I can't access the database schema of the reactome.db package:
> library("reactome.db") > reactome_dbschema() Warning messages: 1: In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former 2: In max(ii) : no non-missing arguments to max; returning -Inf > reactome_dbschema(show.indices=TRUE) Warning message: In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former #I found the following schema, but I can't read it > reactome_dbschema("R/x86_64-pc-linux-gnu-library/3.3/reactome.db/DBschemas/schemas_1.0/REACTOME_DB.sql") Warning messages: 1: In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former 2: In max(ii) : no non-missing arguments to max; returning -Inf # And it doesn't seem to be up to date: > con <- reactome_dbconn() > query <- "SELECT COUNT(DISTINCT reactome_id) AS total_react FROM pathway2gene" > res <- dbGetQuery(con, query) Error in rsqlite_send_query(conn@ptr, statement) : no such column: reactome_id # I could retrieve the actual schema by using the following: > a <- dbGetQuery(con, "select * from sqlite_master") # Which shows that the name of the columns has changed > a[a$name == "pathway2gene", ] type name tbl_name rootpage 761 table pathway2gene pathway2gene 2173887 sql 761 CREATE TABLE pathway2gene (\n DB_ID VARCHAR(10) NOT NULL, -- Reactome DB_ID\n gene_id VARCHAR(10) NOT NULL -- Entrez Gene\n) > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=es_ES.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] reactome.db_1.58.0 AnnotationDbi_1.36.1 IRanges_2.8.1 [4] S4Vectors_0.12.1 Biobase_2.34.0 BiocGenerics_0.20.0 [7] BiocInstaller_1.24.0 loaded via a namespace (and not attached): [1] DBI_0.5-1 tools_3.3.2 memoise_1.0.0 Rcpp_0.12.9 RSQLite_1.1-2 [6] digest_0.6.11