-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.CPTAC.quant_proteome_CPTAC_LSCC_discovery_study_pdc_current`
(
  case_id STRING OPTIONS(description="Unique identifier associated with a specific patient (e.g. 24cb0fcb-63d6-11e8-bcf1-0a2705229b82)"),
  sample_id STRING OPTIONS(description="Unique PDC identifier for this sample (e.g. e8d83eb9-693a-11ea-b1fd-0aad30af8a83)"),
  aliquot_id STRING OPTIONS(description="Unique PDC identifier for this aliquot (e.g. e8db124a-693a-11ea-b1fd-0aad30af8a83)"),
  aliquot_submitter_id STRING OPTIONS(description="Aliquot submitter id assigned by program (e.g. T14)"),
  aliquot_run_metadata_id STRING OPTIONS(description="Uniquely identifies the aliquot by how it was used in the experiment (based on the labelling reagent and/or biological replicate)"),
  study_name STRING OPTIONS(description="Name of the study (e.g. Pediatric Brain Cancer Pilot Study - Phosphoproteome)"),
  protein_abundance_log2ratio FLOAT64 OPTIONS(description="Average log-ratio of sample reporter-ion to common reference of peptide ions associated with the gene in acquisitions from a specific biological sample"),
  gene_id STRING OPTIONS(description="Unique gene identifier assigned by PDC"),
  gene_symbol STRING OPTIONS(description="Gene symbol, sourced by PDC from NCBI"),
  NCBI_gene_id STRING OPTIONS(description="NCBI gene identifier"),
  authority STRING OPTIONS(description="Designating authority for the gene id"),
  authority_gene_id STRING OPTIONS(description="Unique identifier assigned by authority (e.g. HGNC)"),
  gene_description STRING OPTIONS(description="Description of the gene, sourced by PDC from NCBI"),
  organism STRING OPTIONS(description="Gene organism, sourced by PDC from NCBI"),
  chromosome STRING OPTIONS(description="NCBI gene chromosome"),
  locus STRING OPTIONS(description="Gene cytoband, sourced by PDC from NCBI"),
  uniprotkb_id STRING OPTIONS(description="Oldest UniProt id found in 'proteins' column list, derived programmatically"),
  uniprotkb_ids STRING OPTIONS(description="Every UniProt id found in 'proteins' column list"),
  proteins STRING OPTIONS(description="Semi-colon separated list of protein accessions associated with the gene; includes identifiers from multiple sources (e.g. UniProt, NCBI RefSeq database)"),
  assays STRING OPTIONS(description="CPTAC Assay accessions for the peptides associated with the gene")
)
OPTIONS(
  friendly_name="CPTAC3-DISCOVERY LUNG SQUAMOUS CELL CARCINOMA (LSCC) PROTEOME",
  description="Normalized log2ratio protein abundance estimates for the CPTAC LSCC Discovery Study - Proteome study (PDC Study ID: PDC000234) was extracted using PDC API V2.16 in February 2023. These data are part of the CPTAC project. More information on the pipeline and the results generated by it can be found here: https://pdc.cancer.gov/data-dictionary/harmonization.html",
  labels=[("access", "open"), ("data_type", "protein_expression"), ("source", "pdc"), ("program", "cptac3"), ("category", "processed_-omics_data"), ("status", "current"), ("version", "v2_16")]
);

INSERT INTO `isb-cgc-bq.CPTAC.quant_proteome_CPTAC_LSCC_discovery_study_pdc_current` (case_id, sample_id, aliquot_id, aliquot_submitter_id, aliquot_run_metadata_id, study_name, protein_abundance_log2ratio, gene_id, gene_symbol, NCBI_gene_id, authority, authority_gene_id, gene_description, organism, chromosome, locus, uniprotkb_id, uniprotkb_ids, proteins, assays) VALUES ('1c6415e2-d028-11ea-b1fd-0aad30af8a83', '1c651f93-d028-11ea-b1fd-0aad30af8a83', '1c669cae-d028-11ea-b1fd-0aad30af8a83', 'CPT0111000004', '424bca76-d0fd-11ea-b1fd-0aad30af8a83', 'CPTAC LSCC Discovery Study - Proteome', -0.6605, 'f727e28b-b814-11e8-907f-0a2705229b82', 'ATP6', '4508', 'HGNC', '7414', 'ATP synthase F0 subunit 6', 'Homo sapiens', 'MT', '-', 'P00846', 'P00846', 'P00846;YP_003024031.1', NULL), ('1c643c43-d028-11ea-b1fd-0aad30af8a83', '1c657473-d028-11ea-b1fd-0aad30af8a83', '1c66f20c-d028-11ea-b1fd-0aad30af8a83', 'CPT0241210003', '424bd19d-d0fd-11ea-b1fd-0aad30af8a83', 'CPTAC LSCC Discovery Study - Proteome', 0.0927, 'f727e28b-b814-11e8-907f-0a2705229b82', 'ATP6', '4508', 'HGNC', '7414', 'ATP synthase F0 subunit 6', 'Homo sapiens', 'MT', '-', 'P00846', 'P00846', 'P00846;YP_003024031.1', NULL), ('1c643ee9-d028-11ea-b1fd-0aad30af8a83', '1c657bcd-d028-11ea-b1fd-0aad30af8a83', '1c66f9e8-d028-11ea-b1fd-0aad30af8a83', 'CPT0234930004', '424ba538-d0fd-11ea-b1fd-0aad30af8a83', 'CPTAC LSCC Discovery Study - Proteome', 0.721, 'f727e28b-b814-11e8-907f-0a2705229b82', 'ATP6', '4508', 'HGNC', '7414', 'ATP synthase F0 subunit 6', 'Homo sapiens', 'MT', '-', 'P00846', 'P00846', 'P00846;YP_003024031.1', NULL), ('1c63f6e1-d028-11ea-b1fd-0aad30af8a83', '1c64db9d-d028-11ea-b1fd-0aad30af8a83', '1c66633f-d028-11ea-b1fd-0aad30af8a83', 'CPT0205000003', '424bcf68-d0fd-11ea-b1fd-0aad30af8a83', 'CPTAC LSCC Discovery Study - Proteome', 0.0343, 'f727e28b-b814-11e8-907f-0a2705229b82', 'ATP6', '4508', 'HGNC', '7414', 'ATP synthase F0 subunit 6', 'Homo sapiens', 'MT', '-', 'P00846', 'P00846', 'P00846;YP_003024031.1', NULL), ('1c642ffd-d028-11ea-b1fd-0aad30af8a83', '1c6554e4-d028-11ea-b1fd-0aad30af8a83', '1c66d16d-d028-11ea-b1fd-0aad30af8a83', 'CPT0186130003', '424bca04-d0fd-11ea-b1fd-0aad30af8a83', 'CPTAC LSCC Discovery Study - Proteome', -0.3559, 'f727e28b-b814-11e8-907f-0a2705229b82', 'ATP6', '4508', 'HGNC', '7414', 'ATP synthase F0 subunit 6', 'Homo sapiens', 'MT', '-', 'P00846', 'P00846', 'P00846;YP_003024031.1', NULL);