Organisms

Page Sections

There are two ways to create pages for organism. If your organism is already in Chado then you can sync the organism. Sync'ing is the process of creating Drupal pages for content in Chado. If an organism is not in Chado you will need to manually add it using the Tripal web interface. The following two sections describe both methods.  To demonstrate this functionality, step-by-step examples are provided for adding organism pages for two example species: Drosophila melenogaster and Citrus sinsus.

Organisms Already in Chado

Chado comes pre-loaded with a few species, but initially these species do not have pages on the website. First, check to see if the organism is already present. To do this navigate to TripalChado ModulesOrganisms then click the Sync tab.

Tripal2.0 organism1.png

This page has two different options. The first is the top section labeled Sync Organisms. In this section is a list of organisms. These are the organisms that come with the default Chado installation. If the organism is already in the list (e.g. Drosophila melenogaster) then we want to create a web page for the organism. The process of creating pages in Drupal for data housed in Chado is called Syncing. We need to sync Drupal and Chado so that Drupal knows about the organism.  As an example,  click the check box next to Drosophila melenogaster and then click the Submit Sync Job.

As usual we want to run this job manually:

cd /var/www/html
drush trp-run-jobs --user=administrator

Now that the organism is synced we should have a new page for Drosophila melenogaster. To find the page, click the Find Content menu item at the top. A list of all content pages currently available in Drupal should appear. Our new organism page should appear at the top of the list.

Click the link titled Drosophila Melenogaster and the following page should appear:

Tripal2.0 organism2.png

By default all Tripal pages have a table of contents on the left and data in the center. As links in the table of content are clicked the content in the middle updates. Also, messages to the site administrator are contained in blue shaded regions. These blue shaded regions will only appear to users with the Administer Tripal permission. This page, however, is a bit empty. We need to add some details. We want to add a description for this organism and an image. Click the Edit tab next to the page title. In the form that appears add the following text (taken from wikipedia: http://en.wikipedia.org/wiki/Drosophila_melanogaster) for the description:

The genome of D. melanogaster (sequenced in 2000, and curated at the FlyBase database) contains four pairs of chromosomes: an X/Y pair, and three autosomes labeled 2, 3, and 4. The fourth chromosome is so tiny that it is often ignored, aside from its important eyeless gene. The D. melanogaster sequenced genome of 165 million base pairs has been annotated[17] and contains approximately 13,767 protein-coding genes, which comprise ~20% of the genome out of a total of an estimated 14,000 genes. More than 60% of the genome appears to be functional non-protein-coding DNA involved in gene expression control. Determination of sex in Drosophila occurs by the ratio of X chromosomes to autosomes, not because of the presence of a Y chromosome as in human sex determination. Although the Y chromosome is entirely heterochromatic, it contains at least 16 genes, many of which are thought to have male-related functions.

For the image, download this image below and upload it using the Organism image upload field on the page.

Click the Save button. Now we have a more informative page:

Tripal2.0 organism3.png

Manually Adding an Organism

For later sections in this document, examples will be provided for loading data for the Citrus sinensis (sweet orange) species, but this organism is not in Chado by default. We can easily add the organism using the Add Content link in the top administrative menu. The Add Content page now has many more content types than when we first saw it. Previously we only had Page and Story content types. Now we have more content types such as Analysis, Organism, and Feature.

Tripal2.0 Drupal add content2.png

To add a new organism simply click the Organism link and and fill in the fields with these values:

  • Genus: Citrus
  • Species: sinensis
  • Abbreviation: C. 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:

Save the page and view the new Organism:

Tripal2.0 organism4.png

Bulk Loading Organisms

There is no common file format for storing a large number of organisms.  Thus there is no data loader for bulk loading of organisms.   Site developers who need to load a large list of organisms to Chado can do so using the Tripal Bulk Loader which is described later in this document.  An example of loading a list of organisms is provided.