-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.HTAN_versioned.scRNAseq_MSK_immune_cells_r3`
(
  iObs INT64 OPTIONS(description="Index to cell barcodes"),
  iVar INT64 OPTIONS(description="Index to gene IDs"),
  X_value FLOAT64 OPTIONS(description="Expression value for a given gene and cell"),
  n_genes_by_counts INT64 OPTIONS(description="Number of genes detected in a given cell"),
  log1p_n_genes_by_counts FLOAT64 OPTIONS(description="Log (N+1) on the number of genes"),
  total_counts FLOAT64 OPTIONS(description="Total number of gene expression counts (or UMIs mapped) for a given cell"),
  log1p_total_counts FLOAT64 OPTIONS(description="Log (N+1) on the number of gene expression counts (UMIs mapped) for a given cell"),
  mito_frac FLOAT64 OPTIONS(description="Percent of UMIs mapping to mitochondrial genes"),
  RBP_frac FLOAT64 OPTIONS(description="Percent of UMIs mapping to RNA-binding proteins (RBPs)."),
  batch STRING OPTIONS(description="Sample ID"),
  donor_id STRING OPTIONS(description="Identifies a unique individual that data were derived from"),
  treatment STRING OPTIONS(description="The type of treatment recieved by the patient"),
  procedure STRING OPTIONS(description="The method used in sampling the tumor, Biopsy or Resection"),
  histo STRING OPTIONS(description="Histological cancer type"),
  histology_subtype STRING OPTIONS(description="Lung cancer subtype (values: SCLC-A; LUAD; SCLC-P; normal; SCLC-N)"),
  author_cell_type STRING OPTIONS(description="Cell type"),
  clusters STRING OPTIONS(description="Cluster labels assigned to each cell"),
  clusters_fine STRING OPTIONS(description="Sub-cluster labels assigned to each cell"),
  tissue_ontology_term_id STRING OPTIONS(description="Uber-anatomy ontology ID (REF: https://www.ebi.ac.uk/ols/ontologies/uberon) (ex.UBERON:2001190)"),
  disease_ontology_term_id STRING OPTIONS(description="MONDO disease ontology ID (REF: https://www.ebi.ac.uk/ols/ontologies/mondo) (ex. MONDO:0100426 or PATO:0000461 for 'normal')"),
  cell_type_ontology_term_id STRING OPTIONS(description="Cell Ontology ID (i.e. CL:0000784)  (REF: https://www.ebi.ac.uk/ols/ontologies/cl)"),
  organism_ontology_term_id STRING OPTIONS(description="NCBITaxon ID (REF: https://www.ncbi.nlm.nih.gov/taxonomy) (ex. NCBITaxon:9606 for human, NCBITaxon:10090 for mouse)"),
  is_primary_data BOOL OPTIONS(description="Indicates if the sample is primary or not (True/False)"),
  development_stage_ontology_term_id STRING OPTIONS(description="Human Developmental Stages ID (REF: https://www.ebi.ac.uk/ols/ontologies/hsapdv) or Mouse Developmental Stages ID (REF: https://www.ebi.ac.uk/ols/ontologies/mmusdv) (HsapDv if human, MmusDv if mouse, unknown if information unavailable)"),
  assay_ontology_term_id STRING OPTIONS(description="Experimental Factor Ontology ID (REF: https://www.ebi.ac.uk/ols/ontologies/efo)"),
  sex_ontology_term_id STRING OPTIONS(description="Phenotype And Trait Ontology ID, PATO:0000384 for male, PATO:0000383 for female, or unknown if unavailable"),
  self_reported_ethnicity_ontology_term_id STRING OPTIONS(description="If human, the Human Ancestry Ontology ID (i.e. HANCESTRO:0005) (REF: https://www.ebi.ac.uk/ols/ontologies/hancestro); \"multiethnic\" if more than one ethnicity. \"Unknown\" if human and no information, else \"na\" if non-human"),
  suspension_type STRING OPTIONS(description="Cell, nucleus, or na, as corresponding to sample preparation"),
  HTAN_Biospecimen_ID STRING OPTIONS(description="HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)"),
  HTAN_Participant_ID STRING OPTIONS(description="HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )"),
  cell_type STRING OPTIONS(description="The type of cell (i.e. T-cell)"),
  assay STRING OPTIONS(description="An assay based on 10X Genomics. Example : 100x3’ v2"),
  disease STRING OPTIONS(description="Description of disease (example: lung adenocarcinoma) or normal cells"),
  organism STRING OPTIONS(description="The genus and species from which biosamples are derived"),
  sex STRING OPTIONS(description="Phenotypic sex"),
  tissue STRING OPTIONS(description="Derived from UBERON or CL terms that best describes the tissue that the cell was derived from."),
  self_reported_ethnicity STRING OPTIONS(description="Ethnicity of the individual (obtained from HANCESTRO terms for Homo sapiens)"),
  development_stage STRING OPTIONS(description="Human development stage derived from HsapDv term  (Example if data is Homo sapiens, development stage is obtained from Link. HsapDv:0000114 - 20-year-old human stage)"),
