Tripal Tutorial v2.0

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Welcome to the Tripal v2.0 Tutorial. Here you will find instructions for installation, usage and administration of a Tripal-based genome website. This tutorial guides the user through the process of installation, setup and data loading of genomic feature data and annotations.

Note: Tripal is provided free of charge, as-is with no warranty or guarantee of fitness. The developers are committed to creating a platform usable by all and as bug free as possible. However, bugs may be present, especially with the newest features. If you find problems or bugs, please feel free to report them either via the Tripal mailing List or adding a bug report on the Tripal issues tracker.


Note: This tutorial has been updated from the v1.1 tutorial for Tripal v2.0a. It is, however, correct up to the section about importing publications. As Tripal 2.0-alpha matures the tutorial will be completely updated. Thank you for your patience.


Contents

What is Tripal

Tripal is a suite of PHP5 modules that bridges the Drupal Content Managment System (CMS) and GMOD Chado. The goal is to simplify construction of a community genomics, genetics or biological website to enable individual labs or research communities to construct a high-quality, standards-based website for data sharing and collaboration.

600px-WhatisTripal.png

Content Management System

Definition From Wikipedia:

A content management system (CMS) is the collection of procedures used to manage work flow in a collaborative environment. These procedures can be manual or computer-based. The procedures are designed to do the following:

  • Allow for a large number of people to contribute to and share stored data
  • Control access to data, based on user roles (defining which information users or user groups can view, edit, publish, etc.)
  • Aid in easy storage and retrieval of data
  • Reduce repetitive duplicate input
  • Improve the ease of report writing
  • Improve communication between users

In a CMS, data can be defined as nearly anything: documents, movies, pictures, phone numbers, scientific data, and so forth. CMSs are frequently used for storing, controlling, revising, semantically enriching, and publishing documentation. Serving as a central repository, the CMS increases the version level of new updates to an already existing file. Version control is one of the primary advantages of a CMS.

Drupal

Drupal is an open-source freely available CMS with thousands of users and existing sites. Features of Drupal

  • A well-supporting community.
  • Books, tutorials and online forums for help .
  • Hundreds of user-contributed extension modules that are freely available.
  • Hundreds of user-contributed themes to instantly change the look-and-feel of the site
  • User management infrastructure.
  • Allows for non-coding manipulation of the website contents. Anyone can edit content.
  • Easy to install and maintain

Drupal website: http://www.drupal.org Drupal modules: http://www.drupal.org/project/modules Drupal themes: http://www.drupal.org/project/themes

Tripal v2.0 is compatible with Drupal v7.

Chado

You can find more detailed information about Chado here: http://gmod.org/wiki/Chado_-_Getting_Started. However, one thing to remember in regards to Tripal organization is that Chado has a modular structure:

  • Audit - for database audits
  • Companalysis - for data from computational analysis
  • Contact - for people, groups, and organizations
  • Controlled Vocabulary (cv) - for controlled vocabularies and ontologies
  • Expression - for summaries of RNA and protein expresssion
  • General - for identifiers
  • Genetic - for genetic data and genotypes
  • Library - for descriptions of molecular libraries
  • Mage - for microarray data
  • Map - for maps without sequence
  • Organism - for taxonomic data
  • Phenotype - for phenotypic data
  • Phylogeny - for organisms and phylogenetic trees
  • Publication (pub) - for publications and references
  • Sequence - for sequences and sequence features
  • Stock - for specimens and biological collections
  • WWW -

Tripal is also modular following these same designations.

Goals of Tripal

  • Simplify Construction of Biological Databases
    • Reduce time of development
    • Reduce costs
    • Reduce technical resources (i.e. programmers, systems admins).
    • A non-technical site administrator can add content without knowing PHP, HTML, JavaScript.
  • Greater Flexibility of the Biological Website
    • Social Networking
    • Non-biological content
    • Outreach, tutorials, documentation, protocols, publications
  • Expandability
    • Site can be programmatically expanded in any way
    • Changes to base-code are not needed but modules are added.
    • Availability of an Application Programmer Interface (API)
  • Reusability
    • All code can be shared. Expansion modules created by one group can be shared with all.

Structure of Tripal

Tripal is a collection of modules that integrate with Drupal. These modules are divided into hierarchical categories:

TripalLayers.png

The Tripal Core level contains supportive functionality for all other modules. It contains

  • A jobs management utility
  • A utility to manage materialized views
  • An API for these features
  • Functions for managing module specific CV terms
  • Functions for interfacing with Chado.


The Chado-centric modules provide:

  • Edit/Update/Delete for Chado modules.
  • Bulk loaders for these data
  • Basic visualizations for data in Chado specific for the module
  • An API for easily accessing Chado.


Analysis modules provide

  • Custom visualization for specific analyses (e.g. Blast, KEGG, InterProScan, Unigene construction)
  • Uses the API from the Tripal Analysis (Chado-centric) module.


Applications:

  • These are full blown applications that use Tripal, Drupal and Chado and typically consist of several Chado-centric modules, Analysis modules and custom built modules. (e.g. Breeders Toolbox currently under construction).

Sites Running Tripal

Site Name URL
Banana Genome Hub http://banana-genome.cirad.fr/
Pulse Crops Genomics & Breeding http://knowpulse2.usask.ca/portal/
Genome Database for Vaccinium http://www.vaccinium.org
Genome Database for Rosacaee http://www.rosaceae.org
Cool Season Food Legume Database http://www.gabcsfl.org
Cacao Genome Database http://www.cacaogenomedb.org
Fagaceae Genome Web http://www.fagaceae.org
Citrus Genome Database http://www.citrusgenomedb.org
Marine Genomics Project http://www.marinegenomics.org

Resources

The Tripal home site where you can find everything about Tripal: http://tripal.info

GMOD Tripal mailing lists: http://gmod.org/wiki/GMOD_Mailing_Lists

GMOD Tutorials from previous GMOD schools: http://gmod.org/wiki/Tripal

Contributing Organizations

Individuals from these organizations have provided design and coding for Tripal v2.0

150px-USLogo.png 150px-WSULogo.png

Acknowledgments are extended to the Clemson University Genomics Institute where Tripal was first conceived and where development of earlier releases was performed.

150px-CUGILogo.png

Also, special thanks are extended to the GMOD project for logistical support and community interaction!!

Funding

Funding for Tripal v2.0 has been provided through various grants from various sources.


Publications

  1. Lacey-Anne Sanderson, Stephen. P. Ficklin, Chun-Huai Cheng, Sook Jung, Frank A. Feltus, Kirstin E. Bett, Dorrie Main. Tripal v1.1: a Standards-based Platform for Construction of Online Genetic and Genomic Databases. Databases, Sept 2013.
  2. Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret Staton, Taein Lee, Il-Hyung Cho, Sook Jung, Kirstin E Bett, Dorrie Main. Tripal: a construction Toolkit for Online Genome Databases. Database, Sept 2011.

Pre-planning

IT Infrastructure

Tripal requires a server with adequate resources to handle the expected load and systems administration skills to get the machine up and running, applications installed and everything properly secure. Tripal requires a PostgreSQL databases server, Apache (or equivalent) web server, PHP5 and several configuration options to make it all work. However, once these prerequisites are met, working with Drupal and Tripal are quite easy.


There are four ways you could get a Tripal/Drupal/Chado database web server available for your site

  1. Option #1 In-house dedicated servers: You may have access to servers in your own department or group which you have administrative control and wish to install Tripal/Drupal/Chado on these.
  2. Option #2 Institutional IT support: Your institution may provide IT servers and would support your efforts to install a website with database backend.
  3. Option #3 Commercial web-hosting: If options #1 and #2 are not available to you, commercial web-hosting is an affordable option. For large databases you may require a dedicated server. Bluehost.com is a web hosting service that provides hosting compatible with Drupal, Tripal and its dependencies.
  4. Option #4 In the Cloud: Tripal is a part of the GMOD in the cloud Amazon AWS image created by GMOD. It is also accompanied by other GMOD tools such as GBrowse2, JBrowse, Apollo and WebApollo.


After selection of one of the options above you can arrange your database/webserver in the following ways:

  1. Arrangement #1: The database and web server are housed on a single server. This is the approach taken by this course. It is necessary to gain access to a machine with enough memory (RAM), hard disk speed and space, and processor power to handle both services.
  2. Arrangement #2: The database and web server are housed on different servers. This provides dedicated resources to each service (i.e. web and database).


Selection of an appropriate machine

Databases are typically bottle-necked by RAM and disk speed. Selection of the correct balance of RAM, disk speed, disk size and CPU speed is important and dependent on the size of the data. The best advice is to consult an IT professional who can recommend a server installation tailored for the expected size of your data.


Note: Tripal does require command-line access to the web server with adequate local file storage for loading of large data files. Be sure to check with your service provider to make sure command-line access is possible.

Technical Skills

Depending on your needs, you may need additional Technical support....


Tripal already supports my data, what personnel to I need to maintain it?

  • Someone to install/setup the IT infrastructure
  • Someone who understands the data to load it properly


Tripal does not yet support all of my data, but I want to use what's been done and expand on it....?

  • Someone to install/setup the IT infrastructure
  • Someone who understands the data to load it properly
  • PHP/HTML/CSS/JavaScript programmer(s) to write your custom extensions


Why Use Tripal

Tripal v2.0 provides default pages for most Chado data types. It also support all of Chado in terms of data access. So why use Tripal?

  1. You want to use a community-supported common database infrastrcure (i.e. Chado).
  2. You need a web interface but do not want to build one from scratch.
  3. You need content-management capabilities (distributed content editing, user management, social networking... i.e. Drupal)
  4. You want to contribute to a community effort to help build a tool others can use.
  5. You want to participate in a community with other database developers using the same technology and confronting similar problems.
  6. You want to use open-source and free technology!

Development and Production Instances

It is recommended that you have separate development and production instances of Tripal. The staging or development instance allows you to test new functionality, add customizations, or test modification or additions to data without disturbing the production instance. The production instance serves content to the rest of the world. Once you are certain that customizations and new functionality will work well on the development instance you can easily re-implement or copy these over to the production site. Sometimes it may take a few trials to load data in the way you want. A development sites lets you take time to test data loading prior to making it public. The development site can be password-protected to allow only access only to site administrators, developers or collaborators.

Server Installation

The following instructions are for setup of Tripal on an Ubuntu version 12.04 server edition. When possible, alternative command-line statements have been added to this tutorial as users of other Linux version have provided feedback. Unless specifically identified, all commands are for Ubuntu 12.04 linux.

During installation of the Ubuntu 12.04 server please select the following software packages for installation:

  • OpenSSH server
  • LAMP (includes Apache and PHP)
  • PostgreSQL database version 8.4 or higher

Apache Setup

Apache is the web server software. Apache should be installed. On the Ubuntu server, navigate to your new website using this address: http://localhost/. You should see the text "It works!".

ItWorks.png

Drupal works best with the Apache rewrite module enabled. To do this execute the following on the command-line:

   cd /etc/apache2/mods-enabled
   sudo ln -s ../mods-available/rewrite.load

Next we need to edit the apache configuration file to give Drupal full controls of options within the directory root. Edit the /etc/apache2/sites-available/000-default file:

   cd /etc/apache2/sites-available/
   sudo gedit default

And change the AllowOverride option from None to All:

   <Directory /var/www/>
      Options Indexes FollowSymLinks MultiViews
      AllowOverride All
      Order allow,deny
      allow from all
   </Directory>

Now restart your apache again.

sudo /etc/init.d/apache2 restart

Setup PHP

PHP comes loaded onto the server, but we need a few other packages:

Ubuntu.jpg First install php5 using Ubuntu's apt-get utility:

   sudo apt-get install php5-pgsql
   sudo apt-get install php5-gd

For newer versions of Ubuntu (e.g. 13.10) you will also want to install the php5-json package:

   sudo apt-get install php5-json

Suse.png For Suse Linux you may need to install the php-posix package:

   yum install php-posix

Red hat logo big.jpg For RedHat Linux you may also need to install the php-process package:

   yum install php-process

Change some php settings (as root):

   cd /etc/php5/apache2
   sudo gedit php.ini

Set the memory_limit to something larger than 128M (should not exceed physical memory, be conservative but not too much so):

  memory_limit = 2048M;


Now, restart the webserver:

  sudo /etc/init.d/apache2 restart

Install phpPgAdmin

phpPgAdmin is a nice web-based utility for easy administration of a PostgreSQL database. Note: PhpPgAdmin is not required for successful operation of Tripal but is very useful.

   sudo apt-get install phppgadmin

Next, we need to make changes to the configuration settings so that we can remotely access phppgadmin. To do this, edit the phppgadmin config file for apache:

   cd /etc/apache2/conf.d
   sudo gedit phppgadmin

Now, comment out the line that allows access to the local server only, and uncomment the line that allows access to anyone.

