-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.rppa_level3_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"),
  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"),
  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)"),
  Assay_Type STRING OPTIONS(description="The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)"),
  Component STRING OPTIONS(description="Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows."),
  Normalization_Method STRING OPTIONS(description="Description of Normalization Process"),
  Software_and_Version STRING OPTIONS(description="Name of software used to generate expression values. String"),
  File_Format STRING OPTIONS(description="Format of a file (e.g. txt, csv, fastq, bam, etc.)"),
  HTAN_Participant_ID STRING OPTIONS(description="HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )"),
  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 RPPA METADATA LEVEL 3 R5 VERSIONED",
  description="This table contains the file metadata for third level Reverse Phase Protein Array (RPPA) assays. Level 3 RPPA datasets have files that contain intra-batch normalized intensities. 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/standards",
  labels=[("access", "open"), ("data_type", "file_metadata"), ("program", "htan"), ("source", "htan"), ("category", "metadata"), ("status", "current")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.rppa_level3_metadata_r5` (HTAN_Parent_Biospecimen_ID, Filename, HTAN_Parent_Data_File_ID, entityId, Id, HTAN_Data_File_ID, Assay_Type, Component, Normalization_Method, Software_and_Version, File_Format, HTAN_Participant_ID, HTAN_Center, Manifest_Id, Manifest_Version, File_Size, md5, Data_Release, CDS_Release) VALUES ('HTA9_1_23', 'rppa_level_3/HTA9_1_23_Level3.txt', 'HTA9_1_1158', 'syn23639581', '263b6839-47d1-494c-9ccf-1ab6fea32752', 'HTA9_1_1160', 'RPPA', 'RPPALevel3', 'To generate the normalized log2 data, protein measurements were corrected for loading using bidirectional median centering across samples and antibodies; https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887', 'txt', 'HTA9_1', 'HTAN OHSU', 'syn53242447', 6, 7216, 'f4a58f80802a570c98bfc5bc3f107ca1', 'Release 5.0', NULL), ('HTA9_1_36', 'rppa_level_3/HTA9_1_36_Level3.txt', 'HTA9_1_1159', 'syn23639583', 'fccb143c-3c89-47a4-bb50-16cf00a76bc0', 'HTA9_1_1161', 'RPPA', 'RPPALevel3', 'To generate the normalized log2 data, protein measurements were corrected for loading using bidirectional median centering across samples and antibodies; https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887', 'txt', 'HTA9_1', 'HTAN OHSU', 'syn53242447', 6, 7270, '5e98b80dc4b15f723653083b9f9f838c', 'Release 5.0', NULL), ('HTA9_1_120', 'rppa_level_3/RPPA_322079_L3.csv', 'HTA9_1_40582', 'syn53241776', 'abea3f48-4b28-46f4-98f8-986005ad836e', 'HTA9_1_40584', 'RPPA', 'RPPALevel3', 'To generate the normalized log2 data, protein measurements were corrected for loading using bidirectional median centering across samples and antibodies; https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887', 'csv', 'HTA9_1', 'HTAN OHSU', 'syn53242447', 6, 12673, 'eb77cdd0a3a8c1d693b57e323fea27c5', 'Release 5.0', NULL), ('HTA9_1_161', 'rppa_level_3/RPPA_382866_L3.csv', 'HTA9_1_40583', 'syn53241785', 'e8c896c0-6c4a-4ece-aeb4-14eb1a599728', 'HTA9_1_40585', 'RPPA', 'RPPALevel3', 'To generate the normalized log2 data, protein measurements were corrected for loading using bidirectional median centering across samples and antibodies; https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887', 'csv', 'HTA9_1', 'HTAN OHSU', 'syn53242447', 6, 7344, '32aa3b6d480df3325d9c74c44123da5f', 'Release 5.0', NULL), ('HTA9_2_76', 'rppa_level_3/HTA9_2_76_RPPA_Level3.txt', 'HTA9_2_11959', 'syn53241730', '4b025559-04b8-4458-83fc-9732c82092ce', 'HTA9_2_11961', 'RPPA', 'RPPALevel3', 'To generate the normalized log2 data, protein measurements were corrected for loading using bidirectional median centering across samples and antibodies; https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887', 'txt', 'HTA9_2', 'HTAN OHSU', 'syn53242447', 6, 12496, 'a952ca73248b7fc04721bbbd5fef96c3', 'Release 5.0', NULL);