-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.rppa_level2_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"),
  HTAN_RPPA_Antibody_Table STRING OPTIONS(description="A table containing antibody level metadata for RPPA"),
  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."),
  Protocol_Link STRING OPTIONS(description="Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration,  lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated."),
  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 2 R5 VERSIONED",
  description="This table contains the file metadata for second level Reverse Phase Protein Array (RPPA) assays. Level 2 RPPA datasets have files containing dilution curve fitted spot 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_level2_metadata_r5` (HTAN_Parent_Biospecimen_ID, Filename, HTAN_Parent_Data_File_ID, HTAN_RPPA_Antibody_Table, entityId, Id, HTAN_Data_File_ID, Assay_Type, Component, Protocol_Link, Software_and_Version, File_Format, HTAN_Participant_ID, HTAN_Center, Manifest_Id, Manifest_Version, File_Size, md5, Data_Release, CDS_Release) VALUES ('HTA9_13_35', 'rppa_level_2/RPPA_320184_L2.csv', 'HTA9_13_35', 'MDACC_RPPA_Ab_List_Set 175.xlsx', 'syn53213303', 'af419a85-831d-4f50-a9b3-71ae6b90cf10', 'HTA9_13_1021', 'RPPA level2', 'RPPALevel2', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887; doi: 10.1093/bioinformatics/btac665', ' RPPA SPACE was the method used to fit the data to generate raw log2 data;  doi: 10.1093/bioinformatics/btac665', 'csv', 'HTA9_13', 'HTAN OHSU', 'syn53242349', 6, 7864, '4fe7cbee0aea22c2939e8f602f61a1a3', 'Release 5.0', NULL), ('HTA9_13_36', 'rppa_level_2/RPPA_320211_L2.csv', 'HTA9_13_36', 'MDACC_RPPA_Ab_List_Set 175.xlsx', 'syn53213305', 'a68fbf04-7b5a-44a6-9d1b-b70be9269932', 'HTA9_13_1022', 'RPPA level2', 'RPPALevel2', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887; doi: 10.1093/bioinformatics/btac665', ' RPPA SPACE was the method used to fit the data to generate raw log2 data;  doi: 10.1093/bioinformatics/btac665', 'csv', 'HTA9_13', 'HTAN OHSU', 'syn53242349', 6, 7615, 'bd2feed53b167b4ae0d329f161f7941e', 'Release 5.0', NULL), ('HTA9_3_76', 'rppa_level_2/RPPA_272842_L2.csv', 'HTA9_3_76', 'MDACC_RPPA_Ab_List_Set 170-171.xlsx', 'syn53213310', 'f1525fc1-0e3e-4568-b37f-8ea06196e491', 'HTA9_3_16589', 'RPPA level2', 'RPPALevel2', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887; doi: 10.1093/bioinformatics/btac665', ' RPPA SPACE was the method used to fit the data to generate raw log2 data;  doi: 10.1093/bioinformatics/btac665', 'csv', 'HTA9_3', 'HTAN OHSU', 'syn53242349', 6, 7756, '9dca9c9edfae371172f1488cdb0e9554', 'Release 5.0', NULL), ('HTA9_7_45', 'rppa_level_2/RPPA_303010_L2.csv', 'HTA9_7_45', 'MDACC_RPPA_Ab_List_Set 170-171.xlsx', 'syn53213298', '30fd0f1d-f17d-4e2f-b230-9d5b89803bd5', 'HTA9_7_1019', 'RPPA level2', 'RPPALevel2', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887; doi: 10.1093/bioinformatics/btac665', ' RPPA SPACE was the method used to fit the data to generate raw log2 data;  doi: 10.1093/bioinformatics/btac665', 'csv', 'HTA9_7', 'HTAN OHSU', 'syn53242349', 6, 7826, '518c3582579010a63c410d2fd7bae0a8', 'Release 5.0', NULL), ('HTA9_7_46', 'rppa_level_2/RPPA_303164_L2.csv', 'HTA9_7_46', 'MDACC_RPPA_Ab_List_Set 170-171.xlsx', 'syn53213293', 'd1106d74-0769-4515-9433-b9da737c97ef', 'HTA9_7_1020', 'RPPA level2', 'RPPALevel2', 'https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html; DOI: 10.1038/ncomms4887; doi: 10.1093/bioinformatics/btac665', ' RPPA SPACE was the method used to fit the data to generate raw log2 data;  doi: 10.1093/bioinformatics/btac665', 'csv', 'HTA9_7', 'HTAN OHSU', 'syn53242349', 6, 7820, 'c6eb3378bc5db412852e17bdfb43976b', 'Release 5.0', NULL);