#allow from 127.0.0.0/255.0.0.0 ::1/128
allow from all

We also want to password protect PhpPgAdmin using Apache's access control mechanisms. we need to instruct Apache to use password protection for PhpPgAdmin. To do this add the following lines within the Directory stanza just below the line we just uncommented:

AuthType Basic
AuthName "Password Required"
AuthUserFile /usr/share/phppgadmin/.htpasswd
Require User tripaladmin

The lines above instruct apache to use basic authentication, that the password file is located at /usr/share/phppgadmin/.htpasswd and the only user allowed to login is 'tripaladmin'. Save the configuration file. Next we need to create the password file:

   cd /usr/share/phppgadmin
   sudo htpasswd -c .htpasswd tripaladmin

The htpasswd command above will create the .htpasswd file and add the new user 'tripaladmin'. You will need to set a password when requested. Finally, restart the webserver:

sudo /etc/init.d/apache2 restart

Now navigate to the URL [http://localhost/phppgadmin] and you should see the following:

Phppgadmin.png

The username 'tripaladmin' and the password you specified should be required when accessing the PhpPgAdmin page.

Database Setup

Drupal can use a MySQL or PostgreSQL database but Chado prefers PostgreSQL so that is what we will use for both Drupal and Chado. We need to create the Drupal database. The following command can be used to create a new database user and database.


First, become the 'postgres' user:

sudo su - postgres


Next, create the new 'drupal' user account. This account will not be a "superuser' nor allowed to create new roles, but should be allowed to create a database.

createuser -P drupal

When requested, enter an appropriate password:

  
  Enter password for new role: *********
  Enter it again:  *********
  Shall the new role be a superuser? (y/n) n
  Shall the new role be allowed to create databases? (y/n) y
  Shall the new role be allowed to create more new roles? (y/n) n
  


Finally, create the new database:

createdb drupal -O drupal


We no longer need to be the postgres user so exit

exit

Install Drupal

Software Installation

We want to install Drupal into our web document root (/var/www). We want to be able to do this as our 'ubuntu' user. So, first, set the directory permissions to allow this:

  cd /var
  sudo chown -R ubuntu www
  sudo chgrp -R ubuntu www

In the command above we set the owner and group of the directory to be ubuntu (our user group).

Tripal 2.0 requires version 7.x of Drupal. Drupal can be freely downloaded from the http://www.drupal.org website. At the writing of this Tutorial the most recent version of Drupal 7 is version 7.28. The software can be downloaded manually from the Drupal website through a web browser or we can use the 'wget' command to retrieve it:

   cd /var/www
   wget http://ftp.drupal.org/files/projects/drupal-7.28.tar.gz


Next, we want to install Drupal. We will use the tar command to uncompress the software:

  cd /var/www
  tar -zxvf drupal-7.28.tar.gz


Notice that we now have a drupal-7.28 directory with all of the Drupal files. We want the Drupal files to be in our document root, not in a 'drupal-7.28' subdirectory. So, we'll move the contents of the directory up one level:

mv drupal-7.28/* ./
mv drupal-7.28/.htaccess ./
mv index.html index.html.orig


Note: It is extremely important the the hidden file .htaccess is also moved (note the second 'mv' command above. Check to make sure this file is there

   ls -l .htaccess

Notice that the last of the three mv commands renames the index.html file and calls it index.html.orig. The index.html file was serving as the home page for the website. Drupal uses an index.php page for it's home page but the web server has preference for the index.html page. So, we move it out of the way.

Configuration File

Next, we need to tell Drupal how to connect to our database. To do this we have to setup a configuration file. Drupal comes with an example configuration file which we can borrow.


First navigate to the location where the configuration file should go:

  cd /var/www/sites/default/


Next, copy the example configuration that already exists in the directory to be our actual configuration file by renaming it to settings.php.

  cp default.settings.php settings.php


Now, we need to edit the configuration file to tell Drupal how to connect to our database server. To do this we'll use an easy to use text editor gedit

  gedit settings.php


Find the following line

$databases = array();

Add the following just after the above line:

$databases['default']['default'] = array(
  'driver' => 'pgsql',
  'database' => 'drupal',
  'username' => 'drupal',
  'password' => '********',
  'host' => 'localhost',
  'prefix' => '',
);

Replace the text '********' with your database password for the user 'drupal' created previously.

Files directory creation

Finally, we need to create three new directories. The first is the files directory which Drupal uses for storing uploaded files.

  cd /var/www/sites/default
  mkdir files
  sudo chown ubuntu:www-data files
  sudo chmod g+rw files

  cd /var/www/sites/all
  mkdir libraries


The above command creates the directory but sets the group to be the web server (i.e. www) with read/write permissions. This way the web server can write to the directory but so can we.

Web-based Steps

Navigate to the installation page of our new web site http://localhost/install.php

Tripal2.0 install1.png

Ensure that Standard is selected and click Save and Continue. You will next be asked to select the language you want to use. Choose English (which is probably the only choice).

Tripal2.0 install2.png

You will see a progress bar (as shown above) as Drupal is installed. Once it completes, a configuration page with some final settings will be visible.

Tripal2.0 install3.png


Set the following

  • Site Information
    • Site Name: Tripal 2.0
    • Site email: Your email address
  • Site Maintenance Account
    • Username: administrator (all lower-case)
    • Email: Your email address
    • Password: ********
  • Server Settings
    • Default country: (wherever the site is located)
    • Default time zone: (your time zone)
  • Update Notifications (both boxes checked)

Now, click the Save and Continue button. You will see a message about unable to send an email. This is safe to ignore for the tutorial, but for a production site you will need that your server can send emails to a service provider. Now, your site is enabled. Click the link Your new site:

Tripal2.0 install4.png

Drupal Cron Entry

The last step for installing Drupal is setting up the automatted Cron entry. The Drupal cron is used to automatically execute necessary housekeeping tasks on a regular interval. We want to integrate Drupal Cron with the UNIX Cron facility. To do so, we must first get the appropriate URL for the cron by navigating to ConfigurationCron. On this page you will see a link that we will use for cron:


Tripal2.0 cron1.png

In this example the URL is http://localhost/cron.php?cron_key=3979hhoUyiCQ2PhRpWEZc3lrnFbPvPeXSBDSC5kEk0U

To add an entry to the UNIX cron we must use the crontab tool:

  sudo crontab -e
A word on text editors such as nano.


Add this line to the crontab:

  0,30 * * * * /usr/bin/wget -O - -q http://localhost/cron.php?cron_key=3979hhoUyiCQ2PhRpWEZc3lrnFbPvPeXSBDSC5kEk0U


Now save the changes. We have now added a UNIX cron job that will occur every 30 minutes that will execute the cron.php script and cause Drupal to perform housekeeping tasks.

Drush

Drush is a command-line utility that allows for non-graphical access to the Drupal website. You can use it to automatically download and install themes and modules, clear the Drupal cache, upgrade the site and more. Tripal v2.0 supports Drush. For this tutorial we will use Drush and therefore we want the most recent version installed. Drush can be found on a GitHub page at https://github.com/drush-ops/drush. For ubuntu, Drush can be installed simply by issuing the following command:

  apt-get install drush

However, for older version of Ubuntu or other operation systems drush can be manually installed. To install manually, we want Drush to reside in /usr/local which is where 3rd party software is normally installed. We'll download the package to /usr/local/drush:

  cd /usr/local
  sudo git clone https://github.com/drush-ops/drush.git drush

Next, we want the operating system to know about drush. We'll create a symbolic link to the Drush executable in the /usr/local/bin directory where the operating systems looks for executables:

  sudo ln -s /usr/local/drush/drush /usr/local/bin/drush

Finally Drush needs to perform updates the first time it is run, so we'll run it with elevated privileges (using sudo) so that it can perform it's updates. In the future we no longer need 'sudo' to run drush:

  sudo drush

You must always run drush commands within the Drupal installation. It does not matter what subdirectory so long as you are in the Drupal directory sturcture. To see a list of available commands type the following:

  cd /var/www/
  drush

Explore Drupal

User Account Page

All users have an account page. Currently, we are logged in as the administrator. The account page is simple for now. Click the My account link on the left sidebar. You'll see a brief history for the user and an Edit tab. Users can edit their own information using the edit interface:

Tripal2.0 drupal user edit page.png

Creating Content

Creation of content in Drupal is very easy. Click the Add content link on the top administrative menu.

Tripal2.0 Drupal add content.png


You'll see two content types that come default with Drupal: Article and Basic Page. Here is where a user can add simple new pages to the website without knowledge of HTML or CSS. Click the Basic Page content type to see the interface for creating a new page:

Tripal2.0 Drupal add page.png


You'll notice at the top a Title field and a Body text box. All pages require a title and typically have some sort of content entered in the body. Additionally, there are other options that allow someone to enter HTML if they would like, save revisions of a page to preserve a history and to set authoring and publishing information.


For practice, try to create two new pages. A Home page and an About page for our site. First create the home page and second create the about page. Add whatever text you like for the body.

Finding Content

To find any content that has been created on the site, click the Find Content' link on the administrative menu at the top. The page shows all content available on the site. You will see the "About" and "Home" pages you created previously:

Tripal2.0 Drupal find content.png


You'll also notice a set of drop down boxes for filtering the content. For sites with many different content types and pages this helps to find content. You can use this list to click to view each page or to edit.

Site Administration

Site Building

Modules

Click the Modules link on administrative menu at the top of the page:

Tripal2.0 Drupal modules.png

Here is where you see the various modules that make up Drupal. Take a minute to scroll through the list and read some of the descriptions. The modules you see here are core modules that come with Drupal. Those that are checked come pre-enabled. Those that are not checked we will need to install them if we want to use them. To enable or "turn on" a module, check the box next to the desired module, then scroll to the bottom and click 'Save configuration'. Your site will now have the functionality provided by that module. Alternatively, you can search for modules that may be useful to your intended site design at the Drupal module repository, https://drupal.org/project/project_module, and install them by clicking the Install New Module link. Finally, a 3rd method to install modules is by use of the drush tool. We will use drush for this tutorial.

Themes

Next, click the Appearance link on the administrative menu at the top of the page:

Tripal2.0 Drupal appearance.png


Here, you'll see a list of themes that come with Drupal by default. Here you will see the default theme is called Bartik. This theme controls the appearance of all content on the site. You can easily change the way the site looks by changing the default theme to another theme. For this tutorial, we would like to use the Garland theme. If you scroll down you'll see that one theme named Garland. click the link in the Garland theme section titled Enable and set default. The current look of the site is using the Garland theme.

Tripal2.0 Drupal appearance garland.png


Now, click the house icon in the top left. Our home page now uses the Garland theme:

Tripal2.0 Drupal garland home.png

Blocks

Blocks in Drupal are used to provide additional content to any page that already exists. Examples of blocks might be a short overview of recent news items, Twitter feeds, links, recently added content, etc. The blocks interface can be found by navigating to StructureBlocks using the top administrative menu.

On this page you'll see a list of available blocks and where they are located within the site.

Tripal2.0 Drupal blocks.png

Here you can see that the Search form, Navigation, and User Login blocks are all on the left sidebar of Garland theme. There are also a list of other regions available that do not have any blocks and there are many blocks which are Disabled but could be added to a region on the page. For this tutorial, we would like for blocks to appear on the right sidebar rather than the left sidebar. Therefore, change the Search form, Navigation, and User Login to all use the right sidebar by changing the drop down box next to each one. When done, click the Save Blocks button at the bottom. Now when we view our home page the navigation links, search form and user login box (not shown while logged in) all appear on the right side:

Tripal2.0 Drupal garland home2.png

Menus

For this tutorial, we want to add new links in the Main Menu to our new Home and About pages we created earlier. In the Garland theme, the main menu appears in the top right corner and currently only has the link 'Home'. We want to change this link to direct to our new home page. But first, we need to find the path for our home page. The path for a page can be found in the address bar for the page. In Drupal pages of content are generally referred to as nodes. We can find the new home and about pages using the Find content link in the top administrative menu. If we click the link for our home page you'll see the address is http://localhost/node/1. Our about page is http://localhost/node/2 (i.e the first and second pages we created).

