-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.bulkMethylationseq_level1_metadata_r5`
(
  HTAN_Parent_Biospecimen_ID STRING OPTIONS(description="HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated"),
  Total_DNA_Input STRING OPTIONS(description="Overall number of reads for a given sample in digits (microgram, nanogram)."),
  Nucleic_Acid_Source STRING OPTIONS(description="The source of the input nucleic molecule"),
  Filename STRING OPTIONS(description="Name of a file"),
  Replicate_Type STRING OPTIONS(description="A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples."),
  entityId STRING OPTIONS(description="Synapse ID of entity"),
  Id STRING OPTIONS(description="Unique identifier of entity e.g. a96059eb-81af-4b24-ae50-9242c0d8f819"),
  HTAN_Data_File_ID STRING OPTIONS(description="Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)"),
  Component STRING OPTIONS(description="Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows."),
  Bulk_Methylation_Assay_Type STRING OPTIONS(description="Assay types normally determine genomic coverage"),
  Bisulfite_Conversion STRING OPTIONS(description="Name of the kit used in bisulfite conversion."),
  File_Format STRING OPTIONS(description="Format of a file (e.g. txt, csv, fastq, bam, etc.)"),
  Sequencing_Platform STRING OPTIONS(description="A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument."),
  HTAN_Center STRING OPTIONS(description="Name of HTAN Center e.g. HTAN HTAPP"),
  Manifest_Id STRING OPTIONS(description="Synapse ID of manifest containing file annotation"),
  Manifest_Version INT64 OPTIONS(description="Latest version of metadata manifest"),
  File_Size INT64 OPTIONS(description="Size of file (bucket object) in bytes"),
  md5 STRING OPTIONS(description="md5 hash of file"),
  Data_Release STRING OPTIONS(description="Inclusion in HTAN Data Release e.g. Release 1.0"),
  CDS_Release STRING OPTIONS(description="CDS transfer package in which file was included e.g. v22.6.1.seq")
)
OPTIONS(
  friendly_name="HTAN BULKMETHYLATION SEQ LEVEL 1 METADATA R5 VERSIONED",
  description="This table contains the file metadata for the first level Bulk Methyl sequencing. Data was extracted from HTAN Synapse projects in April 2024 and corresponds to HTAN Data Release 5.1. More details: see https://data.humantumoratlas.org/standard/sequencing",
  labels=[("access", "open"), ("data_type", "file_metadata"), ("program", "htan"), ("source", "htan"), ("category", "metadata"), ("status", "current")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.bulkMethylationseq_level1_metadata_r5` (HTAN_Parent_Biospecimen_ID, Total_DNA_Input, Nucleic_Acid_Source, Filename, Replicate_Type, entityId, Id, HTAN_Data_File_ID, Component, Bulk_Methylation_Assay_Type, Bisulfite_Conversion, File_Format, Sequencing_Platform, HTAN_Center, Manifest_Id, Manifest_Version, File_Size, md5, Data_Release, CDS_Release) VALUES ('HTA10_01_004', NULL, 'Bulk Whole Cell', 'bulk_methyl_seq_level_1/A001_C004_120648.fq.gz', 'Not Applicable', 'syn45135795', 'c68b50d7-417e-46b0-a6ed-00e492247858', 'HTA10_01_43208332606526216901477335450321', 'BulkMethylation-seqLevel1', 'Whole genome', 'NEBNext Enzymatic Methyl-seq Kit', 'fastq', 'Ultima Genomics UG100', 'HTAN Stanford', 'syn51718142', 4, 85384456129, 'e32a8ddc6065c6cb69014773dfef03c1', 'Release 4.0', 'v23.10.1.seq'), ('HTA10_01_004', NULL, 'Bulk Whole Cell', 'bulk_methyl_seq_level_1/A001_C004_120655.fq.gz', 'Not Applicable', 'syn45136011', 'd8a770f1-ac5e-4bd5-811f-cf5125ab72ac', 'HTA10_01_31241678407000619453059401802613', 'BulkMethylation-seqLevel1', 'Whole genome', 'NEBNext Enzymatic Methyl-seq Kit', 'fastq', 'Ultima Genomics UG100', 'HTAN Stanford', 'syn51718142', 4, 77772434012, 'd1ceb678ea7a006194530f94a18a2613', 'Release 4.0', 'v23.10.1.seq'), ('HTA10_01_005', NULL, 'Bulk Whole Cell', 'bulk_methyl_seq_level_1/A001_C005_120648.fq.gz', 'Not Applicable', 'syn45137935', '8d0a3213-d7bc-4929-89ae-8e13cb5d32b7', 'HTA10_01_46294077943108131591650144554192', 'BulkMethylation-seqLevel1', 'Whole genome', 'NEBNext Enzymatic Methyl-seq Kit', 'fastq', 'Ultima Genomics UG100', 'HTAN Stanford', 'syn51718142', 4, 68983195386, '46c94077943b081dbf9b6f0beeffe19c', 'Release 4.0', 'v23.10.1.seq'), ('HTA10_01_005', NULL, 'Bulk Whole Cell', 'bulk_methyl_seq_level_1/A001_C005_120655.fq.gz', 'Not Applicable', 'syn45138173', '5f6d6067-fe33-4988-a140-c0074206d98c', 'HTA10_01_54114060048152634471554202053055', 'BulkMethylation-seqLevel1', 'Whole genome', 'NEBNext Enzymatic Methyl-seq Kit', 'fastq', 'Ultima Genomics UG100', 'HTAN Stanford', 'syn51718142', 4, 60541623943, 'f41be06aa481f26dee7bf5eca205da55', 'Release 4.0', 'v23.10.1.seq'), ('HTA10_01_007', NULL, 'Bulk Whole Cell', 'bulk_methyl_seq_level_1/A001_C007_120648.fq.gz', 'Not Applicable', 'syn45138938', '488bb6b6-d6a6-460f-8704-dfe3da21d251', 'HTA10_01_87763024572233951479832245018290', 'BulkMethylation-seqLevel1', 'Whole genome', 'NEBNext Enzymatic Methyl-seq Kit', 'fastq', 'Ultima Genomics UG100', 'HTAN Stanford', 'syn51718142', 4, 68720236239, '877630c4572c3d9fbe798dc2ef0b8290', 'Release 4.0', 'v23.10.1.seq');