-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.scATACseq_level4_metadata_r5`
(
  Workflow_Link STRING OPTIONS(description="Link to workflow or command. DockStore.org recommended. URL"),
  Filename STRING OPTIONS(description="Name of a file"),
  HTAN_Parent_Data_File_ID STRING OPTIONS(description="HTAN Data File Identifier indicating the file(s) from which these files were derived"),
  scATACseq_Workflow_Parameters_Description STRING OPTIONS(description="Parameters used to run the scATAC-seq workflow."),
  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."),
  scATACseq_Workflow_Type STRING OPTIONS(description="Generic name for the workflow used to analyze a data set."),
  File_Format STRING OPTIONS(description="Format of a file (e.g. txt, csv, fastq, bam, etc.)"),
  Workflow_Version STRING OPTIONS(description="Major version of the workflow (e.g. Cell Ranger v3.1)"),
  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 SCATACSEQ LEVEL 4 METADATA R5 VERSIONED",
  description="This table contains the file metadata for the fourth level (t-SNE plot coordinates, etc.) single cell ATAC 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.scATACseq_level4_metadata_r5` (Workflow_Link, Filename, HTAN_Parent_Data_File_ID, scATACseq_Workflow_Parameters_Description, entityId, Id, HTAN_Data_File_ID, Component, scATACseq_Workflow_Type, File_Format, Workflow_Version, HTAN_Center, Manifest_Id, Manifest_Version, File_Size, md5, Data_Release, CDS_Release) VALUES ('https://satijalab.org/seurat/', 'single_cell_ATACseq_level_4_ped_glioma/seurat_atac_Neuroglia_signacIntegrated_bySample_withReference_None.rds', 'HTA4_2010_76721,HTA4_2010_76722,HTA4_2010_76723,HTA4_2007_76700,HTA4_2007_76701,HTA4_2007_76702,HTA4_2005_76682,HTA4_2005_76683,HTA4_2005_76684,HTA4_2010_76724,HTA4_2010_76725,HTA4_2010_76726,HTA4_2001_76667,HTA4_2001_76668,HTA4_2001_76669,HTA4_2003_76673,HTA4_2003_76674,HTA4_2003_76675,HTA4_2002_76670,HTA4_2002_76671,HTA4_2002_76672,HTA4_2003_76676,HTA4_2003_76677,HTA4_2003_76678,HTA4_2012_76733,HTA4_2012_76734,HTA4_2012_76735,HTA4_2007_76703,HTA4_2007_76704,HTA4_2007_76705,HTA4_2007_76706,HTA4_2007_76707,HTA4_2007_76708,HTA4_2009_76715,HTA4_2009_76716,HTA4_2009_76717,HTA4_2009_76718,HTA4_2009_76719,HTA4_2009_76720,HTA4_2013_76739,HTA4_2013_76740,HTA4_2013_76741,HTA4_2008_76709,HTA4_2008_76710,HTA4_2008_76711,HTA4_2013_76742,HTA4_2013_76743,HTA4_2013_76744,HTA4_2005_76685,HTA4_2005_76686,HTA4_2005_76687,HTA4_2006_76694,HTA4_2006_76695,HTA4_2006_76696,HTA4_2014_76745,HTA4_2014_76746,HTA4_2014_76747,HTA4_2016_76760,HTA4_2016_76761,HTA4_2016_76762,HTA4_2016_76763,HTA4_2016_76764,HTA4_2016_76765,HTA4_2008_76712,HTA4_2008_76713,HTA4_2008_76714,HTA4_2015_76748,HTA4_2015_76749,HTA4_2015_76750,HTA4_2015_76751,HTA4_2015_76752,HTA4_2015_76753,HTA4_2005_76688,HTA4_2005_76689,HTA4_2005_76690,HTA4_2005_76691,HTA4_2005_76692,HTA4_2005_76693,HTA4_2015_76754,HTA4_2015_76755,HTA4_2015_76756,HTA4_2015_76757,HTA4_2015_76758,HTA4_2015_76759,HTA4_2011_76727,HTA4_2011_76728,HTA4_2011_76729,HTA4_2006_76697,HTA4_2006_76698,HTA4_2006_76699,HTA4_2012_76736,HTA4_2012_76737,HTA4_2012_76738,HTA4_2011_76730,HTA4_2011_76731,HTA4_2011_76732,HTA4_2016_76766,HTA4_2016_76767,HTA4_2016_76768,HTA4_2004_76679,HTA4_2004_76680,HTA4_2004_76681', 'See paper methods', 'syn51406625', '6df980a2-cbf5-48e2-952b-4a518285c16f', 