Drupal provides an interface for working with menus, including adding new menu items to an existing menu or for creating new menus. You can find the interface for working with menus by navigating to StructureMenus via the administrative top menu:


Tripal2.0 Drupal menu.png


Click the link list links in the operations section for the Main Menu. Here we see that the Home link already exists:


Tripal2.0 Drupal main menu.png

Click edit to change the location of the Home menu item. In the form that appears, we need to set the path for our new home page. The path for each of these nodes is simply node/1 and node/2. Fill out the form fields with these values

  • Menu Link Title: Home
  • Path: node/1
  • Description: Tripal 2.0 Demo Home Page
  • Enabled: checked
  • Show as Expanded: no check
  • Parent item: <Main menu>
  • Weight: 0

Tripal2.0 Drupal main menu home.png

The settings above will give the menu link a title of Home' and put it on the Main menu menu. If we then click the Save button at the bottom our Home menu item now redirects us to our new home page. Now, we also want to add a new menu item for the About page. Return to the Main menu configuration page and add a new link with the following values:

  • Menu Link Title: About
  • Path: node/2
  • Description: About this site
  • Enabled: checked
  • Show as Expanded: no check
  • Parent item: <Main menu>
  • Weight: 0

Click Save and a new menu item should appear. You can then change the order of the menu items by dragging and dropping the link using the cross-hairs next to each menu item.

URL Path

As mentioned previously, the URL paths for our pages have node/1 and node/2 in the address. This is not very intuitive for site visitors.


To set a path, click on our new About page in the new menu link at the top and click the Edit tab (you may have to close the overlay to see the menu item). Scroll to the bottom of the edit page and you'll see a section titled URL path setting. click to open this section. Since this is our about page, we simply want the URL to be http://localhost/about. To do this, just add the word about in the text box and click the Save button. You will now notice that the URL for this page is no longer http://localhost/node/2 but now http://localhost/about. Although, both links will still get you to our About page.

Tripal2.0 drupal edit about page.png

Now, use the instructions described above to set a path of 'home' for our home page.

Site Configuration

There are many options under the Configuration link of the administrative menu at the top. Here we will only look at one of these at the moment--the Site Information page. Here you will find the settings we made when installing the site. You can change the site name, add a slogan, mission and footer text to the. The section titled Front Page is where we can tell Drupal to use our new Home page we created as the first page visitors see when they view the site. We want this to be the same as the home page we created and added a link for in the Main menu. In this text box enter the text node/1. Notice there is no preceeding forward slash. Alternatively we could have used the URL path we added in the previous step. Let's add a slogan: Resources for Community Genomics.

Tripal2.0 Drupal site configuration.png

Now, click the Save configuration button at the bottom. You'll now see the slogan now at the top of the page. Also, if you click the site name or the home icon at the top left we are now redirected to the new home page.

User Accounts

For this tutorial, we will not discuss in depth the user management infrastructure except to point out:

  • User accounts can be created
  • Users are assigned to various roles
  • Permissions for those roles can be set to allow groups of users certain administrative rights or access to specific data.

Explore the Drupal User Management menu to see how users can be created, added to roles with specific permissions.

Prepare Drupal for Tripal

3rd Party Modules

We can install new extension modules which we will need later. For this tutorial we have several modules that we will need to install but which do not yet appear in the list of modules. To do this, we must follow these steps:

  1. Locate the extension modules on the Drupal website (https://drupal.org/)
  2. Retrieve the module using a drush command.
  3. Check for a README.txt or INSTALL.txt for any further instructions for installation of the module
  4. Return the the Drupal AdministerSite BuildingModules page and enable the module.


For an example, let's install the ctools which is a prerequisite for Tripal. The CTools module can be found here: http://drupal.org/project/ctools. We will download the current version using the drush command. On the command-line, execute the following:

  cd /var/www/sites/all/modules
  drush pm-download ctools


Check the README for additional installation instructions

  cd ctools
  ls

There is no README.txt so we are done with installation. Next, return to the Modules page and enable the Chaos Tools module by checking the box next to it:


Tripal2.0 ctools enable.png


Notice that the ctools package provided many modules and they all appear under a Chaos Tools Suite category.

Alternatively, you can enable the module using a simple drush command:

  drush pm-enable ctools


For this tutorial, the CCK, Views, and CKEditor modules should also be downloaded and installed following the same instructions above

drush pm-download views cck ckeditor

For CKEditor, the README file indicates we need to install the CKEditor library before we can enable this module. We must first get this package from online. The wget command can be used to download the file directly using the command-line:

Here is a quick command for downloading this file

  cd /var/www/sites/all/modules/ckeditor
  wget http://download.cksource.com/CKEditor/CKEditor/CKEditor%204.3.2/ckeditor_4.3.2_standard.zip

Now unzip the package and rename it according to the instructions

  unzip ckeditor_4.3.2_standard.zip

Once all installation steps have been completed the Views, CCK and CKEditor modules can be enabled with the following

   drush pm-enable views views_ui
   drush pm-enable cck
   drush pm-enable ckeditor


For reference, the modules installed above can be found here:

Configure CKEditor

Next, we need to configure the CKEditor which provides the MS Word-style interface for adding content. Navigate to ConfigurationCKEditor. You will see a page similar to the following:

Tripal2.0 ckeditor config.png

Click the 'Edit' link beside 'CKEditor Global Profile'. On the page that appears, we want to expand the 'Visibility Settings' and switch the radio button from 'Exclude' to 'Include'. Then clear all of the entries in the textbox named 'Fields to exclude/include':


Tripal-v1.1 ckeditor2.png

Add the following lines to the textbox you just cleared:

page@node/add/page.edit-body
chado_organism@node/add/chado-organism.edit-description
chado_organism@node/*/edit.edit-description
chado_analysis@node/add/chado-analysis.edit-description
chado_analysis@node/*/edit.edit-description

This will disable the CKEditor for all text boxes except for generic pages, organism descriptions and analysis descriptions. We can return later to add any other textareas to the list. You can find the identifier, similar to those we added to the textbox above, underneath any compatible text box. CKEditor puts the identifier under each textbox for your reference. Simply cut-and-paste the identifier. For example, the screenshot from the Create Page page is shown below. Notice the CKEdintifier for the textbox named sky:page@node/add/page.edit-body.. This was one of the identifiers we used in the textbox above, but with the theme name (e.g. sky) removed.

Tripal v1.1-ckeditor3.png

Click the Update global profile button. Next, under the Profiles section. Click the edit link next to Default profile. When the page appears, open the Editor Appearance section, and set the Toolbar by clicking the full link. finally, click the Save button.

Tripal Installation

Get the Software

To download Tripal and the Extension modules change to the directory where Drupal keeps it's modules:

cd /var/www/sites/all/modules

To obtain Tripal, issue the following 'git commands:

git clone http://git.drupal.org/sandbox/spficklin/1337878.git tripal
cd tripal
git checkout 7.x-2.0a

We also want to obtain several Extension modules that will be used in this tutorial. Those modules are available on the Extensions Page of the Tripal website. However, these extension modules are also available via a git repository so we will use a git commands to obtain these.

cd /var/www/sites/all/modules
git clone http://git.drupal.org/sandbox/spficklin/1578226.git tripal_blast_analysis
cd tripal_blast_analysis 
git checkout 7.x-2.0a-tripal_v2.0a

cd /var/www/sites/all/modules
git clone http://git.drupal.org/sandbox/spficklin/1578234.git tripal_kegg_analysis
cd tripal_kegg_analysis 
git checkout 7.x-2.0a-tripal_v2.0a

cd /var/www/sites/all/modules
git clone http://git.drupal.org/sandbox/spficklin/1578232.git tripal_interpro_analysis
cd tripal_interpro_analysis
git checkout 7.x-2.0a-tripal_v2.0a

cd /var/www/sites/all/modules
git clone http://git.drupal.org/sandbox/spficklin/1578230.git tripal_go_analysis
cd tripal_go_analysis 
git checkout 7.x-2.0a-tripal_v2.0a

cd /var/www/sites/all/modules
git clone http://git.drupal.org/sandbox/spficklin/1578246.git tripal_unigene_analysis
cd tripal_unigene_analysis
git checkout 7.x-2.0a-tripal_v2.0a

Applying Patches

A bug exists in Drupal related to the bytea data type in PostgreSQL. At the writing of this document, a fix is not yet incorporated into Drupal, but a patch has been provided. Execute the following commands to patch Drupal:

cd /var/www
wget --no-check-certificat https://drupal.org/files/drupal.pgsql-bytea.27.patch
patch -p1 < drupal.pgsql-bytea.27.patch

There is also a bug in the Drupal Views 3.0 code that prevents Tripal's administrative and search data views from functioning. The patch is provided within the tripal_veiws module. To apply the patch execute the following:

cd /var/www/sites/all/modules/views
patch -p1 < ../tripal/tripal_views/views-sql-compliant-three-tier-naming-1971160-22.patch

Tripal Installation

Previously in this Tutorial we enabled the Path and Search modules. The process for enabling the Tripal modules is the same. The site administrator can navigate to the AdministerSite BuildingModules page and enable each of the Tripal modules. However, Drush make it easier to enable modules from the command-line. First, we must enable the tripal_core module. Enter the following command

drush pm-enable tripal_core

Now that the core module is enabled, A new 'Tripal' menu item appears at the top.

Tripal2.0 install5.png

Next, we must next install Chado. In the web browser, navigate to TripalSetup TripalInstall Chado Schema. Because this is a fresh install, select the option to install Chado v1.2 and click the button Install/ugrapde Chado

Tripal2.0 install6.png

After the button is clicked a message will appear stating "Job 'Install Chado v1.2' submitted. Check the jobs page for status". Click the jobs page link to see the job that was submitted:

Tripal2.0 install7.png

The job is waiting in the queue until the Tripal jobs system wakes and tries to run the job. The jobs management subsystem allows modules to submit long-running jobs, on behalf of site administrators or site visitors. Often, long running jobs can time out on the web server and fail to complete. The jobs system runs separately in the background. In the example above we now see a job for installing Chado. The job view page provides details such as the name of the job, dates that the job was submitted and job status.

Jobs in the queue can be executed in two ways:

  • Manually through a command-line call
  • Using the UNIX cron to automatically launch the command-line

When we installed Drupal we installed a Cron job to allow the software to run housekeeping tasks on a regular bases. Tripal needs a cron entry as well to allow for regular execution of jobs in the queue. We will need to add a second cron entry:

   sudo crontab -e
A word on text editors such as nano.


Add this line to the crontab

   0,15,30,45 * * * * (cd /var/www; drush trpjob-run administrator ) > /dev/null


This entry will run the Tripal cron every 15 minutes as the administrator user. For this tutorial we do not want to wait 15 minutes at the most to execute our jobs. So, we will run the jobs manually. Tripal supports Drush and therefore has it's own commands. We can use drush to manually launch the job:

cd /var/www
drush trpjob-run administrator

As the installation of Chado proceeds, we should see the following text in the terminal window. The final message indicates that the installation of Chado was successful:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_core_install_chado(Install Chado v1.2, 1)
Creating 'chado' schema
Loading sites/all/modules/tripal/tripal_core/chado_schema/default_schema-1.2.sql...
Install of Chado v1.2 (Step 1 of 2) Successful!
Loading sites/all/modules/tripal/tripal_core/chado_schema/initialize-1.2.sql...
Install of Chado v1.2 (Step 2 of 2) Successful.
Installation Complete


Also, we see that the job has completed when refreshing the jobs management page:

Tripal2.0 install8.png

Now that Chado is installed, we can continue with installation of the remaining Tripal modules. These modules should be installed in the following order one at a time. If you install them all at once you may encounter errors later. Install the modules in the following way (and order):

drush pm-enable tripal_views
drush pm-enable tripal_db
drush pm-enable tripal_cv
drush pm-enable tripal_organism
drush pm-enable tripal_analysis
drush pm-enable tripal_feature

In this tutorial we will also discuss adding publications. The Tripal Pub module is dependent on the Tripal Contact module. We can enable both of them together:

drush pm-enable tripal_contact tripal_pub


Now, enable the remaining Tripal extension modules

drush pm-enable tripal_analysis_blast
drush pm-enable tripal_analysis_go
drush pm-enable tripal_analysis_interpro
drush pm-enable tripal_analysis_kegg

There are more Tripal modules that can be enabled (e.g. tripal_project, tripal_stock, etc.). But for this tutorial we will only be using the modules we enabled above.

The Tripal modules create directories in the /var/www/sites/default/files directory. By default, Drupal expects the 'sites/default/files' directory to be writeable by the web server. Because we installed the Tripal modules using Drush we need to reset the permissions for the web user. Execute the following command to give the web user group permission to write to that directory

sudo chown -R ubuntu:www-data /var/www/sites/default/files
sudo chmod -R g+rw /var/www/sites/default/files

Tripal is now installed with a fresh instance of Chado!

