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 local databases/projects, but also to contact other similar
interfaces addressing queries on many resources all at once. Moreover, it can 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, thus acting like a data repository. The extracted data can then be read by
humans or integrated in any other software or pipeline.
The Apache ModeRewrite redirection 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
To access the main query intrface, you should use the URL:
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:
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 by:
You will be asked for a login ID, a password and a database name to
access the interface. You should give your postgreSQLaccount
login and password (password is required unless you set your postgres
server to "trust" TCP/IP localhost connections). 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 (view1, view2).
Apache Mode Rewrite redirection rules
Rewriting redirection rules is not only a nicer way to display URLs within your browser, e.g.
http://my_domain/my_database rather than http://my_domain/cgi-bin/my_database/2d.cgi
but it is before all a far better manner to extract objects and data,
and to formulate queries with the desired parameters, in a much more
rather than http://my_domain/cgi-bin/my_database/2d.cgi?map=plasma
rather than http://my_domain/cgi-bin/my_database/2d.cgi?ac=P12345&format=txt&extract&database=project-1
or (a spot within a database is defined in Make2D-DB II by 'mapName:spotID')
rather than http://my_domain/cgi-bin/my_database/2d.cgi?spot=plasma:123&database=project-1&data=msms
The main advantage, beside the intuitive way to formulate and extract queries, is that any object is clearly defined by its own URI
(Uniform Resource Identifier). Then special actions: how to present the
object, what actions to take, etc.. follow in in a very simple and
Even simple search queries (questions: is there a?..) can be formulated in a similar manner:
rather than http://my_domain/cgi-bin/my_database/2d.cgi2d?author=smith and
By the end of your installation, you
will find two generated files called respectively make2db_map.txt and
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 the 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
contains those rules that have to be included "as is" within this Apchae
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
rewrite_module modules/mod_rewrite.so" or equivalent, then
activate the line "RewriteEngine
on" within the same file by omitting the '#' character it may
have at its beginning.
For more information, have a quick look at the Apache
Module mod_rewrite page. Contact us if you happen to encounter any
problem setting this mode on.
Data defined to be private during the
installation process (or at any later moment using the administration
interface) 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 at the bottom of the home page. Once
activated, it remains active in the browser for 30 days. Users have the
choice to deactivate their access at any moment.
During the installation process,
external up-to-date UniProtKB data should 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 UniProtKB data) from time
to time, to make sure your data is always synchronited with those
external resources (automatisation with a 'crontab' is to be considered).
List of currently available remote Make2D-DB II interfaces
An up-to-datellist of currently available remote Make2D-DB II interfaces, that you may link with your own interfaces,
can always be retrieved from the ExPASy mediator server at:
features and description of the interface should be added to the Readme:
Interface on the ExPASy Make2D-DB II site. Please, visit those
pages for an extended list of description. Those will essentially cover:
A more detailed description of the management
(administration) interface. Currently, there is a fair description of
each operation within the interface itself. Please, do not hesitate to
contact us if you have any question about any of those operations.
A detailed list on how to extract any type of object or data
from a database, in both normal and Mode Rewrite modes. How to extract
local database/project list, protein indexes to link with, maps' list,
species list, how to link to a Make2D-DB II repository, etc..