Organisms

Page Sections

Before we can load our genomic data we must first have an organism to which the data will be associated.  Chado v1.3 does not come preloaded with any organisms (although previous version of Chado do).  For this tutorial we will import genomic data for Citrus sinesis (sweet orange), so we must first create the organism. 

Creating an Organism Page

We can  add the organism using the Add Tripal Content link in the top administrative menu. The Add Tripal Content page has several content types already available, including the Organism content type.

To add a new organism  click the Organism link and a form will appear with multiple fields. Fill in the fields with these values:

  • Abbreviation: C. sinensis
  • Genus: Citrus
  • Species: sinensis
  • Common name: Sweet orange
  • Description: Sweet orange is the No.1 citrus production in the world, accounting for about 70% of the total. Brazil, Flordia (USA), and China are the three largest sweet orange producers. Sweet orange fruits have very tight peel and are classified into the hard-to-peel group. They are often used for juice processing, rather than fresh consumption. Valencia, Navel, Blood, Acidless, and other subtypes are bud mutants of common sweet orange varieties. Sweet orange is considered as an introgression of a natural hybrid of mandarin and pummelo; some estimates shows more mandarin genomic background than pummelo. The genome size is estimated at 380Mb across 9 haploid chromosomes.

And, use the following image:

Leave all remaining fields empty and save the page.  You should now have an organism page that appears as follows:

NOTE: This layout of the organism page is provided by the tripal_ds module that was enabled during Tripal installation.  If you decided not to enable that module then your page will look quite different.  

Notice that this page has three primary sections.  A left sidebar that contains a search box and a block titled Navigation.  To the right of the sidebar is the content section.  Here the content is divided into two columns.  In the first column is a table of contents listing the "Table of Contents" of the page.  Currently this list simply contains the Summary. The second column contains all of the content about the organism.  Clicking the links in the table of contents causes each section to slide to the top of the page for viewing while all other content slides downward.  Users need not scroll the entire page to see all content.  The close link (X) at the top right of each section allows the user to remove sections they may not want to see and which clutter their view. 

There is more information about an organism that does not appear on this page.  Remember, when you created the orgnaism you skiped multiple form elements.  By default, Tripal will not show fields that have no data.  However, if you prefer, you can change this behavior by configuring Tripal to show empty fields.

If you do not like this layout you can change it!  One of the benefits for using Drupal is the ability to customize the entire look and feel of your site.  Tripal v3.x along with Drupal allow you to reorganize this (and any) page however you like.  This default layout is provided by the tripal_ds module to help simplify the process of laying out a page.  If you decided not to enable the tripal_ds module then your page will require manual layout. Later in this tutorial we will present how to reorganize and re-theme the Tripal content pages on your site.  No programming is required to do this.