Controlled Vocabularies: Installing CVs

Before we can proceed with populating our Chado table with genomic data we must first load some controlled vocabularies (i.e. ontologies). To do this, navigate to TripalChado Data LoadersOBO File Loader. You'll see the following page:

Tripal2.0 cv1.png


The Ontology loader will allow you to select a pre-defined ontology from the drop down list or allow you to provide your own to be loaded. If you provide your own, you give the remote URL of the OBO file or provide the full path on the local web server where the OBO file is located. In the case of a remote URL, Tripal first downloads and then parses the OBO file for loading. If you do provide your own OBO file it will appear in the saved drop down list for loading of future updates to the ontology.

For this tutorial, we need to install these ontologies:

  1. Chado feature properties
  2. Relationship ontology
  3. Sequence ontology
  4. Gene ontology.

Do so by selecting an ontology from the drop-down and clicking the Submit button. Repeat this process for each of the four ontologies. You'll notice each time that a job is added to the jobs subsystem.


Now manually launch these jobs

cd /var/www
drush trpjob-run administrator


Note: Loading the Gene Ontology will take several hours.

Setting Perimssions

Because we are logged on to the site as the administrator user we are able to see all content. However, Drupal provides user management and permissions tools that allows the site admin to set which types of users can view the content on the site. By default there are two types of users anonymous and authenticated users. For this tutorial we want to set permissions so that anonymous visitors to the site can see the genomic content. To do this, navigate to PeoplePermissions. Here you will see permissions for all types of content.

Tripal2.0 Drupal permissions.png


Scroll through the list of permissions until you come to those for Tripal. Be sure to give anonymous and authenticated users the following permissions:

  • View Analyses
  • View Features
  • View Organisms

Each time you install a new module you should always check the Permissions page and set any new permissions that may have been added by the new module.

Using Tripal

Creating Organism Pages

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 manually add it using the Tripal web interface. The following two sections describe both methods.

What if Our Organism is Already in Chado?

Now that we have Chado loaded and populated we would like to create pages for our orgnisms. Chado comes pre-loaded with a few species already, so we will check to see if our organism is already present. To do this navigate to TripalChado ModulesOrganismsSync Organisms

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 our organism is already in the list (e.g. Drosophila melenogaster) then we need to inform Drupal that we have data in Chado for which we would like a web page. This is what we call Syncing. We need to sync Drupal and Chado so that Drupal knows about our organism. To do this, 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
drush trpjob-run administrator


Now that our 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.

Dmel.jpg

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

Tripal2.0 organism3.png

Manually Adding an Organism

For this tutorial we will be loading data for Citrus sinensis (sweet orange), 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:

Citrus sinensis.jpg

Save the page and view the new Organism:

Tripal2.0 organism4.png

Creating an Analysis

For this tutorial, we will later import a set of genes, and their associated mRNA, CDS, UTRs, etc. Tripal requires that an analysis be associated with all imported features. This has several advantages, including:

  • The source of features (sequences) can be traced. Even for features simply downloaded from a database, someone else can see where the features came from.
  • Provides a mechanism for describing how the features were created (e.g. whole genome structural and functional annotation description)
  • The analysis links all of the features together which can be useful for querying for specific features from an analysis.

To create an analysis for loading our genomic data, navigate to the Add content and click on the link: Analysis

The analysis creation page will appear:

Tripal2.0 analysis1.png

Here you can provide the necessary details to help others understand the source of your data. For this tutorial, enter the following:

  • Analysis Name: Whole Genome Assembly and Annotation of Citrus Sinensis (JGI)
  • Program, Pipeline Name or Method Name: Performed by JGI
  • Program, Pipeline Name or Method Name: v1.0
  • Source Name: JGI Citrus sinensis assembly/annotation v1.0 (154)
  • Source URI: http://www.phytozome.net/citrus.php
  • Time Executed: Feb 1, 2011
  • Materials and Methods: (if using CKEditor, click the 'Source' button before pasting)
<p>
	<strong><em>Note: </em>The following text comes from phytozome.org:</strong></p>
<p>
	<u>Genome Size / Loci</u><br />
	This version (v.1) of the assembly is 319 Mb spread over 12,574 scaffolds. Half the genome is accounted for by 236 scaffolds 251 kb or longer. The current gene set (orange1.1) integrates 3.8 million ESTs with homology and ab initio-based gene predictions (see below). 25,376 protein-coding loci have been predicted, each with a primary transcript. An additional 20,771 alternative transcripts have been predicted, generating a total of 46,147 transcripts. 16,318 primary transcripts have EST support over at least 50% of their length. Two-fifths of the primary transcripts (10,813) have EST support over 100% of their length.</p>
<p>
	<u>Sequencing Method</u><br />
	Genomic sequence was generated using a whole genome shotgun approach with 2Gb sequence coming from GS FLX Titanium; 2.4 Gb from FLX Standard; 440 Mb from Sanger paired-end libraries; 2.0 Gb from 454 paired-end libraries</p>
<p>
	<u>Assembly Method</u><br />
	The 25.5 million 454 reads and 623k Sanger sequence reads were generated by a collaborative effort by 454 Life Sciences, University of Florida and JGI. The assembly was generated by Brian Desany at 454 Life Sciences using the Newbler assembler.</p>
<p>
	<u>Identification of Repeats</u><br />
	A de novo repeat library was made by running RepeatModeler (Arian Smit, Robert Hubley) on the genome to produce a library of repeat sequences. Sequences with Pfam domains associated with non-TE functions were removed from the library of repeat sequences and the library was then used to mask 31% of the genome with RepeatMasker.</p>
<p>
	<u>EST Alignments</u><br />
	We aligned the sweet orange EST sequences using Brian Haas's PASA pipeline which aligns ESTs to the best place in the genome via gmap, then filters hits to ensure proper splice boundaries.</p>


Note:: Above we entered HTML. This is not the easiest way to enter text, but makes it simple for this tutorial. When the ckeditor module is installed and properly setup the user is provided with editor tools that makes it much easier to add text to any page.

After saving, you should have the following analysis page:

Tripal2.0 analysis2.png

Creating a Database Cross Reference

For our site, we want to create gene pages with sequences and have those pages link back to JGI where we obtained the genes. Therefore, we want to add a database reference for JGI. To add a new external databases, navigate to TripalChado ModulesDatabasesAdd a Database. The resulting page provides fields for adding a new database:

Tripal2.0 db1.png

Enter the following values for the fields:

The URL prefix is important as it will be used to create the links on our gene pages. Our gene name will be appended to this URL to create the link that will take us to the corresponding gene page on Flybase.

Click Add.

We now have added a new database!

Later we will also load Blast data. We need to create two new databases for those as well. Create the following entries for NCBI nr, and ExPASy SwissProt:


  • Name: ExPASy Swiss-Prot
  • Description: A curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases
  • URL: http://expasy.org/sprot/
  • URL prefix: http://www.uniprot.org/uniprot/

Loading Feature Data

Now that we have our organism and whole genome analysis ready, we can being loading genomic data. For this tutorial only a single gene from sweet orange will be loaded into the databsae. This is to ensure we can move through the tutorial rather quickly. The following datasets will be used for this tutorial:


Download these to the /var/www/sites/default/files. The quickest method is to right-click on the links above, then wget to retrieve the file:

  cd /var/www/sites/default/files
  wget http://www.gmod.org/mediawiki/images/d/dc/Citrus_sinensis-orange1.1g015632m.g.gff3
  wget http://www.gmod.org/mediawiki/images/8/87/Citrus_sinensis-scaffold00001.fasta
  wget http://www.gmod.org/mediawiki/images/9/90/Citrus_sinensis-orange1.1g015632m.g.fasta


Loading a GFF3 File

The gene features (e.g. gene, mRNA, 5_prime_UTRs, CDS 3_prime_UTRS) are stored in the GFF3 file downloaded in the previous step. We will load this GFF3 file and consequently load our gene features into the database. Navigate to TripalChado Data LoadersGFF3 file loader.

Tripal2.0 gff3 import.png

Perform the following:

  1. Enter the path on the file system where our GFF file resides (/var/www/sites/default/files/Citrus_sinensis-orange1.1g015632m.g.gff3)
  2. Choose the organism to which the GFF3 file belongs (in this case Citrus sinensis (sweet orange)
  3. Select the analysis named "Whole Genome Assembly and Annotation of Citrus sinensis...".
  4. Leave all other options as default.

Finally, click the Import GFF3 file button. You'll notice a job was submitted to the jobs subsystem. Now, to complete the process we need the job to run. We'll do this manually:

cd /var/www;
drush trpjob-run administrator

You should see output similar to the following:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_feature_load_gff3(/var/www/sites/default/files/Citrus_sinensis-orange1.1g015632m.g.gff3, 13, 10, 0, 1, 0, 0, 1, , , 0, , , , 0, 8)

NOTE: Loading of this GFF file is performed using a database transaction. 
If the load fails or is terminated prematurely then the entire set of 
insertions/updates is rolled back and will not be found in the database

Opening /var/www/sites/default/files/Citrus_sinensis-orange1.1g015632m.g.gff3
Parsing Line 138 (100.00%). Memory: 25,873,800 bytes.
Setting ranks of children...
Setting 10 of 10 (100.00%). Memory: 25,901,976 bytes.
Done

Note: For very large GFF files the loader can take quite a while to complete.

Loading FASTA files

Using the Tripal GFF loader we were able to populate the database with the genomic features for our organism. However, those features now need nucleotide sequence data. To do this, we will load the nucleotide sequences for the mRNA features and the scaffold sequence. Navigate to the TripalChado Data LoadersFASTA file loader Page


Tripal2.0 fasta loader.png


Before loading the FASTA file we must first know the Sequence Ontology (SO) term that describes the sequences we are about to upload. We can find the appropriate SO terms from our GFF file. In the GFF file we see the SO terms that correspond to our FASTA files are 'scaffold' and 'mRNA'.

IMPORTANT: It is important to ensure prior to importing, that the FASTA loader will be able to appropriately match the sequence in the FASTA file with existing sequences in the database. Before loading FASTA files take special care to ensure the definition line of your FASTA file can uniquely identify the feature for the specific organism and sequence type. For example, in our GFF file an mRNA feature appears as follows:

scaffold00001   phytozome6      mRNA    4058460 4062210 .       +       .       ID=PAC:18136217;Name=orange1.1g015632m;PACid=18136217;Parent=orange1.1g015632m.g

Note that for this mRNA feature the ID is PAC:18136217 and the name is orange1.1g015632m. In Chado, features always have a human readable name which does not need to be unique, and also a unique name which must be unique for the organism and SO type. In the GFF file, the ID becomes the unique name and the Name becomes the human readable name.

In our FASTA file the definition line for this mRNA is:

>orange1.1g015632m PAC:18136217 (mRNA) Citrus sinensis


By default Tripal will match the sequence in a FASTA file with the feature that matches the first word in the definition line. In this case the first word is orange1.1g015632m. As defined in the GFF file, the name and unique name are different for this mRNA. However, we can see that the first word in the definition line of the FASTA file is the name and the second is the unique name. Therefore, when we load the FASTA file we should specify that we are matching by the name because it appears first in the definition line.

If however, we cannot guarantee the that feature name is unique then we can use a regular expressions in the Advanced Options to tell Tripal where to find the name or unique name in the definition line of your FASTA file.

IMPORTANT: When loading FASTA files to update existing features, always choose "Update only" as the import method. Otherwise, Tripal may add the features in the FASTA file as new features if it cannot properly match them to existing features.


Now, enter the following values in the fields on the web form:

  • FASTA file: /var/www/sites/default/files/Citrus_sinensis-scaffold00001.fasta
  • Organism: Citrus sinensis (Sweet orange)
  • Sequence type: supercontig (scaffold is an alias for supercontig in the sequence ontology)
  • Method: Update only (we do not want to insert these are they should already be there)
  • Name Match Type: Name
  • Analysis: Whole Genome Assembly and Annotation of Citrus sinensis....

Click the Import Fasta File, and a job will be added to the jobs system. Run the job:

cd /var/www
drush trpjob-run administrator

Next do the same for the genes GFF:

  • FASTA file: /var/www/sites/default/files/Citrus_sinensis-orange1.1g015632m.g.fasta
  • Organism: Citrus sinensis (Sweet orange)
  • Sequence type: mRNA
  • Method: Update only
  • Name Match: Name
  • Analysis: Whole Genome Assembly and Annotation of Citrus sinensis....


