{"database": "WtMTA", "private": false, "path": "/WtMTA-4fd108c", "size": 52227317760, "tables": [{"name": "genomes", "columns": ["taxonomy_id", "species", "family", "order", "phylum", "accession", "n_minor_introns", "n_major_introns", "percent_minor_introns", "busco_score", "minor_snRNAs", "genome_version", "source_url", "source_metadata", "minor_intron+"], "primary_keys": ["taxonomy_id"], "count": 1575, "hidden": false, "fts_table": "genomes_fts", "foreign_keys": {"incoming": [{"other_table": "introns", "column": "taxonomy_id", "other_column": "taxonomy_id"}, {"other_table": "transcripts", "column": "taxonomy_id", "other_column": "taxonomy_id"}], "outgoing": []}, "private": false}, {"name": "introns", "columns": ["id", "dinucleotide_pair", "is_minor", "score", "length", "transcript_id", "ordinal_index", "start", "end", "taxonomy_id", "scored_motifs", "phase", "in_cds", "relative_position"], "primary_keys": ["id"], "count": 214855132, "hidden": false, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": [{"other_table": "genomes", "column": "taxonomy_id", "other_column": "taxonomy_id"}, {"other_table": "transcripts", "column": "transcript_id", "other_column": "id"}]}, "private": false}, {"name": "transcripts", "columns": ["id", "taxonomy_id", "transcript_id", "gene_id", "chromosome", "strand", "start", "end", "coding_length", "introns_per_kbp_cds", "proportion_minor_introns", "n_introns", "n_minor_introns"], "primary_keys": ["id"], "count": 38837229, "hidden": false, "fts_table": "transcripts_fts", "foreign_keys": {"incoming": [{"other_table": "introns", "column": "id", "other_column": "transcript_id"}], "outgoing": [{"other_table": "genomes", "column": "taxonomy_id", "other_column": "taxonomy_id"}]}, "private": false}, {"name": "genomes_fts", "columns": ["species", "source_metadata", "phylum", "order", "family", "genomes_fts", "rank"], "primary_keys": [], "count": 1575, "hidden": true, "fts_table": "genomes_fts", "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts_config", "columns": ["k", "v"], "primary_keys": ["k"], "count": 1, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts_data", "columns": ["id", "block"], "primary_keys": ["id"], "count": 126, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts_docsize", "columns": ["id", "sz"], "primary_keys": ["id"], "count": 1575, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "genomes_fts_idx", "columns": ["segid", "term", "pgno"], "primary_keys": ["segid", "term"], "count": 104, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "sqlite_stat1", "columns": ["tbl", "idx", "stat"], "primary_keys": [], "count": 21, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts", "columns": ["transcript_id", "gene_id", "transcripts_fts", "rank"], "primary_keys": [], "count": null, "hidden": true, "fts_table": "transcripts_fts", "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts_config", "columns": ["k", "v"], "primary_keys": ["k"], "count": 1, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts_data", "columns": ["id", "block"], "primary_keys": ["id"], "count": 325698, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts_docsize", "columns": ["id", "sz"], "primary_keys": ["id"], "count": 38837229, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}, {"name": "transcripts_fts_idx", "columns": ["segid", "term", "pgno"], "primary_keys": ["segid", "term"], "count": 221798, "hidden": true, "fts_table": null, "foreign_keys": {"incoming": [], "outgoing": []}, "private": false}], "hidden_count": 11, "views": [], "queries": [{"params": ["species", "min_score", "max_score"], "sql": "select\n  t.chromosome,\n  i.start,\n  i.\"end\",\n  i.id,\n  i.score,\n  t.strand\nfrom\n  introns i\n  JOIN transcripts t ON i.transcript_id = t.id\n  JOIN genomes g ON i.taxonomy_id = g.taxonomy_id\nwhere\n  g.taxonomy_id = (\n    select taxonomy_id from genomes\n    where\n      CASE\n        WHEN CAST(:species AS INTEGER) > 0 AND CAST(:species AS TEXT) = :species\n        THEN taxonomy_id = CAST(:species AS INTEGER)\n        ELSE species LIKE '%' || :species || '%'\n      END\n    limit 1\n  )\n  and (\n    select count(distinct taxonomy_id) from genomes\n    where\n      CASE\n        WHEN CAST(:species AS INTEGER) > 0 AND CAST(:species AS TEXT) = :species\n        THEN taxonomy_id = CAST(:species AS INTEGER)\n        ELSE species LIKE '%' || :species || '%'\n      END\n  ) = 1\n  and i.score > :min_score\n  and i.score <= :max_score\norder by\n  t.chromosome, i.start", "title": "BED-formatted introns", "description": "Retrieve introns for a single species in BED format. The species parameter accepts a taxonomy ID (e.g. \"9606\") or a partial species name (e.g. \"Homo sapiens\" or \"sapiens\"), but must match exactly one species or no rows are returned. For minor introns, use min_score=90 and max_score=100.", "name": "bed_format", "private": false}, {"params": ["search"], "sql": "select species, taxonomy_id\nfrom genomes\nwhere species LIKE '%' || :search || '%'\norder by species", "title": "Search species", "description": "Search for species by partial name. Returns matching species names and taxonomy IDs.", "name": "species_search", "private": false}, {"sql": "select species, taxonomy_id\nfrom genomes\norder by species", "title": "Species names <--> taxonomy IDs", "description": "List all species names and taxonomy IDs.", "name": "species_list", "private": false}], "allow_execute_sql": true, "query_ms": 31.99834600673057, "source": "Larue & Roy, 2023", "source_url": "https://doi.org/10.1093/nar/gkad797", "license": "ODbL", "license_url": "https://opendatacommons.org/licenses/odbl/"}