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cgcMetadataSparqlQuery.rq
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prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix tcga: <https://www.sbgenomics.com/ontologies/2014/11/tcga#>
select distinct ?file_name ?gdc_file_uuid ?file_submitter_id ?case_name ?aliquot_name ?ref_genome_label ?sample_type_label ?experimental_strategy_label ?data_type_label ?data_format_label ?gender_label ?race_label ?ethnicity_label ?ageAtDiagnosis ?disease_type_label ?sample_label ?investigation_label ?histological_diagnosis_label ?primary_site_label ?prior_dx ?clinical_m_label ?clinical_n_label ?clinical_t_label ?pathologic_m_label ?pathologic_n_label ?pathologic_t_label ?pathologic_stage_label ?perf_score_karnofsky_label ?perf_score_eastern_cancer_oncology_group_label ?perf_score_timing_label ?primary_therapy_outcome_success_label ?vital_status_label ?new_tumor_event_label ?new_tumor_event_after_initial_trtmt ?radiation_therapy_code_label ?radiation_therapy_site_label ?radiation_therapy_type_label ?days_to_last_followup ?year_of_diagnosis ?icd10 ?icd03_histology_label ?icd03_histology_site ?data_submitting_center_label ?seq_platform_label ?aliquot_concentration ?analyte_A260A280Ratio ?analyte_type_label ?analyte_amount ?analyte_well_number ?spectrophotometer_method_label ?file_upload_date ?file_published_date ?file_last_modified_date ?portion_weight ?portion_is_ffpe ?portion_number ?portion_slide_label ?freezing_method_label ?tissue_source_site_label ?country_of_sample_procurement
where
{
?file a tcga:File .
?file rdfs:label ?file_name .
?file tcga:hasGDCFileUUID ?gdc_file_uuid .
?file tcga:hasSubmitterId ?file_submitter_id .
?file tcga:hasCase ?case .
?case rdfs:label ?case_name .
?file tcga:hasAliquot ?aliquot .
?aliquot rdfs:label ?aliquot_name .
?file tcga:hasReferenceGenome ?ref_genome .
?ref_genome rdfs:label ?ref_genome_label .
?file tcga:hasSample ?sample .
?sample tcga:hasSampleType ?st .
?st rdfs:label ?sample_type_label
filter(?sample_type_label='Primary Tumor' || ?sample_type_label='Additional - New Primary' || ?sample_type_label='Additional Metastatic' || ?sample_type_label='Metastatic' || ?sample_type_label='Primary Blood Derived Cancer - Peripheral Blood' || ?sample_type_label='Recurrent Tumor' || ?sample_type_label='Blood Derived Normal' || ?sample_type_label='Bone Marrow Normal' || ?sample_type_label='Buccal Cell Normal' || ?sample_type_label='Solid Tissue Normal')
?file tcga:hasExperimentalStrategy ?xs .
?xs rdfs:label ?experimental_strategy_label .
filter(?experimental_strategy_label='RNA-Seq' || ?experimental_strategy_label='WGS') .
?file tcga:hasDataType ?type .
?type rdfs:label ?data_type_label .
filter(?data_type_label='Raw sequencing data') .
?file tcga:hasDataFormat ?format .
?format rdfs:label ?data_format_label .
filter(?data_format_label='BAM') .
?file tcga:hasCase ?case .
?case tcga:hasGender ?gender .
?gender rdfs:label ?gender_label .
?file tcga:hasCase ?case .
?case tcga:hasEthnicity ?ethnicity .
?ethnicity rdfs:label ?ethnicity_label .
?file tcga:hasCase ?case .
?case tcga:hasRace ?race .
?race rdfs:label ?race_label .
?file tcga:hasCase ?case .
?case tcga:hasAgeAtDiagnosis ?ageAtDiagnosis .
?file tcga:hasCase ?case .
?case tcga:hasDiseaseType ?diseaseType .
?diseaseType rdfs:label ?disease_type_label .
?file tcga:hasCase ?case .
?case tcga:hasSample ?sample .
?sample rdfs:label ?sample_label .
?file tcga:hasCase ?case .
?case tcga:hasInvestigation ?investigation .
?investigation rdfs:label ?inv_label .
?file tcga:hasCase ?case .
?case tcga:hasHistologicalDiagnosis ?hd .
?hd rdfs:label ?histological_diagnosis_label .
?file tcga:hasCase ?case .
?case tcga:hasPrimarySite ?primary_site .
?primary_site rdfs:label ?primary_site_label .
?file tcga:hasCase ?case .
?case tcga:hasPriorDiagnosis ?prior_dx_base .
?prior_dx_base rdfs:label ?prior_dx .
?file tcga:hasCase ?case .
?case tcga:hasClinicalM ?clinical_m .
?clinical_m rdfs:label ?clinical_m_label .
?file tcga:hasCase ?case .
?case tcga:hasClinicalM ?clinical_n .
?clinical_n rdfs:label ?clinical_n_label .
?file tcga:hasCase ?case .
?case tcga:hasClinicalM ?clinical_t .
?clinical_t rdfs:label ?clinical_t_label .
?file tcga:hasCase ?case .
?case tcga:hasClinicalStage ?clinical_stage .
?clinical_stage rdfs:label ?clinical_stage_label .
?file tcga:hasCase ?case .
?case tcga:hasPathologicM ?pathologic_m .
?pathologic_m rdfs:label ?pathologic_m_label .
?file tcga:hasCase ?case .
?case tcga:hasPathologicN ?pathologic_n .
