trial_system + +co_investigator_email + +co_investigator_name + +crdc_id + +data_access_level + +data_types + +email + +file_types + +file_types_and_format + +first_name + +funding_agency + +funding_source_program_name + +grant_id + +index_date + ++ 20 properties + + - + program - -program - - - -crdc_id - -institution - -program_acronym - -program_external_url - -program_full_description - -program_name - -program_short_description - -program_short_name - -program_sort_order - - + +program + + + +crdc_id + +institution + +program_acronym + +program_external_url + +program_full_description + +program_name + +program_short_description + +program_short_name + +program_sort_order + + - + study->program - - -of_program + + +of_program + + + +NonDICOMradiologyAllModalities + +NonDICOMradiologyAllModalities + + + +NonDICOMradiologyAllModalities_id + +performed_imaging_study_acquisitionTypeCode + +performed_imaging_study_admittingDiagnosisCode + +performed_imaging_study_algorithmCode + +performed_imaging_study_bodyPositionCode + +performed_imaging_study_cardiacSynchronizationTechniqueCode + +performed_imaging_study_dataCollectionDiameter + +performed_imaging_study_description + +performed_imaging_study_lossyImageCompressionIndicator + +performed_imaging_study_nonAcquisitionModalitiesInStudyCode + +performed_imaging_study_primaryAnatomicSiteCode + +performed_imaging_study_reconstructionDiameter + +performed_imaging_study_reconstructionFieldOfViewHeight + +performed_imaging_study_reconstructionFieldOfViewWidth + +performed_imaging_study_reconstructionInterval + +performed_imaging_study_respiratoryMotionTechniqueCode + +performed_imaging_study_sliceThickness + +performed_imaging_study_summary + + + + + +NonDICOMradiologyAllModalities->image + + +of_image NonDICOMMRimages - -NonDICOMMRimages - - - -MRImageAcquisitionProtocolElement_acquisitionContrastCode - -MRImageAcquisitionProtocolElement_arterialSpinLabelingContrastCode - -MRImageAcquisitionProtocolElement_diffusionBValue - -MRImageAcquisitionProtocolElement_diffusionDirectionalityCode - -MRImageAcquisitionProtocolElement_echoPlanarPulseSequenceIndicator - -MRImageAcquisitionProtocolElement_echoPulseSequenceCategoryCode - -MRImageAcquisitionProtocolElement_inversionRecoveryIndicator - -MRImageAcquisitionProtocolElement_magneticFieldStrength - -MRImageAcquisitionProtocolElement_multipleSpinEchoIndicator - -MRImageAcquisitionProtocolElement_phaseContrastIndicator - -MRImageAcquisitionProtocolElement_pulseSequenceName - -MRImageAcquisitionProtocolElement_resonantNucleusCode - -MRImageAcquisitionProtocolElement_saturationRecoveryIndicator - -MRImageAcquisitionProtocolElement_spectrallySelectedSuppressionCode - -MRImageAcquisitionProtocolElement_steadyStatePulseSequenceCode - -MRImageAcquisitionProtocolElement_timeOfFlightContrastIndicator - -MRImageReconstructionProtocolElement_complexImageComponentCode - -NonDICOMMRimages_id - - + +NonDICOMMRimages + + + +MRImageAcquisitionProtocolElement_acquisitionContrastCode + +MRImageAcquisitionProtocolElement_arterialSpinLabelingContrastCode + +MRImageAcquisitionProtocolElement_diffusionBValue + +MRImageAcquisitionProtocolElement_diffusionDirectionalityCode + +MRImageAcquisitionProtocolElement_echoPlanarPulseSequenceIndicator + +MRImageAcquisitionProtocolElement_echoPulseSequenceCategoryCode + +MRImageAcquisitionProtocolElement_inversionRecoveryIndicator + +MRImageAcquisitionProtocolElement_magneticFieldStrength + +MRImageAcquisitionProtocolElement_multipleSpinEchoIndicator + +MRImageAcquisitionProtocolElement_phaseContrastIndicator + +MRImageAcquisitionProtocolElement_pulseSequenceName + +MRImageAcquisitionProtocolElement_resonantNucleusCode + +MRImageAcquisitionProtocolElement_saturationRecoveryIndicator + +MRImageAcquisitionProtocolElement_spectrallySelectedSuppressionCode + +MRImageAcquisitionProtocolElement_steadyStatePulseSequenceCode + +MRImageAcquisitionProtocolElement_timeOfFlightContrastIndicator + +MRImageReconstructionProtocolElement_complexImageComponentCode + +NonDICOMMRimages_id + + - + NonDICOMMRimages->image - - -of_image - - - -sample - -sample - - - -biosample_accession - -crdc_id - -derived_from_specimen - -sample_age_at_collection - -sample_anatomic_site - -sample_description - -sample_id - -sample_tumor_status - -sample_type - -sample_type_category - - - - - -sample->participant - - -of_participant + + +of_image - + participant->study - - -of_study + + +of_study - + genomic_info - -genomic_info - - - -avg_read_length - -bases - -coverage - -crdc_id - -custom_assembly_fasta_file_for_alignment - -design_description - -genomic_info_id - -instrument_model - -library_id - -library_layout - -library_selection - -library_source - -library_source_material - -library_source_molecule - -library_strategy - -methylation_platform - -number_of_reads - -platform - -reference_genome_assembly - -reporter_label - -sequence_alignment_software - - + +genomic_info + + + +avg_read_length + +bases + +coverage + +crdc_id + +custom_assembly_fasta_file_for_alignment + +design_description + +genomic_info_id + +instrument_model + +library_id + +library_layout + +library_selection + +library_source + +library_source_material + +library_source_molecule + +library_strategy + +methylation_platform + +number_of_reads + +platform + +reference_genome_assembly + +reporter_label + +sequence_alignment_software + + - -genomic_info->file - - -of_file - - - -file->study - - -of_study - - -file->sample - - -from_sample - - - -file->participant - - -of_participant - - - -file->file - - -associated_with +genomic_info->file + + +of_file - + NonDICOMPETimages - -NonDICOMPETimages - - - -NonDICOMPETimages_id - -PETImagingAcquisitionProtocolElement_gantryDetectorTilt - -Radiopharmaceutical_radionuclideCode - - + +NonDICOMPETimages + + + +NonDICOMPETimages_id + +PETImagingAcquisitionProtocolElement_gantryDetectorTilt + +Radiopharmaceutical_radionuclideCode + + - + NonDICOMPETimages->image - - -of_image + + +of_image + + + +diagnosis + +diagnosis + + + +age_at_diagnosis + +crdc_id + +days_to_last_followup + +days_to_last_known_disease_status + +days_to_last_known_status + +days_to_recurrence + +diagnosis_id + +disease_type + +incidence_type + +last_known_disease_status + +morphology + +primary_diagnosis + +primary_site + +progression_or_recurrence + +site_of_resection_or_biopsy + +study_diagnosis_id + +tissue_or_organ_of_origin + +tumor_grade + +tumor_stage_clinical_m + +tumor_stage_clinical_n + +tumor_stage_clinical_t + +vital_status + + + + + +diagnosis->participant + + +of_participant - + MultiplexMicroscopy - -MultiplexMicroscopy - - - -MultiplexMicroscopy_id - -acquisition_method_type - -antibody_name - -catalog_number - -channel_id - -channel_metadata_file_url_in_cds - -channel_metadata_filename - -channel_name - -clone - -concentration - -cycle_number - -dilution - -embedding_medium - -emission_bandwidth - -emission_wavelength - -excitation_bandwidth - -excitation_wavelength - -fluorophore - -imaging_assay_type - -immersion - -lens_numerical_aperture - -lot - -metal_isotope_element_abbreviation - -metal_isotope_element_mass - -nominal_magnification - -+ 19 properties - - + +MultiplexMicroscopy + + + +MultiplexMicroscopy_id + +acquisition_method_type + +antibody_name + +catalog_number + +channel_id + +channel_metadata_file_url_in_cds + +channel_metadata_filename + +channel_name + +clone + +concentration + +cycle_number + +dilution + +embedding_medium + +emission_bandwidth + +emission_wavelength + +excitation_bandwidth + +excitation_wavelength + +fluorophore + +imaging_assay_type + +immersion + +lens_numerical_aperture + +lot + +metal_isotope_element_abbreviation + +metal_isotope_element_mass + +nominal_magnification + ++ 19 properties + + - + MultiplexMicroscopy->image - - -of_image + + +of_image + + + +NonDICOMCTimages + +NonDICOMCTimages + + + +CTAquisitionProtocolElement_ctdiPhantomTypeCode + +CTAquisitionProtocolElement_ctdiVol + +CTAquisitionProtocolElement_exposureModulationType_Code + +CTAquisitionProtocolElement_gantryDetectorTilt + +CTAquisitionProtocolElement_kVp + +CTAquisitionProtocolElement_singleCollimationWidth + +CTAquisitionProtocolElement_spiralPitchFactor + +CTAquisitionProtocolElement_totalCollimationWidth + +CTImageReconstructionProtocolElement_convolutionKernel + +CTImageReconstructionProtocolElement_convolutionKernelGroupCode + +NonDICOMCTimages_id + + + + + +NonDICOMCTimages->image + + +of_image + + + +sample + +sample + + + +biosample_accession + +crdc_id + +derived_from_specimen + +sample_age_at_collection + +sample_anatomic_site + +sample_description + +sample_id + +sample_tumor_status + +sample_type + +sample_type_category + + + + + +sample->participant + + +of_participant + + + +image->file + + +of_file - + version version @@ -687,71 +725,33 @@ - - -treatment - -treatment - - - -crdc_id - -days_to_treatment - -response - -therapeutic_agents - -treatment_id - -treatment_type - - - - + -treatment->participant - - -of_participant +file->study + + +of_study - - -NonDICOMpathologyImages - -NonDICOMpathologyImages - - - -NonDICOMpathologyImages_id - -acquisition_method_type - -embedding_medium - -immersion - -lens_numerical_aperture - -nominal_magnification - -objective - -staining_method - -tissue_fixative - -tumor_tissue_type - - + + +file->participant + + +of_participant - - -NonDICOMpathologyImages->image - - -of_image + + +file->sample + + +from_sample + + + +file->file + + +associated_with diff --git a/docs/model-desc/cds-model.txt b/docs/model-desc/cds-model.txt index 3ad84b7..462225c 100644 --- a/docs/model-desc/cds-model.txt +++ b/docs/model-desc/cds-model.txt @@ -1,5 +1,5 @@ repo https://github.com/CBIIT/cds-model -commit 70f5e5e +commit a5b570d node property value_or_TYPE MultiplexMicroscopy MultiplexMicroscopy_id STRING MultiplexMicroscopy acquisition_method_type STRING @@ -2502,6 +2502,7 @@ diagnosis primary_site Vulva diagnosis primary_site Waldeyer's Ring diagnosis primary_site Wrist Joint diagnosis primary_site Zygomatic Bone +diagnosis progression_or_recurrence Censored diagnosis progression_or_recurrence No diagnosis progression_or_recurrence Not Allowed To Collect diagnosis progression_or_recurrence Not Reported @@ -9126,22 +9127,22 @@ version model_version STRING relationship source_node destination_node property value_or_TYPE associated_with file file NA NA from_sample file sample NA NA -of_file image file NA NA -of_file genomic_info file NA NA of_file proteomic file NA NA -of_image NonDICOMPETimages image NA NA +of_file genomic_info file NA NA +of_file image file NA NA of_image MultiplexMicroscopy image NA NA -of_image NonDICOMCTimages image NA NA of_image NonDICOMradiologyAllModalities image NA NA of_image NonDICOMMRimages image NA NA of_image NonDICOMpathologyImages image NA NA -of_participant treatment participant NA NA -of_participant sample participant NA NA -of_participant file participant NA NA +of_image NonDICOMPETimages image NA NA +of_image NonDICOMCTimages image NA NA of_participant diagnosis participant NA NA +of_participant file participant NA NA +of_participant sample participant NA NA +of_participant treatment participant NA NA of_program study program NA NA -of_study file study NA NA of_study participant study NA NA +of_study file study NA NA property description CTAquisitionProtocolElement_ctdiPhantomTypeCode The type of phantom to use for CTDI measurement according to IEC 60601-2-44 diff --git a/docs/model-desc/cds-model.yml b/docs/model-desc/cds-model.yml index 6293989..f990638 100644 --- a/docs/model-desc/cds-model.yml +++ b/docs/model-desc/cds-model.yml @@ -1,5 +1,5 @@ Handle: CDS -Version: v5.0.0 +Version: v5.0.1 Nodes: program: Desc: "Program in the Cancer Data Service refer to a broad framework of goals under which related projects or other research activities are grouped. Example - Clinical Proteomic Tumor Analysis Consortium (CPTAC)"