Collect information about the package annotation DB

Description

Some convenience functions for getting a connection object to (or collecting information about) the package annotation DB.

Usage

  org.Dm.eg_dbconn()
  org.Dm.eg_dbfile()
  org.Dm.eg_dbschema(file="", show.indices=FALSE)
  org.Dm.eg_dbInfo()

Arguments

Details

org.Dm.eg_dbconn returns a connection object to the package annotation DB. IMPORTANT: Don't call dbDisconnect on the connection object returned by org.Dm.eg_dbconn or you will break all the AnnDbObj objects defined in this package!

org.Dm.eg_dbfile returns the path (character string) to the package annotation DB (this is an SQLite file).

org.Dm.eg_dbschema prints the schema definition of the package annotation DB.

org.Dm.eg_dbInfo prints other information about the package annotation DB.

Value

org.Dm.eg_dbconn: a DBIConnection object representing an open connection to the package annotation DB.

org.Dm.eg_dbfile: a character string with the path to the package annotation DB.

org.Dm.eg_dbschema: none (invisible NULL).

org.Dm.eg_dbInfo: none (invisible NULL).

See Also

dbGetQuery, dbConnect, dbconn, dbfile, dbschema, dbInfo

Examples

  library(DBI)
  ## Count the number of rows in the "genes" table:
  dbGetQuery(org.Dm.eg_dbconn(), "SELECT COUNT(*) FROM genes")

  org.Dm.eg_dbschema()

  org.Dm.eg_dbInfo()

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(org.Dm.eg.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/org.Dm.eg.db/org.Dm.eg_dbconn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Dm.eg_dbconn
> ### Title: Collect information about the package annotation DB
> ### Aliases: org.Dm.eg_dbconn org.Dm.eg_dbfile org.Dm.eg_dbschema
> ###   org.Dm.eg_dbInfo
> ### Keywords: utilities datasets
> 
> ### ** Examples
> 
>   library(DBI)
>   ## Count the number of rows in the "genes" table:
>   dbGetQuery(org.Dm.eg_dbconn(), "SELECT COUNT(*) FROM genes")
  COUNT(*)
1    25074
> 
>   org.Dm.eg_dbschema()
CREATE TABLE metadata (name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) );
CREATE TABLE map_metadata (
      map_name VARCHAR(80) NOT NULL,
      source_name VARCHAR(80) NOT NULL,
      source_url VARCHAR(255) NOT NULL,
      source_date VARCHAR(20) NOT NULL
    );
CREATE TABLE map_counts (
      map_name VARCHAR(80) PRIMARY KEY,
      count INTEGER NOT NULL
    );
CREATE TABLE genes (
      _id INTEGER PRIMARY KEY,
      gene_id VARCHAR(10) NOT NULL UNIQUE           -- Entrez Gene ID
    );
CREATE TABLE sqlite_stat1(tbl,idx,stat);
CREATE TABLE gene_info (
      _id INTEGER NOT NULL UNIQUE,                  -- REFERENCES  genes 
      gene_name VARCHAR(255) NOT NULL,              -- gene name
      symbol VARCHAR(80) NOT NULL,                  -- gene symbol
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE chromosomes (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      chromosome VARCHAR(2) NOT NULL,               -- chromosome name
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE accessions (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      accession VARCHAR(20) NOT NULL,               -- GenBank accession number
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE cytogenetic_locations (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      cytogenetic_location VARCHAR(20) NOT NULL,    -- cytoband location
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE refseq (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      accession VARCHAR(20) NOT NULL,               -- RefSeq accession number
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE pubmed (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      pubmed_id VARCHAR(10) NOT NULL,               -- PubMed ID
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE unigene (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      unigene_id VARCHAR(10) NOT NULL,              -- UniGene ID
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE chrlengths (
      chromosome VARCHAR(2) PRIMARY KEY,                   -- chromosome name
      length INTEGER NOT NULL
    );
CREATE TABLE go_bp (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      go_id CHAR(10) NOT NULL,                      -- GO ID
      evidence CHAR(3) NOT NULL,                    -- GO evidence code
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE go_mf (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      go_id CHAR(10) NOT NULL,                      -- GO ID
      evidence CHAR(3) NOT NULL,                    -- GO evidence code
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE go_cc (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      go_id CHAR(10) NOT NULL,                      -- GO ID
      evidence CHAR(3) NOT NULL,                    -- GO evidence code
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE go_bp_all (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      go_id CHAR(10) NOT NULL,                      -- GO ID
      evidence CHAR(3) NOT NULL,                    -- GO evidence code
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE go_mf_all (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      go_id CHAR(10) NOT NULL,                      -- GO ID
      evidence CHAR(3) NOT NULL,                    -- GO evidence code
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE go_cc_all (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      go_id CHAR(10) NOT NULL,                      -- GO ID
      evidence CHAR(3) NOT NULL,                    -- GO evidence code
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE kegg (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      path_id CHAR(5) NOT NULL,                     -- KEGG pathway short ID
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE ec (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      ec_number VARCHAR(13) NOT NULL,               -- EC number 
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE chromosome_locations (
      _id INTEGER NOT NULL,                      -- REFERENCES  genes 
      seqname VARCHAR(20) NOT NULL,              -- sequence name
      start_location INTEGER NOT NULL,
      end_location INTEGER NOT NULL,
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE alias (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      alias_symbol VARCHAR(80) NOT NULL,            -- gene symbol or alias
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE ensembl (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      ensembl_id VARCHAR(20) NOT NULL,              -- ensembl id
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE ensembl_prot (
      _id INTEGER NOT NULL,                          -- REFERENCES  genes 
      prot_id VARCHAR(20) NOT NULL,                  -- Ensembl Protein ID
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE ensembl_trans (
      _id INTEGER NOT NULL,                          -- REFERENCES  genes 
      trans_id VARCHAR(20) NOT NULL,                  -- Ensembl Transcript ID
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE uniprot (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      uniprot_id VARCHAR(20) NOT NULL,              -- uniprot id
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE flybase (
      _id INTEGER NOT NULL,                         -- REFERENCES  genes 
      flybase_id VARCHAR(80) NOT NULL,              -- FlyBase ID
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE flybase_cg (
      _id INTEGER NOT NULL,                          -- REFERENCES  genes 
      flybase_cg_id VARCHAR(10) NOT NULL,            -- FlyBase CG ID
      FOREIGN KEY (_id) REFERENCES  genes  (_id)
    );
CREATE TABLE flybase_prot (
      _id INTEGER NOT NULL,                          -- REFERENCES  genes 
      prot_id VARCHAR(20) NOT NULL,                  -- Flybase Protein ID
      FOREIGN KEY (_id) REFERENCES  genes (_id)
    );