Now run this job:

cd /var/www;
drush trpjob-run administrator

Now the scaffold sequence and mRNA sequences are loaded

Note It is not necessary to load the mRNA sequences as those can be derived from their alignments with the scaffold sequence. However, in Chado the feature table has a 'residues' column. Therefore, it is best practice to load the sequence when possible.


The FASTA loader has some advanced options which we will not cover in this tutorial. But briefly, the advanced options allow you to create relationships between features and associate them with external databases. For example, the definition line for an mRNA is:

>orange1.1g015632m PAC:18136217 (mRNA) Citrus sinensis

Here we have more information than just the feature name. We have a unique Phytozome accession number (e.g. PAC ID) for the mRNA. Using the External Database Reference section under Advanced Options we can provide the name of the database and a regular expression to tell the loader how to find the accession number in the definition line.

If the name of the gene to which this mRNA belonged was also on the definition line, we could use the Relationships section to link this mRNA with it's gene parent. Fortunately, this information is also in our GFF file and these relationships have already been made.

Creating Feature Pages

Now that we've loaded our feature data, we must "sync" them. Loading of the GFF file in the previous step has populated the feature tables of Chado for us, but now Drupal must know about these features. To sync features, navigating to TripalChado ModulesFeaturesSync.

Tripal2.0 feature sync.png

Here we can specify the types of features to sync and the organism. This allows us to create feature pages for different types of features for different organisms. In our case, we want gene and mRNA pages (these types were present in our GFF file). To only create pages for genes and mRNA we want to enter the sequence ontology terms gene and mRNA in the Feature Types box. Place each term on a separate line.

Next, select the organism "Citrus sinensis", and click the "Sync Features" button. A job is then added to the jobs management system which we need to manually run rather than wait on the cron entry to run it.

cd /var/www
drush trpjob-run administrator


Our features are now synced:


Tripal-Features-Synced.png

Note: It is not necessary to sync all types of features in the GFF file. For example, do not sync the scaffold. The feature is large and would have many relationships to other features. Only sync features that you will want users to view. For example, each mRNA is composed of several CDS features. These CDS features do not need their own page and therefore do not need to be synced..


Now, we can view our gene and mRNA pages. Click the Find Content link. to see the newly added features. Click the new page titled orange1.1g015615m, PAC:18136219 (mRNA) Citrus sinensis. Here we can see the gene feature we added and its corresponding mRNA's.

Tripal2.0 feature2.png

Materialized Views

Chado is efficient as a data warehouse but queries can become slow depending on the number of table joins and amount of data. To help simplify and speed these queries, materialized views can be employed. For a materialized view, a table is created and then populated with the results of a pre-defined SQL query. Therefore, rather than execute the pre-defined query which may take a long time, the query on the materialized view is more simple and faster. A side effect, however is redundant data, with the materialized view becoming stale if not updated regularly.

Tripal provides a mechanism for populating and updating these materialized views. These can be found on the TripalChado SchemaMaterialized Views page.

Tripal2.0 mviews.png


Here we see several materialized views. These were installed automatically by the various Tripal modules. To update these views, click the Populate button for each one.

This will submit jobs to populate the views with data. Now, run the jobs:

cd /var/www
drush trpjob-run administrator


You can now see that all views are up-to-date on the Materialized Views Page. The number of rows in the view table is shown:

Tripal-MViews-Populated.png


Materialized views are most useful when creating custom pages where data is queried in novel ways.

Feature Page Configuration

The feature configuration page allows us to perform configuration changes for the entire site. Navigate to the TripalChado ModulesFeaturesSettings page.

Feature URLs

First on the configuration page is the Feature URL Path settings. In this section, you can use tokens to create the URL path for each feature. By default, the URL string is /feature/[genus]/[species]/[type]/[uniquename]. The tokens in this URL string are [genus], [species], [type] and [uniquename]. These tokens are substituted by the genus, species, type and uniquename of the feature respectively. All other characters are left as is. Thus, for feature orange1.1g015615m the URL becomes: http://localhost/feature/citrus/sinensis/mRNA/PAC%3A18136219. You can change the tokens as desired. But, be certain to always create a URL that is guaranteed to be unique. The URL string provided by default will always be unique.

Tripal2.0 feature configure.png

Note: Additionally, Tripal uses these URLs for any feature /feature/[name] or feature/[uniquename]. These allow for more simple linking from external sites to the features in a Tripal site. For example, GBrowse can be configured to link to features in Tripal. If two or more features have the same name then Tripal will present a table of matching features for the user to select from.

Feature Browser

Next on the configuration page are Feature Browser settings. By default, Tripal will provide a browser on the organism page that allows a visitor to easily find a feature. For large sites with many features this would be an inefficient way to find a specific feature, but it does allow visitors who simply want to explore the site to quickly find example pages. This browser will only show synced features and will only show features of the type specified in the Feature Types box. We want to show genes pages so alter the contents of this box to contain only the word gene.

Tripal2.0 feature browser.png

Feature Summary Report

Next on the configuration page is the Feature Summary Report setting. By default, on the organism page, Tripal will provide a list of all features belonging to an organism and provide a pie-chart of this list. For example, below is a screen shot of the Feature Summary on the Citrus sinensis page for the data we loaded. This is only useful when data from a single analysis is associated with an organism. For sites with only a single unigene (transcriptome analysis) or a single whole genome then this summary would be appropriate. For sites with multiple analyses it may confuse site visitors who see mulitple counts.


Tripal2.0 feature summary.png

On the feature settings page, you can also specify which feature types should appear and rename them to be more meaningful. We want to provide a list of the total number of scaffolds, genes and mRNA. To do this, enter the following contents in the Map feature types box"

supercontig = Scaffolds
gene = Genes
mRNA

Cick the Save configuration button at the bottom. Now the Feature Summary on the organism page appears as:

Tripal2.0 feature summary2.png


Note The feature summary is only available when the organism_feature_count materialized view is populated. Each time new data is added, this materialized view should be re-populated to capture the changes and have those shown in the summary.

Loading Functional Data Using Extension Modules

For this tutorial we will be loading functional data for our gene. To do this we will use the Blast, KEGG, and InterPro extension modules. These modules were installed previously. Blast, KEGG and InterPro analyses were completed prior to this tutorial and results files are avaialble for downloading:

Download these files to the /var/www/sites/default/files directory. To do so quickly run these commands:

cd /var/www/sites/default/files
wget http://www.gmod.org/mediawiki/images/0/0c/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml
wget http://www.gmod.org/mediawiki/images/1/13/Citrus_sinensis-orange1.1g015632m.g.KEGG.heir.tar.gz
wget http://www.gmod.org/mediawiki/images/e/e8/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out
wget http://www.gmod.org/mediawiki/images/2/24/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_nr.out

Loading BLAST Results

Configuring BLAST Databases

Now that we have our features loaded we want to add some functional data as well. We need to create a new analysis page for our BLAST results. The Tripal Blast Analysis extension module will parse BLAST results and load them into Chado after a BLAST analysis page is created. However, before we create the page we need to ensure that the BLAST module can properly parse the BLAST hits. To do this, navigate to TripalExtension ModulesTripal Blast Analyses. On this page will be configuration settings for the Tripal BLAST Analysis extension module.

This page allows you to specify a different, more meaningful name for the sequence library file (a.k.a. database) used for BLASTing. This name will be displayed with BLAST results. You can also provide regular expressions for parsing BLAST hits. For example, the following is an line for a match from SwissProt:

sp|P43288|KSG1_ARATH Shaggy-related protein kinase alpha OS=Arabidopsis thaliana GN=ASK1 PE=2 SV=3

Here the hit name is "KSG1_ARATH", the accession is "P43288", the hit description is "Shaggy-related protein kinase alpha OS=Arabidopsis thaliana" and the organism is "Arabidopsis thaliana". We need regular expressions to tell Tripal how to extract these unique parts from the match text. Because Tripal is a PHP application, the syntax for regular expressions follows the PHP method. Documentation for regular PHP expressions can be found here. The following regular expressions can be used to extract the hit name, the accession, hit description and organism for the example SwissProt line above:

Element RE
Hit Name
^sp\|.*?\|(.*?)\s.*?$
Hit Description
^sp\|.*?\|.*?\s(.*)$
Hit Accession
^sp\|(.*?)\|.*?\s.*?$
Hit Organism
^.*?OS=(.*?)\s\w\w=.*$


In this tutorial, we will be adding BLAST results for the two databases we created earlier in the tutorial: ExPASy SwissProt and NCBI nr. First, select ExPASy SwissProt from the drop-down menu. A form will appear:

Tripal2.0 Blast settings.png

In the form fields, add the following values:

  • Title for the BLAST analysis: (leave blank)
  • Regular expression for Hit Name: ^sp\|.*?\|(.*?)\s.*?$
  • Regular expression for Hit Description: ^sp\|.*?\|.*?\s(.*)$
  • Regular expression for Hit Accession: ^sp\|(.*?)\|.*?\s.*?$
  • Regular expression for Organism: ^.*?OS=(.*?)\s\w\w=.*$
  • Organism Name: (leave blank)

Click Save Settings.

Note: The match accession will be used for building web links to the external database. The accession will be appended to the URL Prefix set earlier when the database record was first created.

Now select the NCBI nr database from the drop-down and click the radio button. NCBI databases use a format that is compatible with BLAST. Therefore, the hit name, accession and description are handled differently in the BLAST XML results. To correctly parse results from an NCBI database click the Use Genebank style parser checkbox. This should disable all other fields and is all we need for this database.

Load the BLAST Results

Now we can create out analysis page. Navigate to Create Content page and select the Analysis: BLAST content type. Add the following values for this analysis. In the fields set the following values:

  • Analysis Name: blastx Citrus sinensis v1.0 genes vs ExPASy SwissProt
  • Program: blastall
  • Program Version: 2.2.25
  • Algorithm: blastx
  • Source name: C. sinensis mRNA vs ExPASy SwissProt
  • Time Executed: (today's date)
  • Materials & Methods: C. sinensis mRNA sequences were BLAST'ed against the ExPASy SwissProt protein database using a local installation of BLAST on in-house linux server. Expectation value was set at 1e-6
  • BLAST Settings
    • Database: ExPASy SwissProt
    • BLAST XML File/Directory: /var/www/sites/default/files/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_uniprot_sprot.fasta.out
    • Parameters: -p blastx -e 1e-6 -m 7
    • Submit a job to parse the XML output: checked
    • Keywords for custom search: checked

Click the Save button. You can now see our new Analysis.

Tripal2.0 Blast analysis.png


Now we need to manually run the job to parse the BLAST results:

cd /var/www
drush trpjob-run administrator


The results should now be loaded. if we visit our feature page, for feature 'orange1.1g015615m' (http://localhost/feature/citrus/sinensis/mRNA/PAC%3A18136219) we should now see BLAST results by clicking the 'Homology' link in the left table of contents.

Tripal2.0 feature homology.png


Now we want to add the results for NCBI nr. Repeat the steps above to add a new analysis with the following details:

  • Analysis Name: blastx Citrus sinensis v1.0 genes vs NCBI nr
  • Program: blastall
  • Program Version: 2.2.25
  • Algorithm: blastx
  • Source name: C. sinensis mRNA vs NCBI nr
  • Time Executed: (today's date)
  • Materials & Methods: C. sinensis mRNA sequences were BLAST'ed against the NCBI nr protein database using a local installation of BLAST on in-house linux server. Expectation value was set at 1e-6
  • Blast Settings
    • Database: NCBI nr
    • Blast XML File/Directory: /var/www/sites/default/files/Blastx_citrus_sinensis-orange1.1g015632m.g.fasta.0_vs_nr.out
    • Parameters: -p blastx -e 1e-6 -m 7
    • Submit a job to parse the XML output: checked
    • Keywords for custom search: checked

Click the Save button and manually run the job:

cd /var/www
drush trpjob-run administrator

Return to the example feature page to view the newly added results: http://localhost/feature/citrus/sinensis/mRNA/PAC%3A18136219

Loading InterProScan Results

Now we want to load results from an InterProScan. For this tutorial, these results were obtained by using a local installation of InterProScan installed on a computational cluster. However, you may choose to use Blast2GO or the online InterProScan utility. Results should be saved in XML format.


To create an analysis, click the Add Content link in the administrative menu and select the content type Analysis: Interpro. Add the following values for this analysis

  • Analysis Name: InterPro Annotations of C. sinensis v1.0
  • Program: InterProScan
  • Program Version: 4.8
  • Algorithm: iprscan
  • Source name: C. sinensis v1.0 mRNA
  • Time Executed: (today's date)
  • Materials & Methods: C. sinensis mRNA sequences were mapped to IPR domains and GO terms using a local installation of InterProScan executed on a computational cluster. InterProScan date files used were MATCH_DATA_v32, DATA_v32.0 and PTHR_DATA v31.0.
  • InterPro Settings
    • InterProScan XML File/Directory: /var/www/sites/default/files/Citrus_sinensis-orange1.1g015632m.g.iprscan.xml
    • Check the box 'Submit a job to parse the Interpro XML output'
    • Check the box 'Load GO terms'
    • Parameters: iprscan -cli -goterms -ipr -format xml


Click the Save button. You can now see our new Analysis.