?pathologic_n rdfs:label ?pathologic_n_label .
?file tcga:hasCase ?case .
?case tcga:hasPathologicT ?pathologic_t .
?pathologic_t rdfs:label ?pathologic_t_label .
?file tcga:hasCase ?case .
?case tcga:hasPathologicStage ?pathologic_stage .
?pathologic_stage rdfs:label ?pathologic_stage_label .
?file tcga:hasCase ?case .
?case tcga:hasPerformanceStatusScoreKarnofsky ?perf_score_karnofsky .
?perf_score_karnofsky rdfs:label ?perf_score_karnofsky_label .
?file tcga:hasCase ?case .
?case tcga:hasPerformanceStatusScoreECOG ?perf_score_eastern_cancer_oncology_group .
?perf_score_eastern_cancer_oncology_group rdfs:label ?perf_score_eastern_cancer_oncology_group_label .
?file tcga:hasCase ?case .
?case tcga:hasPerformanceStatusScoreTiming ?perf_score_timing .
?perf_score_timing rdfs:label ?perf_score_timing_label .
?file tcga:hasCase ?case .
?case tcga:hasPrimaryTherapyOutcomeSuccess ?primary_therapy_outcome_success .
?primary_therapy_outcome_success rdfs:label ?primary_therapy_outcome_success_label .
?file tcga:hasCase ?case .
?case tcga:hasVitalStatus ?vital_status .
?vital_status rdfs:label ?vital_status_label .
?file tcga:hasCase ?case .
?case tcga:hasNewTumorEvent ?new_tumor_event .
?new_tumor_event rdfs:label ?new_tumor_event_label .
?file tcga:hasCase ?case .
?case tcga:hasRadiationTherapy ?radiation_therapy .
?radiation_therapy rdfs:label ?radiation_therapy_code_label .
?file tcga:hasCase ?case .
?case tcga:hasRadiationTherapy ?radiation_therapy .
?radiation_therapy tcga:hasRadiationTherapySite ?radiation_therapy_site .
?radiation_therapy_site rdfs:label ?radiation_therapy_site_label .
?file tcga:hasCase ?case .
?case tcga:hasRadiationTherapy ?radiation_therapy .
?radiation_therapy tcga:hasRadiationType ?radiation_therapy_type .
?radiation_therapy_type rdfs:label ?radiation_therapy_type_label .
?file tcga:hasCase ?case .
?case tcga:hasNewTumorEventAfterInitialTreatment ?new_tumor_event_after_initial_trtmt .
?file tcga:hasCase ?case .
?case tcga:hasDaysToLastFollowUp ?days_to_last_followup .
?file tcga:hasCase ?case .
?case tcga:hasYearOfDiagnosis ?year_of_diagnosis .
?file tcga:hasCase ?case .
?case tcga:hasIcd10 ?icd10 .
?file tcga:hasCase ?case .
?case tcga:hasIcdO3Histology ?icd03_histology_label .
?file tcga:hasCase ?case .
?case tcga:hasIcdO3Site ?icd03_histology_site .
?file tcga:hasDataSubmittingCenter ?data_submitting_center .
?data_submitting_center rdfs:label ?data_submitting_center_label .
?file tcga:hasPlatform ?seq_platform .
?seq_platform rdfs:label ?seq_platform_label .
?file tcga:hasAliquot ?aliquot .
?aliquot tcga:hasConcentration ?aliquot_concentration .
?file tcga:hasAnalyte ?analyte .
?analyte tcga:hasA260A280Ratio ?analyte_A260A280Ratio .
?file tcga:hasAnalyte ?analyte .
?analyte tcga:hasAnalyteType ?analyte_type .
?analyte_type rdfs:label ?analyte_type_label .
?file tcga:hasAnalyte ?analyte .
?analyte tcga:hasAmount ?analyte_amount .
?file tcga:hasAnalyte ?analyte .
?analyte rdfs:label ?analyte_well_number .
?file tcga:hasAnalyte ?analyte .
?analyte tcga:hasSpectrophotometerMethod ?spectrophotometer_method .
?spectrophotometer_method rdfs:label ?spectrophotometer_method_label .
?file tcga:uploadDate ?file_upload_date .
?file tcga:publishedDate ?file_published_date .
?file tcga:lastModifiedDate ?file_last_modified_date .
?file tcga:hasAnalyte ?analyte .
?analyte tcga:hasPortion ?portion .
?portion tcga:hasWeight ?portion_weight .
?file tcga:hasAnalyte ?analyte .
?analyte tcga:hasPortion ?portion .
?portion tcga:hasIsFFPE ?portion_is_ffpe .
?file tcga:hasAnalyte ?analyte .
?analyte tcga:hasPortion ?portion .
?portion tcga:hasPortionNumber ?portion_number .
?file tcga:hasAnalyte ?analyte .
?analyte tcga:hasPortion ?portion .
?portion tcga:hasSlide ?portion_slide .
?portion_slide rdfs:label ?portion_slide_label .
?file tcga:hasCase ?case .
?case tcga:hasSample ?sample .
?sample tcga:hasFreezingMethod ?freezing_method .
?freezing_method rdfs:label ?freezing_method_label .
?file tcga:hasCase ?case .
?case tcga:hasSample ?sample .
?sample tcga:hasTissueSourceSite ?tissue_source_site .
?tissue_source_site rdfs:label ?tissue_source_site_label .
?file tcga:hasCase ?case .
?case tcga:hasSample ?sample .
?sample tcga:hasCountryOfSampleProcurement ?country_of_sample_procurement .
}