Query Examples

Querying datasets in GEO OmixAtlas

1. To identify datasets belonging to the tissue Breast, disease Breast Neoplasms and organism Homo sapiens

       query = """SELECT * FROM geo.datasets
                           WHERE CONTAINS(curated_disease, 'Breast Neoplasms')
                           AND CONTAINS(curated_tissue, 'Breast')
                           AND CONTAINS(curated_organism, 'Homo sapiens')
                           """
   

2. Fetch datasets from Depmap which has gene dependency information according to CRISPR screening experiments

       query = """ SELECT dataset_id FROM depmap.datasets
       WHERE
           data_type = 'Gene dependency' AND
           data_repository_version = '2021_Q4' AND
           platform = 'CRISPR Screening'"""
   

3. Identify all transcriptome datasets in Hepatocellular Carcinoma disease in Human and Mouse

       query = """SELECT * FROM geo.datasets
                           WHERE CONTAINS(curated_disease, 'Carcinoma, Hepatocellular')
                           AND (CONTAINS(curated_organism, 'Homo sapiens' OR CONTAINS(curated_organism, 'Mus musculus')
                           AND data_type LIKE '%Transcriptomics%')
                     """
   

Querying samples in GEO OmixAtlas

1. Get the name of samples, dataset ID and extract_protocol_ch1 where spectroscopy is mentioned in the extract_protocol_ch1

       query = """SELECT name, src_dataset_id, extract_protocol_ch1 FROM geo.samples
        WHERE LOWER(extract_protocol_ch1) LIKE '%spectroscopy%'"""
   

2. IGet the name of disease and number of samples where information about particular disease is curated

       query = """SELECT curated_disease, COUNT(*) AS count FROM geo.samples 
       GROUP BY curated_disease ORDER BY count DESC """
   

Querying data matrix in GEO OmixAtlas

1. Fetch data matrix for selected genes for a dataset ID of interest

       gene = ('hbb-y', 'fth1', 'bbip1', 'actb')
       query = f"SELECT * FROM data_matrices.geo__GSE4230_GPL1261 WHERE 
       LOWER(rid) IN {gene}"
   

Other Query Examples

1. Select a few feature level metadata for selected genes from Mutation datasets of TCGA where dataset_id contains BRCA

   query = """SELECT src_dataset_id, disease, protein_position, amino_acids, sequencer, impact, variant_class, consequence, name
       FROM tcga.features AS features
       JOIN (
       SELECT dataset_id AS dataset_id, curated_disease AS disease FROM tcga.datasets WHERE data_type LIKE 'Mutation') AS datasets
       ON features.src_dataset_id = datasets.dataset_id
       WHERE hugo_symbol IN ('TP53','PIK3CA','CDH1','GATA3') AND features.src_dataset_id LIKE '%BRCA%'
       ORDER BY features.src_dataset_id"""
   

Tutorial Notebooks

Example queries have been given in various notebooks in this github folder.