Tripal2.0 feature interpro.png


Now we need to manually run the job to parse the Inetpro results:

cd /var/www
drush trpjob-run administrator


The results should now be loaded. if we visit our feature page, http://localhost/orange1.1g015615m, we should now see interpro results by clicking on the "Interpro Report" link on the right sidebar.

Tripal2.0 feature interpro2.png

Loading KEGG Analysis Results

Now we want to load results from a KEGG/KAAS analysis (http://www.genome.ad.jp/tools/kaas/). The KAAS server receives as input a FASTA file of sequences and annotates those with KEGG orthologs and pathways. The tool also generates an heirarchy (heir) output file. This output file can be read directly by the Tripal Analysis KEGG module.

To create an analysis,click the Add Content link in the administrative menu and select the content type Analysis: KEGG. Add the following values for this analysis

  • Analysis Name: KEGG analysis of C. sinensis v1.0
  • Program, Pipeline Name or Method Name : KEGG Automatic Annotation Server (KAAS)
  • Program, Pipeline or Method version : 1.64a
  • Source name: C. sinensis v1.0 genes
  • Time Executed: (todays date)
  • Materials & Methods: C. sinensis mRNA sequences were uploaded to the KEGG Automatic Annotation Server (KAAS) where they were mapped to KEGG pathways and orthologs. The SBH (single-directional best hit) was used with the genes data set being the defaults for genes.
  • KEGG Settings
    • KAAS hier.tar.gz Output File: /var/www/sites/default/files/Citrus_sinensis-orange1.1g015632m.g.KEGG.heir.tar.gz
    • Check the box "Submit a job to parse the kegg output into Chado"


Click the Save button. You can now see our new Analysis.

Tripal2.0 kegg analysis.png

Now we need to manually run the job to parse the KEGG results:

cd /var/www;
drush trpjob-run administrator


A KEGG report is avilable on the analysis and the organism page. Navigate to the Citrus sinensis organism page and click the KEGG Reports in the Resources sidebar. A page with instructions is visible:

Tripal2.0 organism kegg.png


We have already loaded the data, therefore, we only need to popluate the kegg_by_organism materialized view. Click the link to populate the view. After populating the view we can now return to the organism page and view the KEGG report:

Tripal2.0 organism kegg2.png


Site visitors can browse KEGG results by expanding the trees correspoding to the the heirarchy terms. This same report is also visible on the KEGG analysis page.

Viewing Assigned Terms

When we imported the InterPro analysis results, the InterPro terms were assigned to the mRNA features. We also requested when we created the InterPro Analysis page that it parse GO terms from the results. As a result, GO terms have also been assigned. Also, when importing the KEGG results, KEGG orthologs and pathways were assigned to features. Therefore, we now have a new Annotated Terms item in the table of contents. For our example feature (http://localhost/feature/citrus/sinensis/mRNA/PAC%3A18136219), the results are as follows:

Tripal2.0 feature terms.png

NOTE: the remainder of this section is not yet accurate for Tripal v2.0-alpha. The GO Reports have not yet been fully ported. Once that work is completed, this part of the tutorial will be updated

Because we now have GO terms associated with features we can setup the GO report that appears on the organism page. Navigate to the Citrus sinensis organism page and click the Go Analysis Reports in the Resources sidebar. A page appears with instructions to the site administrator that gives details to make the report visible.

Triapl-GO-Report-NotSetup.png

Follow the instructions as presented on the page. Briefly, you need to

  1. Set the CV term paths for the three GO vocabularies. This should have been done automatically when you loaded the Gene Ontology earlier in the Tutorial.
  2. Populate the go_count_analysis materialized view.

When complete the following report will be visible:

Tripal-GO-Report.png

The GO report provides pie charts and an expandable tree for browsing results. Clicking on a GO term in the true will cause a box to appear with details about the term and a link to download a FASTA file of all features annotated with the term. Notice that the graphs are quite simple and the graph for the cellular component is missing. This is because we only loaded GO assignments for a single gene.

Adding Publications

Tripal provides an interface for automatically and manually adding publications. First we will manually add a new publication. To do this, we must first enable the Tripal Pub module. We have previously used Drush to install modules in this tutorial and the commands to install the Tripal Pub module are similar. The Tripal Contact module is a dependency of the Tripal Pub module, so we must enable both:

cd /var/www
drush pm-enable tripal_contact tripal_pub

You should see the following output in the terminal:

The following extensions will be enabled: tripal_pub, tripal_contact
Do you really want to continue? (y/n): y
tripal_contact was enabled successfully.                                                                   [ok]
tripal_pub was enabled successfully.                                                                       [ok]
The directory sites/default/files/tripal/tripal_pub has been created.                                      [status]
Job 'Load OBO Tripal Publication' submitted.  Check the jobs page for status                               [status]
The directory sites/default/files/tripal/tripal_contact has been created.                                  [status]
Job 'Load OBO Tripal Contacts' submitted.  Check the jobs page for status                                  [status]

You will notice that two jobs were submitted. These jobs will load a contact and publication ontology. The Tripal Contact and Pub ontologies are custom vocabularies used for organizing information about publications and contact information. So, before we can add publications (or contacts) we need to run these jobs:

cd /var/www
drush trpjob-run administrator

Note: Always remember to set permissions for any new modules that are installed.

Manually Adding a Publication

Now that the Tripal publication and contact ontologies are loaded we can add publications. First, we will manually add a publication. Click the Add Content link in the administrative menu and then Publication.

Tripal2.0 pub create.png

We will add information about the Tripal publication. Enter the following values:

  • Publication Title: Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.
  • Publication Type: Journal Article
  • Publication Year: 2013
  • Citation: Sanderson LA, Ficklin SP, Cheng CH, Jung S, Feltus FA, Bett KE, Main D. Tripal: a construction Toolkit for Online Genome Databases. Database, Oct 25 2013. bat075

To further describe the publication we will add all other details as properties. Select the property in the drop-down, add the text and click the add button for each of the following properties:

  • Journal Name: Database
  • Abstract: Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. DATABASE URL: http://tripal.info/.
  • Publication Date: 2013 Oct 25
  • Authors: Sanderson LA, Ficklin SP, Cheng CH, Jung S, Feltus FA, Bett KE, Main D


Next, to link this publication to it's record in PubMed we need to add an entry in the section titled Relationships. Add the following

  • PMID: 24163125


Now click the Save button at the bottom

Our publication has been added and you should see the following page:

Tripal2.0 pub new.png


Now we have a publication page, but the title links to the PubMed page for the article. If we want to change this link to be at the online journal. We can edit the publication by clicking the Edit link and adding a new property of type URL with the value:

http://database.oxfordjournals.org/content/2013/bat075.long

After saving the page, the title is now linked to the article on the Journal site rather than the PubMed site. However, the link to PubMed is still found under the Cross References link.

Searching for Publications

By default, Tripal provides simple search tools for many data types (e.g. organisms, analyses, features, etc). These can be found in the menu under Search Data. To search for publications, click the Publications link under Search Data.

On the search form, clicking the search button without providing any criteria will provide a list of all publications. For this tutorial, we only have a single publication:

Tripal2.0 pub search.png

However, you will notice that if you try to select a criteria that nothing is available. Tripal allows you to set which fields a user can use as criteria. In some cases not all fields will be appropriate given the publications available on the site. All of the properties available when adding a publication can be searched, but some properties like the URL may not be necessary for searching. You can specify which fields to use for search criteria by clicking the Publication Module Settings Page in the administrator information box just above the search form. At the top of the resulting page you will see a section for Searching Options:

Tripal2.0 pub search options.png

Here you can select which properties a user can use for searching. For this tutorial, find and check these options:

  • Abstract
  • Authors
  • Journal Name
  • Title

Then click the Save configuration button at the bottom. If we return to the publication search page, we now have criteria for searching.

Bulk Import of Publications

Tripal supports bulk importing of publications from remote databases such as NCBI PubMed and the USDA National Agricultural Library (AGL). Support of PubMed is built-in to the Tripal module, but support for AGL requires some additional setup on the server. You can find instructions for preparing the server for AGL on the TripalChado ModulesPublicationsHelp page. For this tutorial we will create an importer for PubMed.

Creation of an importer is an administrative function. A publication importer is created by the site administrator and consists of a set of search criteria for finding multiple publications at one time. When the importer is run, it will query the remote database, retrieve the publications that match the criteria and add them to the database. Because we loaded genomic data for Citrus sinensis we will create an importer that will find all publications related to this species.

First, navigate to TripalChado ModulesPublicationsPublication Importers and click the link New Importer. You will see the following page:

Tripal2.0 pub new importer.png

Enter the following values in the fields:

  • Remote Database: PubMed
  • Loader Name: Pubs for Citrus sinensis
  • Criteria #1:
    • Scope: Abstract/Title
    • Search Terms: Citrus sinensis
    • is Phrase?: checked

Now, click the 'Test Importer' button. This will connect to PubMed and search for all publications that match our provided criteria. On the date this portion of the tutorial was written, 532 publications were found:

Tripal2.0 pub new importer test.png

Now, save this importer. You should see that we have one importer in the list:

Tripal2.0 pub importer list.png

We can use this importer to load all 532 publications related to Citrus sinensis from PubMed into our database (how to load these will be shown later). However, what if new publications are added? We would like this importer to be run monthly so that we can automatically add new publications as they become available. But we do not need to try to reload these 532 again. So, we will create a new importer that only finds publications within the last 30 days. To do this, click the link New Importer. Now, add the following criteria:

  • Remote Database: PubMed
  • Loader Name: Pubs for Citrus sinensis last 30 days
  • Days since record modified: 30
  • Criteria #1:
    • Scope: Abstract/Title
    • Search Terms: Citrus sinensis
    • is Phrase?: checked

Now, when we test the importer we find only 1 publications that have been add (created) in PubMed in the last 30 days:

Tripal2.0 pub new importer test30.png


Save this importer.

Next, there are two ways to import these publications. The first it to manually import them. There is a Drush command that is used for importing publications. Return to the terminal and run the following command:

cd /var/www
drush tpubs-import

You should see output to the terminal that begins like this:

NOTE: Loading of publications is performed using a database transaction. 
If the load fails or is terminated prematurely then the entire set of 
insertions/updates is rolled back and will not be found in the database

Importing: Pubs for Citrus sinensis

And as publications are imported each one is printed to the screen. The importer will pause while it requests 100 publications. It will then load those, then pause to request another 100 until it imports all publications that match the criteria.

Some things to know about the publication importer:

  1. The importer keeps track of publications from the remote database using the publication accession (e.g. PubMed ID).
  2. If a publication with an accession (e.g. PubMed ID) already exists in the local database, the record will be updated.
  3. If a publication in the local database matches by title, journal and year with one that is to be imported, then the record will be updated. You can change the requirement of which fields to match at the TripalChado ModulesPublicationsSettings page. On the settings page, look for the Import Settings section.


The second way to import publications is to add an entry to the UNIX cron. We did this previously for the Tripal Jobs management system when we first installed Tripal. We will add another entry for importing publications. But first, now that we have imported all of the relevant pubs, we need to return to the importers list at TripalChado ModulesPublicationsPublication Importers and disable the first importer we created. We do not want to run that importer again, as we've already imported all historical publications on record at PubMed. Click the edit button next to the importer named Pubs for Citrus sinensis, click the disable checkbox and then save the template. The template should now be disabled.

Tripal2.0 pub impoter disabled.png

Now we have the importer titled Pubs for Citrus sinensis last 30 days enabled. This is the importer we want to run on a monthly basis. The cron entry will do this for us. On the terminal open the crontab with the following command:

sudo crontab -e

Now add the following line to the bottom of the crontab:

30 8 1,15 * *  su - www-data -c '/usr/local/drush/drush -r /var/www -l http://[site url] tpubs-import --report=[your email] > /dev/null'

Where

  • [site url] is the full URL of your site
  • [your email] is the email address of the user that should receive an email containing a list of publications that were imported. You can separate multiple email addresses with a comma.

The cron entry above will launch the importer at 8:30am on the first and fifteenth days of the month. We will run this importer twice a month in the event it fails to run (e.g. server is down) at least one time during the month.