  feature_is_filtered BOOL OPTIONS(description="Indicates if the feature (gene) was/should be filtered in analysis"),
  feature_name STRING OPTIONS(description="Gene name from HUGO Human Gene Nomenclature Committee (https://www.genenames.org/)"),
  feature_reference STRING OPTIONS(description="A reference to the feature: NCBI Taxonomy ID"),
  feature_biotype STRING OPTIONS(description="Biological type of feature (e.g. gene)")
)
OPTIONS(
  friendly_name="MSK IMMUNE CELLS R3 VERSIONED",
  description="Data was derived in April 2023 from an H5AD file (Synapse ID: syn51298602) submitted by the MSK HTAN Center. This dataset is subsetted from the combined dataset based on cluster-based PTPRC (CD45) positivity. It contains both raw gene expression counts and log2(X+1) transformed, median-normalized expression (N=73,047 cells).",
  labels=[("access", "open"), ("reference_genome", "hg38"), ("data_type", "gene_expression"), ("program", "htan"), ("source", "htan-msk"), ("category", "processed_-omics_data"), ("status", "current")]
);

INSERT INTO `isb-cgc-bq.HTAN_versioned.scRNAseq_MSK_immune_cells_r3` (iObs, iVar, X_value, n_genes_by_counts, log1p_n_genes_by_counts, total_counts, log1p_total_counts, mito_frac, RBP_frac, batch, donor_id, treatment, procedure, histo, histology_subtype, author_cell_type, clusters, clusters_fine, tissue_ontology_term_id, disease_ontology_term_id, cell_type_ontology_term_id, organism_ontology_term_id, is_primary_data, development_stage_ontology_term_id, assay_ontology_term_id, sex_ontology_term_id, self_reported_ethnicity_ontology_term_id, suspension_type, HTAN_Biospecimen_ID, HTAN_Participant_ID, cell_type, assay, disease, organism, sex, tissue, self_reported_ethnicity, development_stage, feature_is_filtered, feature_name, feature_reference, feature_biotype) VALUES (27786, 3662, 3.51444149017334, 1143, 7.042286171939743, 1918.0, 7.559559345245361, 0.02669404447078705, 0.25804242491722107, 'RU1038_Sort-Freeze', 'RU1038', 'Naive', 'Resection', 'LUAD', 'LUAD', 'NK', '8', '10', 'UBERON:0002048', 'MONDO:0005061', 'CL:0000623', 'NCBITaxon:9606', False, 'HsapDv:0000210', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'cell', 'HTA8_1001_1', 'HTA8_1001', 'natural killer cell', '10x 3'' v2', 'lung adenocarcinoma', 'Homo sapiens', 'female', 'lung', 'European', '84-year-old human stage', False, 'CIB1', 'NCBITaxon:9606', 'gene'), (29552, 3662, 2.563546657562256, 1031, 6.939253946041508, 2036.0, 7.61923360824585, 0.03585657477378845, 0.21115538477897644, 'RU1038_Sort-Freeze', 'RU1038', 'Naive', 'Resection', 'LUAD', 'LUAD', 'NK', '32', '42', 'UBERON:0002048', 'MONDO:0005061', 'CL:0000623', 'NCBITaxon:9606', False, 'HsapDv:0000210', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'cell', 'HTA8_1001_1', 'HTA8_1001', 'natural killer cell', '10x 3'' v2', 'lung adenocarcinoma', 'Homo sapiens', 'female', 'lung', 'European', '84-year-old human stage', False, 'CIB1', 'NCBITaxon:9606', 'gene'), (33048, 3662, 3.5394060611724854, 979, 6.887552571664617, 1882.0, 7.540621757507324, 0.032830189913511276, 0.17886792123317719, 'RU1038_Sort-Freeze', 'RU1038', 'Naive', 'Resection', 'LUAD', 'LUAD', 'NK', '37', '42', 'UBERON:0002048', 'MONDO:0005061', 'CL:0000623', 'NCBITaxon:9606', False, 'HsapDv:0000210', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'cell', 'HTA8_1001_1', 'HTA8_1001', 'natural killer cell', '10x 3'' v2', 'lung adenocarcinoma', 'Homo sapiens', 'female', 'lung', 'European', '84-year-old human stage', False, 'CIB1', 'NCBITaxon:9606', 'gene'), (50300, 3662, 3.0944857597351074, 844, 6.739336627357174, 1326.0, 7.190676212310791, 0.03113648109138012, 0.1172807440161705, 'RU1038_Sort-Freeze', 'RU1038', 'Naive', 'Resection', 'LUAD', 'LUAD', 'NK', '37', '8', 'UBERON:0002048', 'MONDO:0005061', 'CL:0000623', 'NCBITaxon:9606', False, 'HsapDv:0000210', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'cell', 'HTA8_1001_1', 'HTA8_1001', 'natural killer cell', '10x 3'' v2', 'lung adenocarcinoma', 'Homo sapiens', 'female', 'lung', 'European', '84-year-old human stage', False, 'CIB1', 'NCBITaxon:9606', 'gene'), (55387, 3662, 2.6978793144226074, 1095, 6.999422467507961, 1822.0, 7.508238792419434, 0.04096204414963722, 0.1638481765985489, 'RU1038_Sort-Freeze', 'RU1038', 'Naive', 'Resection', 'LUAD', 'LUAD', 'NK', '37', '38', 'UBERON:0002048', 'MONDO:0005061', 'CL:0000623', 'NCBITaxon:9606', False, 'HsapDv:0000210', 'EFO:0009899', 'PATO:0000383', 'HANCESTRO:0005', 'cell', 'HTA8_1001_1', 'HTA8_1001', 'natural killer cell', '10x 3'' v2', 'lung adenocarcinoma', 'Homo sapiens', 'female', 'lung', 'European', '84-year-old human stage', False, 'CIB1', 'NCBITaxon:9606', 'gene');