# ---------------------------------------------------------------------------
# Rice Reactome - CHEBI Ontology Mapping Script
#
-# Justin Preece, 10/06/10
+# Justin Preece, 10/06q/10
# v1.0: 10/13/10 (svn rev. 66)
# v1.1: 10/20/10 (svn rev. 70)
+# v2.0: 10/21/10 (svn rev. ?)
#
# Purpose: Map CHEBI ontology terms onto Rice Reactome database.
#
# (Header) [ReactomeID] [Compound_Name] [CAS] [LIGAND] [RiceCyc]
# (Row) 923893 S-adenosyl-L-methionine 29908-03-0 C00019 S-ADENOSYLMETHIONINE ** the '-' (dash) symbol will be applied to any empty columns
#
-# Outputs: tab-del mapping file (reactome_chebi_mapping.txt)
+# Outputs: tab-del mapping file (reactome_chebi_mapping_results_sorted.txt)
#
# [ReactomeID] [CHEBI] [XREF_Type] [XREF_ID]
# 923893 15414 CAS 29908-03-0
# ---------------------------------------------------------------------------
# set paths to data files
-my $data_path = "/home/preecej/Documents/projects/reactome/";
+my $data_path = "/Users/cindypreece/Desktop/work/Documents/projects/reactome/";
+#my $data_path = "/home/preecej/Documents/projects/reactome/";
my $chebi_obo_file = "chebi.obo";
my $reactome_file = "RiceReferenceMolecules.txt";
-my $mapped_output_file = "1.1_reactome_chebi_mapping_complete.txt";
-my $sorted_output_file = "1.1_reactome_chebi_mapping_complete_sorted.txt";
-my $unique_mappings = "1.1_reactome_unique_mappings.txt";
-my $sorted_no_match_file = "1.1_reactome_entries_with_no_chebi_match.txt";
+my $mapped_output_file = "2.0_reactome_chebi_mapping_complete.txt";
+my $sorted_output_file = "2.0_reactome_chebi_mapping_complete_sorted.txt";
+my $unique_mappings = "2.0_reactome_unique_mappings.txt";
+my $sorted_no_match_file = "2.0_reactome_entries_with_no_chebi_match.txt";
# options
my $allow_obsolete_terms = 1;
--- /dev/null
+<?php
+
+# This file was automatically generated by the MediaWiki installer.
+# If you make manual changes, please keep track in case you need to
+# recreate them later.
+#
+# See includes/DefaultSettings.php for all configurable settings
+# and their default values, but don't forget to make changes in _this_
+# file, not there.
+#
+# Further documentation for configuration settings may be found at:
+# http://www.mediawiki.org/wiki/Manual:Configuration_settings
+
+# If you customize your file layout, set $IP to the directory that contains
+# the other MediaWiki files. It will be used as a base to locate files.
+if( defined( 'MW_INSTALL_PATH' ) ) {
+ $IP = MW_INSTALL_PATH;
+} else {
+ $IP = dirname( __FILE__ );
+}
+
+$path = array( $IP, "$IP/includes", "$IP/languages" );
+set_include_path( implode( PATH_SEPARATOR, $path ) . PATH_SEPARATOR . get_include_path() );
+
+require_once( "$IP/includes/DefaultSettings.php" );
+
+if ( $wgCommandLineMode ) {
+ if ( isset( $_SERVER ) && array_key_exists( 'REQUEST_METHOD', $_SERVER ) ) {
+ die( "This script must be run from the command line\n" );
+ }
+}
+
+
+
+# BEGIN 09/30/10: Justin Preece - added for Semantic MediaWiki and related extensions
+
+# added for Semantic public notification value recommended by Semantic MediaWiki
+$wgServerName = "palea.cgrb.oregonstate.edu";
+
+# Semantic MediaWiki extension
+include_once("$IP/extensions/SemanticMediaWiki/SemanticMediaWiki.php");
+enableSemantics($wgServerName);
+
+# Semantic Forms extension
+include_once("$IP/extensions/SemanticForms/SemanticForms.php");
+$sfgAutocompletionURLs['remote_species'] = 'http://palea.cgrb.oregonstate.edu/AnnoWiki/prototyping/remote_autocomplete.php?q=<substr>';
+
+# Data Transfer extension
+include_once("$IP/extensions/DataTransfer/DataTransfer.php");
+
+# External Data extension
+include_once("$IP/extensions/ExternalData/ExternalData.php");
+
+# END 09/30/10: Justin Preece - added for Semantic MediaWiki and related extensions
+
+
+
+## Uncomment this to disable output compression
+# $wgDisableOutputCompression = true;
+
+$wgSitename = "AnnoWiki";
+
+## The URL base path to the directory containing the wiki;
+## defaults for all runtime URL paths are based off of this.