> 
>   org.Dm.eg_dbInfo()
                 name
1     DBSCHEMAVERSION
2             Db type
3  Supporting package
4            DBSCHEMA
5            ORGANISM
6             SPECIES
7        EGSOURCEDATE
8        EGSOURCENAME
9         EGSOURCEURL
10          CENTRALID
11              TAXID
12       GOSOURCENAME
13        GOSOURCEURL
14       GOSOURCEDATE
15     GOEGSOURCEDATE
16     GOEGSOURCENAME
17      GOEGSOURCEURL
18     KEGGSOURCENAME
19      KEGGSOURCEURL
20     KEGGSOURCEDATE
21       GPSOURCENAME
22        GPSOURCEURL
23       GPSOURCEDATE
24       FBSOURCEDATE
25       FBSOURCENAME
26        FBSOURCEURL
27       ENSOURCEDATE
28       ENSOURCENAME
29        ENSOURCEURL
                                                               value
1                                                                2.1
2                                                              OrgDb
3                                                      AnnotationDbi
4                                                             FLY_DB
5                                            Drosophila melanogaster
6                                                                Fly
7                                                         2016-Mar14
8                                                        Entrez Gene
9                               ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
10                                                                EG
11                                                              7227
12                                                     Gene Ontology
13 ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
14                                                          20160305
15                                                        2016-Mar14
16                                                       Entrez Gene
17                              ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
18                                                       KEGG GENOME
19                              ftp://ftp.genome.jp/pub/kegg/genomes
20                                                        2011-Mar15
21              UCSC Genome Bioinformatics (Drosophila melanogaster)
22                      ftp://hgdownload.cse.ucsc.edu/goldenPath/dm6
23                                                        2014-Dec12
24                                                        2016-Dec21
25                                                           Flybase
26   ftp://ftp.flybase.net/releases/current/precomputed_files/genes/
27                                                         2016-Mar9
28                                                           Ensembl
29                           ftp://ftp.ensembl.org/pub/current_fasta
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>