'HTA4_000_86667', 'ScATAC-seqLevel4', 'Seurat', 'RData', 'Seurat v4', 'HTAN CHOP', 'syn53253226', 6, 11108268668, 'c3747c691de5915c96a36308830fd379', 'Release 5.0', NULL), ('https://satijalab.org/seurat/', 'single_cell_ATACseq_level_4_ped_glioma/seurat_atac_signacIntegrated_bySample_withReference_4036_4037.rds', 'HTA4_2010_76721,HTA4_2010_76722,HTA4_2010_76723,HTA4_2007_76700,HTA4_2007_76701,HTA4_2007_76702,HTA4_2005_76682,HTA4_2005_76683,HTA4_2005_76684,HTA4_2010_76724,HTA4_2010_76725,HTA4_2010_76726,HTA4_2001_76667,HTA4_2001_76668,HTA4_2001_76669,HTA4_2003_76673,HTA4_2003_76674,HTA4_2003_76675,HTA4_2002_76670,HTA4_2002_76671,HTA4_2002_76672,HTA4_2003_76676,HTA4_2003_76677,HTA4_2003_76678,HTA4_2012_76733,HTA4_2012_76734,HTA4_2012_76735,HTA4_2007_76703,HTA4_2007_76704,HTA4_2007_76705,HTA4_2007_76706,HTA4_2007_76707,HTA4_2007_76708,HTA4_2009_76715,HTA4_2009_76716,HTA4_2009_76717,HTA4_2009_76718,HTA4_2009_76719,HTA4_2009_76720,HTA4_2013_76739,HTA4_2013_76740,HTA4_2013_76741,HTA4_2008_76709,HTA4_2008_76710,HTA4_2008_76711,HTA4_2013_76742,HTA4_2013_76743,HTA4_2013_76744,HTA4_2005_76685,HTA4_2005_76686,HTA4_2005_76687,HTA4_2006_76694,HTA4_2006_76695,HTA4_2006_76696,HTA4_2014_76745,HTA4_2014_76746,HTA4_2014_76747,HTA4_2016_76760,HTA4_2016_76761,HTA4_2016_76762,HTA4_2016_76763,HTA4_2016_76764,HTA4_2016_76765,HTA4_2008_76712,HTA4_2008_76713,HTA4_2008_76714,HTA4_2015_76748,HTA4_2015_76749,HTA4_2015_76750,HTA4_2015_76751,HTA4_2015_76752,HTA4_2015_76753,HTA4_2005_76688,HTA4_2005_76689,HTA4_2005_76690,HTA4_2005_76691,HTA4_2005_76692,HTA4_2005_76693,HTA4_2015_76754,HTA4_2015_76755,HTA4_2015_76756,HTA4_2015_76757,HTA4_2015_76758,HTA4_2015_76759,HTA4_2011_76727,HTA4_2011_76728,HTA4_2011_76729,HTA4_2006_76697,HTA4_2006_76698,HTA4_2006_76699,HTA4_2012_76736,HTA4_2012_76737,HTA4_2012_76738,HTA4_2011_76730,HTA4_2011_76731,HTA4_2011_76732,HTA4_2016_76766,HTA4_2016_76767,HTA4_2016_76768,HTA4_2004_76679,HTA4_2004_76680,HTA4_2004_76681', 'See paper methods', 'syn51406640', 'e470fd06-242b-4454-96e0-6a06cd74581c', 'HTA4_000_86668', 'ScATAC-seqLevel4', 'Seurat', 'RData', 'Seurat v4', 'HTAN CHOP', 'syn53253226', 6, 13836652353, '13e3a1585f3eab0fba9dc9eb7bbce7bf', 'Release 5.0', NULL), ('https://satijalab.org/seurat/', 'single_cell_ATACseq_level_4_NBL/seurat_atac_malignant_withTransferLabels.rds', 'HTA4_1004_73337', 'See paper Methods', 'syn53335811', '1a2c7f25-924e-406d-982e-c2bd535fcb13', 'HTA4_000_83337', 'ScATAC-seqLevel4', 'Seurat', 'RData', 'Seurat v4', 'HTAN CHOP', 'syn53398038', 2, 4581882685, '5b54e841c49410dca26cae14b6a7af4e', 'Release 5.0', NULL), ('https://satijalab.org/seurat/', 'single_cell_ATACseq_level_4_NBL/seurat_atac_non_binary_vap20000.rds', 'HTA4_1004_73337', 'See paper Methods', 'syn51690871', '9e4c89a0-d0a8-4bec-ac6e-eb83f1d7afcb', 'HTA4_000_83338', 'ScATAC-seqLevel4', 'Seurat', 'RData', 'Seurat v4', 'HTAN CHOP', 'syn53398038', 2, 33737403285, 'f1630f81e8865bb578a04f34d303db0c', 'Release 5.0', NULL), ('https://satijalab.org/seurat/', 'single_cell_ATACseq_level_4_NBL/seurat_atac_signac_byPatient_cellTypeAnnotated.rds', 'HTA4_1004_73337', 'See paper Methods', 'syn53335800', '5272d932-5e8e-4dc2-857e-7e74862a6bb7', 'HTA4_000_83339', 'ScATAC-seqLevel4', 'Seurat', 'RData', 'Seurat v4', 'HTAN CHOP', 'syn53398038', 2, 17836739912, '498bcdbc8e822224b2bb47477a7405c2', 'Release 5.0', NULL);