Drupal Views Integration

Drupal Views is a powerful 3rd-party module that allows an authorized user to query database tables in novel and unique ways and to create custom pages and search forms. Tripal has fully integrates the Chado database tables with Drupal Views.

Adding a New View

As an introduction to Drupal Views, we will create a new page without any PHP or HTML programming. To create a new view navigate to Structure'Views and click the Add new view link near the top of the page. Here you see brief configuration page:

Tripal2.0 views new.png

Suppose we want to create a Species page for our site that lists all of the available species that our site houses. Tripal provides "teasers" for all of its pages. A teaser is a brief set of contents about a page. So, we want the Species page to be a list of organism page teasers. To do this, enter the following

  1. View name: All species
  2. Show: Content
  3. of type: Organism
  4. sorted by: Title
  5. Page title: Species
  6. Path: http://localhost/species
  7. Display format: Unformatted, list of teasers, with links, without comments
  8. Items to Display: 10
  9. Use a Pager: checked
  10. Create a menu link: checked
    1. Menu: Main menu
    2. Link text: Species

Despite that we will be creating a list of species, we select Show as Content. This is because all nodes (nodes are pages in Drupal lingo) have teasers. So, we want to use the node teasers. If however, we wanted to use content directly from the Chado organism table then we would have selected Chado Organism. The settings above also specify a page title, a filter to include only nodes (pages) of the Organism type, a URL for the page and details for adding the page to the main menu of the site.

Now we see the same form we saw before when editing an existing view, but there are no fields, sort criteria, or filters for this view. The first thing we want to do is indicate to the view that we will be using Node teasers. To do this, click the Row style link in the Basic Settings section. A box appears towards the bottom with radio buttons. Click the Save & Exit button. There should now be a link in the main menu at the top left of the page titled Species. If we click that link we can now see our new species page:

Tripal2.0 views species.png

Editing Existing Views

Many of the basic search tools available under the Search Data menu item are Drupal Views and hence can be customized using the Views interface. As a brief introduction to views we will examine one of these views and customize it. In order to use Views you need a basic understanding of the Chado tables.

First, navigate to StructureViews

Tripal2.0 views1.png

Here we see the list of the views that have already been created. All of the tripal views were created automatically by Tripal modules when they were enabled. At the bottom of the page are inactive views that come by default with the Views module. Scroll to the view titled Feature User Search and click the 'Edit' button to the right of it. You will see the following page:

Tripal2.0 views feature search.png

On this page you will see several sections: Title, Format, Fields, Filter Criteria, Sort Criteria, Page Settings and a few others. This tutorial will not describe all of these settings. There are tutorials on the web that better explains these fields. For this tutorial we will discuss only a few of them.

Breifly, the Fields section lists the fields that will be used for the view. For example, in this view we will be using the feature's uniquename, name, type, organism common name and a few other fields from the Chado feature table. We also have the node ID of the Drupal node that corresponds to the feature.

The Sort criteria section lists the order in which results will be shown. The results will be sorted by organism common name, feature type and feature name, in that order.

The Filters section provides a set of criteria for limiting which records will be shown. We want to limit the results by common name, feature type and feature name. The filters are used to create the search form at the top of the features search page:


Suppose we do not like the way our search pages behaves. Currently, for features, when search results are returned we see the unique name, name, feature type, common name of the organism, sequence length, if the sequence is obsolete and the date it was accessioned. We do not want the sequence length, or if the sequence is obsolete or the date it was accessioned to appear in our search results. And, suppose we want the genus and species to be listed instead of the common name. We can make these changes by editing the view settings.

First, we need to add the genus and species as fields to show. To do this, click Add in the header of the Fields' section. In the overlay a list of available fields will appear:

Tripal2.0 views fields.png

In the Filter Drop down you can see the Groups of fields associated with features. These groups correspond to Chado tables. Select the group Chado Organism. This reduces the list of fields to only those associated with the Chado orgnaism table. Click the checkbox for Chado Organism: Genus and Chado Organism: Species and click Apply (all displays).

Next we see a set of configuration settings for the fields we selected. In this case, we see configuration settings for the Genus field first.

Tripal2.0 views fields configure.png

Views will let you control a lot of how the field is seen (or not seen) in the page results. Here we want to leave all the defaults. click the Apply (all displays) button at the bottom. The configuration settings for the Species field now appears. Leave the defaults as well and click Apply (all displays). Now that we are done configuring our new fields we can preview the changes by viewing the example at the bottom of the page. Below is a screen shot of the view after we have added our new fields:

Tripal2.0 views preview.png

Now, we want to remove the unwanted fields. In the Fields section, click on the field named Chado Feature: Seqlen (Sequence Length). A configuration page appears similar to what we saw previously for Genus and Species. Check the box Exclude from display. This will leave the field present in the list of fields but will not show it in the resulting view. Click the Apply (all displays) button. Do the same for the common name, and is obsolete fields. Alternatively, if we no longer want to keep this field in the view, then we could remove the field by clicking the Remove button. Our view now appears as follows:

Tripal2.0 views preview2.png

Next, we want to limit results to only those with synced pages. Currently any feature present in the database is visible in the list, but we only have pages for genes and mRNA features. To limit the results only to synced features first locate the Filter Criteria' section and click the Add button in the header. In the Filter dropdown, select Content. The list of available fields for a Drupal node are available to select. All nodes must have a node ID. Therefore, we can filter results to exclude those that do not have a node ID. Look for the element titled Content: Nid, select it, and click the Apply (all displays button. A configuration screen appears:

Tripal2.0 views filters.png

We want to only show features that have a page which means that the Node ID (Nid) must not be empty. Therefore, select the is not empty(NOT NULL) from the operator dropdown and click Apply (all displays). Now, only synced features (those with pages) will appear in the list.

Tripal2.0 views preview3.png

Next, in the view preview the Type Id dropdown field used for filtering the results by feature type contains all available feature types. However, because we have limited our view to only show features with pages we also need to limit this list. We can easily do this by clicking the Chado Feature: Type Id field in the Filter Criteria section. On the configuration overlay that appears, click the Grouped Filters radio button under Filter type to expose. A new box appears that allows you to add the values that should appear in the drop down. We will limist search capabilities to just mRNA and genes as these are the two types of features that we have pages for. Add these two values as shown in the screen shot below and click the Apply (all displays button.

Tripal2.0 views filters2.png

Now, the Type Id dropdown only contains gene and mRNA. We can similarly limit the values that appear in the Organism Common Name dropdown as well.


If we click the Save button at the top right of the page, then this will save all of the changes we have made to the view and the Features search page under Search Data will be updated.

We have only touched on a few of the capabilities of the Views interface. You can create advanced looking forms and pages using Views.

Using the Bulk Loader

The bulk loader is a tool that Tripal provides for loading of data contained in tab delimited files. We have loaded files in standard file formats (e.g. FASTA, GFF, OBO), but Chado can support a variety of different biological data types and there are often no community standard file formats for loading these data. For example, there is no file format for importing genotype and phenotype data. Those data can be stored in the feature, stock and natural diversity tables of Chado. As another example, there is also no file format for bulk loading of organisms. The Bulk Loader was introduced in Tripal v1.1 and provides a web interface for building custom data loader. The site developer creates the bulk loader "template". This template can then be used and re-used for any tab delimited file that follows the format described by the template. Additionally, bulk loading templates can be exported allowing Tripal sites to share loaders with one another.

Before we can use the bulk loader we must enable the module. We can do this using a typical drush command:

cd /var/www/
drush pm-enable tripal_bulk_loader

Note: The bulk loader images shown here are from Tripal v2.0-alpha which looks very similar to the bulk loader in Tripal v1.1. There are plans to simplify the interface before a stable release of Tripal v2. Therefore, keep in mind that the interface may change

Plan How to Store Data

This tutorial will show a brief example of how to use the Tripal bulk loader to import a list of organisms and associate them with their NCBI taxonomy IDs. The input file we will use contains the list of all Fragaria (strawberry) species in NCBI at the time of the writing of this tutorial. Click the file and download

Download this file to the /var/www/sites/default/files. The quickest method is to right-click on the link above to copy the URL location, then use wget to retrieve the file:

cd /var/www/sites/default/files
wget http://gmod.org/mediawiki/images/a/a9/Fragaria.txt

This file has three columns: NCBI taxonomy ID, genus and species:

3747    Fragaria        x ananassa              
57918   Fragaria        vesca           
60188   Fragaria        nubicola                
64939   Fragaria        iinumae         
64940   Fragaria        moschata                
64941   Fragaria        nilgerrensis            
64942   Fragaria        viridis        


To use the bulk loader you must be familiar with the Chado database schema and have an idea for where data should be stored. It is best practice to consult the GMOD website or consult the Chado community (via the gmod-schema mailing list) when deciding how to store data. For this example, we want to add the species in the input file to Chado, and we want to associate the NCBI taxonomy ID with these organisms. The first step, therefore, is to decide where in Chado these data should go. In Chado, organisms are stored in the organism table. This table has the following fields:

organism Structure
FK Name Type Description
organism_id serial PRIMARY KEY
abbreviation character varying(255)
genus character varying(255) UNIQUE#1 NOT NULL
species character varying(255) UNIQUE#1 NOT NULL

A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.
common_name character varying(255)
comment text

We can therefore store the second and third columns of the tab-delimited input file in the genus and species columns of the organism table.

In order to store a database external reference (such as for the NCBI Taxonomy ID) we need to use the following tables: db, dbxref, and organism_dbxref'. The db table will house the entry for the NCBI Taxonomy; the dbxref table will house the entry for the taxonomy ID; and the organism_dbxref table will link the taxonomy ID stored in the dbxref table with the organism housed in the organism table. For reference, the fields of these tables are as follows:


db Structure
F-Key Name Type Description
db_id serial PRIMARY KEY
name character varying(255) UNIQUE NOT NULL
description character varying(255)
urlprefix character varying(255)
url character varying(255)


dbxref Structure
F-Key Name Type Description
dbxref_id serial PRIMARY KEY

db

db_id integer UNIQUE#1 NOT NULL
accession character varying(255) UNIQUE#1 NOT NULL

The local part of the identifier. Guaranteed by the db authority to be unique for that db.
version character varying(255) UNIQUE#1 NOT NULL DEFAULT ''::character varying
description text


organism_dbxref Structure
FK Name Type Description
organism_dbxref_id serial PRIMARY KEY

organism

organism_id integer UNIQUE#1 NOT NULL

dbxref

dbxref_id integer UNIQUE#1 NOT NULL


For our bulk loader template, we will therefore need to insert values into the organism, db, dbxref and organism_dbxref tables. In our input file we have the genus and species and taxonomy ID so we can import these with a bulk loader template. However, we do not have information that will go into the db table (e.g. "NCBI Taxonomy"). This is not a problem as the bulk loader can use existing data to help with import. We simply need to add the "NCBI Taxonomy" to Chado prior to creating the bulk loader template. We can do this using Tripal by navigating to TripalChado ModulesDatabases and click Add Database. We did this earlier in the tutorial when adding databases used for BLAST. Add a database with the following fields:

Creating a New Bulk Loader Template

Now that we know where all of the data in the input file will go and we have the necessary dependencies in the database (i.e. the NCBI Taxonomy database), we can create a new bulk loader template. Navigate to TripalChado Data LoadersBulk LoaderTemplates and click the link Add Template. The following page appears:

Tripal2.0 bulk loader new.png

We need to first provide a name for our template. Try to name templates in a way that are meaningful for others. Currently only site administrators can load files using the bulk loader. But, future versions of Tripal will provide functionality to allow other privileged users the ability to use the bulk loader templates. Thus, it is important to name the templates so that others can easily identify the purpose of the template. For this example, enter the name NCBI Taxonomy Importer (taxid, genus, species). The following page appears:

Tripal2.0 bulk loader create1.png

Notice that the page is divided into two sections: Current Records and Current Fields. Before we continue with the template we need a bit of explanation as to the terminology used by the bulk loader. A record simply refers to a table and an action on that table. For example, to insert the data from the input file we will need to select the database we just added from the db table and insert entries into the dbxref, organism and dbxref_organism tables. Therefore, we will have four records:

  • An insert into the organism table
  • A select from the db table (to get the database id (db_id) of the "NCBI Taxonomy" database needed for the insert into the dbxref table)
  • An insert into the dbxref table
  • An insert into the organism_dbxref table.

Each record contains a set of fields on which the action is performed. Thus, when we insert an entry into the organism table we will insert into two fields: genus and species.

