return a SQLite connection (read only) to an INCAtools Semantic SQL ontology

Usage

retrieve_semsql_conn(
  ontology = "efo",
  cache = BiocFileCache::BiocFileCache(),
  cacheid = NULL,
  ...
)

Arguments

ontology: character(1) short string prefixing .db.gz in the INCAtools collection
cache: a BiocFileCache instance, defaulting to BiocFileCache::BiocFileCache()
cacheid: character(1) or NULL; if non-null, the associated SQLite resource will be used from cache
...: passed to download.file

Value

an RSQLite DBI connection instance

Note

When the cache is searched, the string given as 'ontology' will be prefixed with '^'. This helps avoid confusion between pcl.db and cl.db, for example.

Examples

# first time will involve a download and decompression
aionto = retrieve_semsql_conn("aio")
head(DBI::dbListTables(aionto))
#> [1] "all_problems"                    "annotation_property_node"       
#> [3] "anonymous_class_expression"      "anonymous_expression"           
#> [5] "anonymous_individual_expression" "anonymous_property_expression"  
dplyr::tbl(aionto, "class_node") |> head() 
#> # Source:   SQL [?? x 1]
#> # Database: sqlite 3.51.2 [/Users/vincentcarey/Library/Caches/org.R-project.R/R/BiocFileCache/4561637cb3e4_aio.db]
#>   id                             
#>   <chr>                          
#> 1 aio:AbstractRNNCell            
#> 2 aio:ActivationLayer            
#> 3 aio:ActiveLearning             
#> 4 aio:ActivityBias               
#> 5 aio:ActivityRegularizationLayer
#> 6 aio:AdaptiveAvgPool1DLayer