+## For more information on customizing the URLs please see:
+## http://www.mediawiki.org/wiki/Manual:Short_URL
+$wgScriptPath = "/AnnoWiki";
+$wgScriptExtension = ".php";
+
+## The relative URL path to the skins directory
+$wgStylePath = "$wgScriptPath/skins";
+
+## The relative URL path to the logo. Make sure you change this from the default,
+## or else you'll overwrite your logo when you upgrade!
+$wgLogo = "$wgStylePath/common/images/A1_sterileflowers_wiki_icon.jpg";
+
+## UPO means: this is also a user preference option
+
+$wgEnableEmail = true;
+$wgEnableUserEmail = true; # UPO
+
+$wgEmergencyContact = "preecej@science.oregonstate.edu";
+$wgPasswordSender = "preecej@science.oregonstate.edu";
+
+$wgEnotifUserTalk = true; # UPO
+$wgEnotifWatchlist = true; # UPO
+$wgEmailAuthentication = true;
+
+## Database settings
+$wgDBtype = "mysql";
+$wgDBserver = "floret.cgrb.oregonstate.local";
+$wgDBname = "annowiki";
+$wgDBuser = "annowikiuser";
+$wgDBpassword = "annowikiuser-pw";
+
+# MySQL specific settings
+$wgDBprefix = "";
+
+# MySQL table options to use during installation or update
+$wgDBTableOptions = "ENGINE=InnoDB, DEFAULT CHARSET=binary";
+
+# Experimental charset support for MySQL 4.1/5.0.
+$wgDBmysql5 = true;
+
+## Shared memory settings
+$wgMainCacheType = CACHE_NONE;
+$wgMemCachedServers = array();
+
+## To enable image uploads, make sure the 'images' directory
+## is writable, then set this to true:
+$wgEnableUploads = false;
+$wgUseImageMagick = true;
+$wgImageMagickConvertCommand = "/usr/bin/convert";
+
+## If you use ImageMagick (or any other shell command) on a
+## Linux server, this will need to be set to the name of an
+## available UTF-8 locale
+$wgShellLocale = "en_US.utf8";
+
+## If you want to use image uploads under safe mode,
+## create the directories images/archive, images/thumb and
+## images/temp, and make them all writable. Then uncomment
+## this, if it's not already uncommented:
+# $wgHashedUploadDirectory = false;
+
+## If you have the appropriate support software installed
+## you can enable inline LaTeX equations:
+$wgUseTeX = false;
+
+## Set $wgCacheDirectory to a writable directory on the web server
+## to make your wiki go slightly faster. The directory should not
+## be publically accessible from the web.
+#$wgCacheDirectory = "$IP/cache";
+
+$wgLocalInterwiki = strtolower( $wgSitename );
+
+$wgLanguageCode = "en";
+
+$wgSecretKey = "469aad58c7cc5ab0ec223dbf1316d16a6ded21cfa01f9e23d6ef22dee92a3224";
+
+## Default skin: you can change the default skin. Use the internal symbolic
+## names, ie 'vector', 'monobook':
+$wgDefaultSkin = 'monobook';
+
+## For attaching licensing metadata to pages, and displaying an
+## appropriate copyright notice / icon. GNU Free Documentation
+## License and Creative Commons licenses are supported so far.
+# $wgEnableCreativeCommonsRdf = true;
+$wgRightsPage = ""; # Set to the title of a wiki page that describes your license/copyright
+$wgRightsUrl = "";
+$wgRightsText = "";
+$wgRightsIcon = "";
+# $wgRightsCode = ""; # Not yet used
+
+$wgDiff3 = "/usr/bin/diff3";
+
+# When you make changes to this configuration file, this will make
+# sure that cached pages are cleared.
+$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
projects / old-jaiswallab-svn / .git / commitdiff