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The Make2D-DB II query interface is the entry point from which users and database managers access the potsgreSQL databases and related documents.
Beside being an interactive interface to address queries, it offers many other features. It has the ability to manage simultaneously several databases, to contact other similar interfaces addressing queries on several resources all at once. It can also be used in non interactive mode as an extractor for data and objects (maps, gels, spots, experimental results, etc..) and export them in different formats. The extracted data can then be read by humans or integrated in any other software or pipeline.
The Apache ModeRewrite mode is another included feature that makes queries (specially in non interactive mode) very intuitive. This tends to give data extraction an aspect of URI (unified resource identifier) object extraction. All the needed rules for mode rewriting are generated by the tool.

When the server installation part is executed, all the needed scripts and documents are built inside your Apache server directories and your database is ready to be accessed via the Web.

To access the main query intrface, you should use the URL:

http://your_domain/2d

Where your_domain is the domain address of your sever and 2d is the Web server reference name you would have defined in your configuration files (the $web_server_ref_name variable), e.g. of a test database:

http://mordor.isb-sib.ch/2d_test

In some systems, you may need to preceed the server reference name by 'html': http://your_domain/html/2d, or any other prefix, depending on your server files location.

The administration (management) interface is accessible via:

http://your_domain/2d/admin

You will be asked for a login ID, a password and a database name to access the interface. You should give your postgreSQL account login and password. The database name is also the postgreSQL database name. You may logout at any moment. After 30 minutes of non-activity, your login will expire. The login data is highly *encrypted* and is time and system dependant (view).

By the end of your installation, you will find two generated files called respectively make2db_map.txt and mod_rewrite.txt. Those files are located in your database server directory ../cgi-bin/2d/inc (or similar - another copy from your last installation will be in the Make2D-DB temp directory). The first file, make2db_map.txt, contains a mapping functions that will be used by the Apache server. This file also contains a summary of the directives on how to include the rewrite rules within the Apache configuration file. The second file, mod_rewrite.txt, contains those rules that have to be included within this Apchae configuration file.
You should copy all the instructions given in this mod_rewrite.txt file to the end of your Apache httpd.conf file (usually in /etc/httpd/conf/httpd.conf) and restart your server (you should have permissions to do so, or ask your system administrator to do this task). You should verify that the Apache httpd.conf file has an instruction: "LoadModule rewrite_module modules/mod_rewrite.so" or equivalent, then activate the line "RewriteEngine on" within the same file by omiiting the '#' character it may have at its beginning.

For more information, have a look at the Apache Module mod_rewrite page. Contact us if you happen to encounter any problem setting this mode.

Data defined to be private during the installation process will only be accessible to adminstrators. If you have set a value for the $private_data_password variable in your configuration file 2d_include.pl, then users may also access those data by entering the appropriate password from the main interface home page. A button labeled 'Private data' is located under the text of this main page. Once activated, it remains active in the browser for 30 day. Users have the choice to deactivate their access at any moment.

During the installation process, external UniProtKB data would have been already integrated within your data. Other external 2D resources may also be contacted to establish links between your database and their data. This operation is not launched by default during the installation process. Instead, you should select "Managing External data" from the management interface and then choose "Update external 2D data".

You may re-execute such updates (as well as for UniProt data) from time to time, to make sure you data is always synchronited with those external resources.

Many other features and description of the interface will be added to the Readme: Interface on the ExPASy Make2D-DB II site. Please, visit those pages for an extended list of description.