intBuilder_DB          package:PAnnBuilder          R Documentation

_B_u_i_l_d _D_a_t_a _P_a_c_k_a_g_e _f_o_r _I_n_t_e_r_a_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Given the URL to protein-protein or domain-domain interaction
     database,  this function creates a SQLite-based annotation data
     package.

_U_s_a_g_e:

     intBuilder_DB(src=c("geneint","intact","mppi","3DID","DOMINE"), 
                prefix, pkgPath, version, author) 

_A_r_g_u_m_e_n_t_s:

     src: a character string to indicate which protein-protein or 
          domain-domain interaction database will be used. 

  prefix: the prefix of the name of the data package to be built. (e.g.
           "hsaSP"). The name of builded package is prefix+".db". 

 pkgPath: a character string for the full path of an existing directory
          where the built backage will be stored.

 version: a character string for the version number.

  author: a list with named elements "authors" containing a character
          vector of author names and "maintainer" containing the
          complete character string for the maintainer field, for
          example, "Jane Doe <jdoe@doe.com>".

_D_e_t_a_i_l_s:

     Build annotation data packages for protein-protein or
     domain-domain interaction.  Supported databases are: "geneint":
     <URL: ftp://ftp.ncbi.nih.gov/gene/GeneRIF/interactions.gz> ;
     "intact": <URL: http://www.ebi.ac.uk/intact> ; "mppi": <URL:
     http://mips.gsf.de/proj/ppi> ; "3DID": interacting protein domains
     of known three-dimensional structure,  <URL: http://3did.embl.de>
     ; "DOMINE": <URL: http://domine.utdallas.edu/cgi-bin/Domine> ;

     'intBuilder_DB' employes functions  'writeGENEINTData_DB',
     'writeINTACTData_DB',  'writeMPPIData_DB', 'write3DIDData_DB' and 
     'writeDOMINEData_DB' to parse and write data.

     Data files in the database will be automatically downloaded to the
     tmp directory, so enough space is needed for the data files. After
     downloading, files are parsed by perl, so perl must be installed. 
     It may  take a long time to parse database and build R package.
     Alternatively, we have  produced diverse R packages by
     PAnnBuilder, and you can download appropriate  package via <URL:
     http://www.biosino.org/PAnnBuilder>.

_V_a_l_u_e:

     This function does not return any value.

_A_u_t_h_o_r(_s):

     Hong Li

_E_x_a_m_p_l_e_s:

     # Set path, version and author for the package.
     pkgPath <- tempdir()
     version <- "1.0.0"
     author <- list()
     author[["authors"]] <- "Hong Li"
     author[["maintainer"]] <- "Hong Li <sysptm@gmail.com>"

     ## It may take a long time to parse database and build R package.
     if(interactive()){
         # Build annotation data package "int.geneint" for interaction data from NCBI.
         intBuilder_DB(src="geneint", 
         prefix="int.geneint", pkgPath, version, author) 
         
         # Build annotation data package "int.intact" for IntAct database.
         intBuilder_DB(src="intact", 
         prefix="int.intact", pkgPath, version, author) 
         
         # Build annotation data package "int.mppi" for interaction data from MIPS.
         intBuilder_DB(src="mppi", 
         prefix="int.mppi", pkgPath, version, author) 
         
         # Build annotation data package "int.did" for 3DID database.
         intBuilder_DB(src="3DID", 
         prefix="int.did", pkgPath, version, author) 
         
         # Build annotation data package "int.domine" for DOMINE database.
         intBuilder_DB(src="DOMINE", 
         prefix="int.domine", pkgPath, version, author) 
     }

