-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.pancancer_atlas.Filtered_jhu_usc_edu_PANCAN_merged_HumanMethylation27_HumanMethylation450_betaValue_whitelisted`
(
  ParticipantBarcode STRING OPTIONS(description="TCGA barcode identifier for the study participant, eg TCGA-02-0001"),
  SampleBarcode STRING OPTIONS(description="Barcode of the biospecimen sample, eg TCGA-13-1489-02A"),
  AliquotBarcode STRING OPTIONS(description="TCGA aliquot barcode, eg TCGA-12-1089-01A-01D-0517-28"),
  SampleTypeLetterCode STRING OPTIONS(description="Letter code of the sample type using the TCGA standards, eg TPN, EBV. Full list available at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes"),
  SampleType STRING OPTIONS(description="There are 10 sample types: Blood Derived Normal, Primary solid Tumor, Solid Tissue Normal, Recurrent Solid Tumor, Metastatic, Additional - New Primary, Primary Blood Derived Cancer - Peripheral Blood, Buccal Cell Normal, Additioanal Metastatic, Bone Marrrow Normal"),
  Study STRING OPTIONS(description="TCGA study abbreviation, eg LAML. Full list available at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations"),
  ID STRING OPTIONS(description="Unique probe identifier (eg cg04676771) from the Illumina Human Methylation array -- please refer to the annotation table (isb-cgc-bq.annotations.methylation_annotation_hg19_illumina_current) for more details about any particular probe"),
  Beta FLOAT64 OPTIONS(description="Normalized DNA methylation beta value (between 0 and 1, where 0 indicates completely un-methylated and 1 indicates fully methylated)")
)
OPTIONS(
  friendly_name="PanCancer Filtered DNA Methylation (Merged 27K+450K Only)",
  description="Data extracted from the PanCancer Atlas initiative on the GDC in April 2018. Contains DNA Methylation (Merged from the 27K and 450K tables) annotated with pertinent TCGA barcodes.  \n\nNote: The data was filtered from the BigQuery table isb-cgc-bq:pancancer_atlas.Original_jhu_usc_edu_PANCAN_merged_HumanMethylation27_HumanMethylation450_betaValue_whitelisted, using the PanCancer Atlas whitelist (table Whitelist_ParticipantBarcodes)  \n\nMore details: BigQuery Table: isb-cgc-bq:pancancer_atlas.Original_jhu_usc_edu_PANCAN_merged_HumanMethylation27_HumanMethylation450_betaValue_whitelisted \nand https://gdc.cancer.gov/about-data/publications/pancanatlas",
  labels=[("category", "processed_-omics_data"), ("status", "current"), ("access", "open"), ("source_0", "gdc"), ("data_type", "dna_methylation"), ("program", "pancancer_atlas"), ("reference_genome", "hg19"), ("source_1", "literature")]
);

INSERT INTO `isb-cgc-bq.pancancer_atlas.Filtered_jhu_usc_edu_PANCAN_merged_HumanMethylation27_HumanMethylation450_betaValue_whitelisted` (ParticipantBarcode, SampleBarcode, AliquotBarcode, SampleTypeLetterCode, SampleType, Study, ID, Beta) VALUES ('TCGA-01-0628', 'TCGA-01-0628-11A', 'TCGA-01-0628-11A-01D-0383-05', 'NT', 'Solid Tissue Normal', 'OV', 'cg25264554', 0.014019597658378), ('TCGA-01-0628', 'TCGA-01-0628-11A', 'TCGA-01-0628-11A-01D-0383-05', 'NT', 'Solid Tissue Normal', 'OV', 'cg12269343', 0.0197464851425526), ('TCGA-01-0628', 'TCGA-01-0628-11A', 'TCGA-01-0628-11A-01D-0383-05', 'NT', 'Solid Tissue Normal', 'OV', 'cg02425732', 0.033633891941717), ('TCGA-01-0628', 'TCGA-01-0628-11A', 'TCGA-01-0628-11A-01D-0383-05', 'NT', 'Solid Tissue Normal', 'OV', 'cg09852871', 0.788843878492672), ('TCGA-01-0628', 'TCGA-01-0628-11A', 'TCGA-01-0628-11A-01D-0383-05', 'NT', 'Solid Tissue Normal', 'OV', 'cg23953831', 0.864616977642031);