Genex Tutorial

# Tutorial for Genex.pm

This is an ever expanding tutorial on the use of the Genex.pm module. If you have suggestions for improving this content, please mail the author.

# Overview

Genx is distributed with an Application Programmer's Interface (API) written in Perl and distributed under the perl package, Genex.pm. The API was built with a one class per table approach, so that each table in the database (DB) is represented by a single perl class in the 'Genex' namespace (listed in table 1). A large subset of the classes represent the Genex controlled vocabulary tables--each of which regulates the accepted values of a single column for a single table (listed in table 2). Lastly, there are three utility modules (listed in table 3) for help with common data access and data conversion tasks.

A common task would be to investigate the data in a single row in a DB table, for example the ExperimentSet table. To accomplish this we would create a Bio::Genex::ExperimentSet instance and set it's 'id' attribute to the value desired:

    $exp_set =  Bio::Genex::ExperimentSet->new(id=>$pkey);

Now that we have the object we can access the data stored in that row of the DB by simply using accessor methods on the object. Each method has the same name as the DB column it accesses:

    $bio_desc = $exp_set->biology_description();
    $rel_date = $exp_set->release_date();

For situtations were it is necessary to fetch multiple rows from the DB, each class provides a get_object() method that can be utilized in three modes: 1) passing a list of primary key values to fetch; 2) passing the keyword 'ALL', to retrieve all entries from the table, and 3) specifying a column and value to use for restricting the objects:

    @exp_sets1 = Bio::Genex::ExperimentSet->get_objects(4,7,21);
    @exp_sets2 = Bio::Genex::ExperimentSet->get_objects('ALL');
    @exp_sets3 = Bio::Genex::ExperimentSet->get_objects({column=>'is_public',
                                                    value=>1});

## More Complex Queries

This interface works well for simple DB queries, but many applications need access to a richer set of DB commands. Genex is designed so that it can be implemented on top of many different database management systems (DBMSs). So far it has been tested on Sybase and PostgreSQL. One problem with this approach is the heterogenious nature of the Structured Query Lanquage (SQL) accross differrent DBMSs. To handle this problem, a simple SQL wrapper layer is provided by the Bio::Genex::DBUtils module for creating SQL for DB inserts and selects:

    $dbh = Bio::Genex::current_connection(); # get a DB handle
    $sql = create_insert_sql($dbh,
                             TABLE=>'Contact',
                             COLUMNS=>['contact_person','url']);
    $sth = $dbh->prepare($sql);
    $sth->execute('Patrick O. Brown','http://www.stanford.edu/')

    $sql = create_select_sql($dbh,
                             COLUMNS=>['name'],
                             FROM=>['ArrayMeasurement'],
                             WHERE=>"am_pk = 34");
    @arrays = $dbh->selectall_array($sql);

The Bio::Genex::current_connection() function provides a cached DB handle to the default Genex DB that was specified during installation. This makes it simple to change the location and name of the DB and not have to modify any of the applications built to access it.

## Writing Output as XML or HTML

One of the primary uses of the Genex DB is as a data repository that users around the world can use to retrieve information. We have written an XML based exchanged format, the Genex Expression Markup Language (GEML), as the medium of data transmission. To facilitate data input and output from XML, we have included an XMLUtils module.

Another important use is to display the contents of data in the DB to the users, and since the WWW browser has become the de facto standard for information retrieval and browsing we have included an HTMLUtils module to render Genex objects as HTML.

## CGI Example

To provide a final concrete example for using the Genex modules we will build a simple perl CGI script that will enable browsing of any DB table, displaying either a single entry from a table or all entries:

    use Bio::Genex;
    use Bio::Genex::HTMLUtils qw(objs2html);

    # start a DB connection
    $dbh = Bio::Genex::current_connection();

    # start the HTML page and get the DB accession number from the script
    $query = new CGI;
    $pkey = param('AccessionNumber');
    $table = param('Table');

    # start the output
    print $query->header, $query->h2("$table Entries Retrieved from GeneX");
    print $query->p("Your query returned " . scalar @objects . " $table entries");

    # import the namespace for this class, and retrieve the objects
    $class = 'Bio::Genex::' . $table;
    eval "require $class";
    if ($pkey eq 'ALL') {
      push(@objects, $class->get_objects('ALL'));
    } else {
      push(@objects, $class->new(id=>$pkey));
    }

    # make the table, and end the page
    $html = objs2table(HEADER=>1,CGI=>$query,OBJECTS=>\@objects);
    print $query->table({-border=>''},$html), $query->end_html;

An example of the output of this script is shown in Figure 1.

Figure 1. Output of sample code

## More Details

Each module has accompanying documentation in both Perl pod format (Plain Old Documentation) and HTML, as well as a general overview of the entire API, and a short tutorial for using the Genex classes. Each module also includes a set of automated regression tests which allows testing of the entire system before installation, which provide further details of how to use the Genex.pm API. See the main index for more details.

### Author and Copyright

This tutorial was written by Jason E. Stewart (jes@ncgr.org), and all the material is copyright © 2000 the National Center for Genome Resources.