To create the first record for inserting an organism, click the button New Record/Field. The following page appears:

Tripal2.0 bulk loader create2.png

By default, when adding a new record the bulk loader also provides the form elements for adding the first field of the record as well. Because we are adding the organism record we will first add the field for the genus. The first section at the top of the page is titled Type of Field. Here we specify the source of the field. Because the genus value comes from the input file, select the first radio button titled Data.

We are adding a field to a new record, so we can leave the Record drop-down as New Record. Next, give this record a human-readable name. Because we are inserting into the organism table, enter the name Organism into the Unique Record Name box. Next we need a human-readable name for the field. This field is the genus field so we will enter Genus into the Human-readable Title for Field box.

Next, we need to specify the Chado table for this record. In the Chado table drop down box, choose the organism table, and in the Chado Field/Column drop down box select genus.

In the next section, titled Data File Column, we need to indicate the column in the tab-delimited file where the genus is found. For the example file this is column 2 (columns are ordered beginning with number 1). Therefore, enter the number 2 in the Column box. There are additional options to expose the field to the user, but for now we can ignore those options. Finally, open the Additional options section and check the box Make this field required. This is important because if the field is missing from the input file then the bulk loader will throw an error and stop loading. Click the Save Changes button at the bottom. We now see that the organism record and the first field have been added to our bulk loader template.

Tripal2.0 bulk loader create3.png

We also see that the Mode (or action) for this record has been set to insert by default. Before continuing we should edit the settings for the record so that it is more fault tolerant. Click the Edit link to the left of the new organism record. On the resulting page we see the record details we already provided, but now there is a section titled Action to take when Loading Record. By default, the INSERT option is selected. This is correct. We want to perform an insert. Also, the SELECT if duplicate (no insert) is also selected. This is a good option to keep because it prevents the bulk loader from failing if the record already exists in the table.

Tripal2.0 bulk loader create4.png

Click the Edit Record button to save these settings. Now, you will see that the Mode is now set to insert or select if duplicate. Previously the Mode was just insert.

Next, we need to add the species field. Click the Add Field link to the left of the organism record name. Here we are presented with the same form we used when first adding the organism record. However, this time, the Record drop down already has the Organism record as we are not creating a new record. Provide the following values and click the Save Changes button:

  • Type of field: Data
  • Record: Organism (should already be set)
  • Human-readable Title for Field: Species
  • Chado table: organism (should already be set)
  • Chado Field/Column: species
  • Column: 3
  • Additional Options: check make this field required

We now have two fields for our organism record: Tripal2.0 bulk loader create5.png

At this point our organism record is complete, however there are still a few fields in the organism table of Chado that are not present in our record. These include the organism_id, abbreviation, common_name and comment fields. We do not have values in our input file for any of these fields. Fortunately, the organism_id field is a primary key field and is auto generated when a record is submitted. We do not need to provide a value for that field. The other fields are not part of the unique constraint of the table. Therefore, those fields are optional and we do not need to specify them. Ideally, if we did have values for those non-required fields we would add them as well.

To this point, we have built the loader such that it can load two of the three columns in our input file. We have one remaining column: the NCBI taxonomy ID. In order to associate an organism with the taxonomy ID we must first insert the taxonomy ID into the dbxref table. Examining the dbxref table, we see that a db_id field is a required value in a foreign key relationship. We must first retrieve the db_id from the db table of Chado before we can add the entry to the dbxref table. Therefore, we will create a second record that will do just that. On the Edit Template page click the button New Record/Field. Here we see the same form we used for adding the first organism record. Provide the following values:

  • Type of field: Constant
  • Record: New Record
  • Unique Record Name: NCBI Taxonomy DB
  • Human-readable Title for Field: DB name
  • Chado table: db
  • Chado field/column: name
  • Constant Value: NCBI Taxonomy


Here we use a field type of Constant rather than Data. This is because we are providing the value to be used in the record rather than using a value from the input file. The value we are providing is "NCBI Taxonomy" which is the name of the database we added previously. We select the db table and the field name from the db table. The goal is to match the name "NCBI Taxonomy" with an entry in the db table. Click the Save Changes button.

We now see a second record on the Edit Template page. However, the mode for this record is insert. We do not want to insert this value into the table, we want to select it because we need the corresponding db_id for the dbxref record. To change this, click the Edit link to the left of the NCBI Taxonomy DB record. Here we want to select only the option SELECT ONCE. We choose this option because the database entry that will be returned by the record will apply for the entire input file. Therefore, we only need to select it one time. Otherwise, the select statement would execute for each row in the input file causing excess queries. Finally, click Save Record. The NCBI Taxonomy DB record now has a mode of select once:

Tripal2.0 bulk loader create6.png

Now that we have a record that selects the db_id' we can now create the dbxref record. For the dbxref record there is a unique constraint that requires the accession, db_id and version. The version record has a default value so we just need to create two fields for this new record: the db_id and the accession'. We will use the db_id from the NCBI Taxonomy DB record and the accession is the first column of the input file. First, we will add the db_id record. Click the New Record/Field button and set the following:

  • Type of field: Record referral
  • Record: New Record
  • Unique Record Name: Taxonomy ID
  • Human-readable Title for Field: NCBI Taxonomy DB ID
  • Chado table: dbxref
  • Chado Field/Column: db_id
  • Record to refer to: NCBI Taxonomy DB
  • Field to refer to: db_id

Click the Save Changes button. The Edit Template page appears. Again, we need to edit the record. Click the Edit link to the left of the Taxonomy ID record. Select the following:

  • Insert
  • Select if duplicate

To complete this record, we need to add the accession field. Click the Add field link to the left of the Taxonomy ID record name. Provide the following values:

  • Type of Field: Data
  • Record: Taxonomy ID
  • Human-readable Title for Field: Accession
  • Chado table: dbxref
  • Chado field/column: accession
  • Column: 1
  • Additional Options: check make this field required

After saving, edit this record and make the necessary changes so that it is of mode insert or select if duplicate.

At this state, we should have three records: Organism, NCBI Taxonomy DB, and Taxonomy ID. We can now add the final record that will insert a record into organism_dbxref table. Create this new record with the following details:

Create Record with first field:

  • Type of Field: Record Referral
  • Record: New Record
  • Unique Record Name: Taxonomy/Organism Linker
  • Human-readable Title for Field: Accession Ref
  • Chado table: organism_dbxref
  • Chado field/column: dbxref_id
  • Record to refer to: Taxonomy ID
  • Field to refer to: dbxref_id

Create the second field:

  • Type of Field: Record Referral
  • Record: Taxonomy/Organism Linker
  • Human-readable Title for Field: Organism ID
  • Chado table: organism_dbxref
  • Chado field/column: organism_id
  • Record to refer to: Organism
  • Field to refer to: organism_id
  • Additional Options: check make this field required

Change the record mode to:

  • insert or select if duplicate

We are now done! We have created a bulk loader template that reads in a file with three columns containing an NCBI taxonomy ID, a genus and species. The loader places the genus and species in the organism table, adds the NCBI Taxonomy ID to the dbxref table and links it to the NCBI Taxonomy entry in the db table, and then adds an entry to the organism_dbxref table that links the organism to the NCBI taxonomy Id. The following screen shots show how the template should appear:

Record section:

Tripal2.0 bulk loader create7.png

Fields Section:

Tripal2.0 bulk loader create8.png

To save the template, click the Save Template link at the bottom of the page.

Creating a Bulk Loader Job (importing a file)

Now that we have created a bulk loader template we can use it to import a file. We will import the Fragaria.txt file downloaded in the previous section. To import a file using a bulk loader template, click the Add Content link in the administrative menu and click the Bulk Loading Job. A bulk loading job is required each time we want to load a file. Below is a screen shot of the page used for creating a bulk loading job.

Tripal2.0 bulk loader job.png

Provide the following values:

  • Import of Fragaria species
  • /var/www/sites/default/files/Fragaria.txt
  • Keep track of inserted IDs: No
  • File has a header: No

Click Save the page then appears as follows:

Tripal2.0 bulk loader job2.png


You can see details about constants that are used by the template and the where the fields from the input file will be stored by clicking the Data Fields tab in the table of contents on the left sidebar.

Tripal2.0 bulk loader job3.png

Now that we have created a job, we can submit it for execution by clicking the Submit Job button. This adds a job to the Tripal Jobs systems and we can launc the job as we have previously in this tutorial:

cd /var/www
drush trpjob-run administrator

After execution of the job you should see similar output to the terminal window:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_bulk_loader_load_data(62, 24)
Template: NCBI Taxonomy Importer (taxid, genus, species) (1)
File: /var/www/sites/default/files/Fragaria.txt (45 lines)

Preparing to load...
Loading...
	Preparing to load the current constant set...
		Open File...
		Start Transaction...
		Defer Constraints...
		Acquiring Table Locks...
			ROW EXCLUSIVE for organism
			ROW EXCLUSIVE for dbxref
			ROW EXCLUSIVE for organism_dbxref
	Loading the current constant set...
Progress:
[|||||||||||||||||||||||||||||||||||||||||||||||||||] 100.00%. (45 of 45) Memory: 29077528

Our Fragaira species should now be loaded, and we return to the Tripal site to see them. Click on the Organisms link in the Search Data menu, and in the Genus text box type Fragaria and click the Filter button. We should see the list of newly added Fragaria species.

Tripal2.0 org search fragaria.png

These Fragaria species are not synced and do not have pages which is why there are no links for them in the search results. To check if the NCBI taxonomy IDs are properly associated, we can sync all or some of them. We can sync organisms as per the instructions earlier in this Tutorial, but in short, navigate to TripalChado ModulesOrganismsSync and select the species you would like to sync and then execute the sync job. Once complete, return to the search form, find a Fragaria species that has been synced and view it's page. You should see a Cross References link in the left table of contents. If you click that link you should see the NCBI Taxonomy ID with a link to the page:

Tripal2.0 org f chiloensis.png

Customizing Tripal

Tripal is designed to be fully customizable such that a site developer can alter the look-and-feel or the data presented on any Tripal page. There are two ways to customize Tripal:

  1. Edit the available template files that control what and how data is presented
  2. Create a custom module to support more complex search forms, custom tables, visualiations, or alternate data views.

There are several resources available to assist developers extend Tripal

  1. The Tripal API contains a set of functions for accessing Chado data and just about all functionality provided by Tripal.
  2. The Tripal Developer's Handbook contains instructions for customizing templates and creating custom modules
  3. Tripal 2.0 comes with a new Tripal Example module as part of the source code. This module contains all of the hooks and logic needed to create a custom Tripal module.

Note: The developer's handbook is still for v1.1 a version for v2.0 will be coming soon

Customizing The Look-and-Feel of Tripal

The default look-and-feel of data presented by Tripal is set in Drupal-style template files. When logged on as a site administrator, each of the Tripal pages contains a blue box that gives the path to the template file that provides the content. For example, the following screen shot of a feature page shows a blue box at the bottom indicating that the template file that provides the Overview content can be found in the Drupal installation at: sites/all/modules/tripal/tripal_feature/theme/templates/tripal_feature_base.tpl.php. Clicking each link in the table of contents on the left sidebar shows that each type of content has a differnet template file.

Tripal2.0 feature admin notice.png


You can alter a template file by:

  1. Copying it to your default theme directory.
  2. Customizing the code in the default theme directory.
  3. Clear the Drupal cache (use the 'drush cc all command in the terminal window to clear the cache.

Despite that the template file exists in both the Tripal module directory and your default theme directory, Drupal selects the template in the theme directory first. The reason for copying the templates out of the Tripal directory is to allow for future updates to the Tripal code without overwriting any of your customizations. If you are using one of Drupal's default themes, such as Garland, then you may have the same problem with loosing customizations if you upgrade Drupal. In this case, be sure to backup your theme templates before proceeding with an upgrade.

When editing a Tripal template file there are a few best practices to follow:

  1. Do not use SQL statements in the template. Tripal makes all data from any Chado table available within the templates.
  2. If you find you must write an SQL statement because the data query is too complex for the API functions, consider creating a custom module rather than adding SQL to template file. Drupal provides function "hooks" for "preprocessing" of variables available to template files. It is in these function hooks where you can create custom SQL for a template.
  3. Tripal Developer's Mailing List: This list is intended for developers who need help creating custom modules.
  4. Use the Drupal theming functions. An important feature of Tripal is that changing a site's theme can change the look and feel of the entire site. If you use the Drupal theme functions in your customizations then you are guaranteed to maintain consistency in the look-and-feel of the site. For example, Drupal provides theme functions for tables and ordered lists. Using these, rather than creating your own HTML code for tables and lists ensures consistency.

Creating Custom Modules

This tutorial will not cover how to create a custom module. But, once created, custom modules that conform the the Tripal API and Drupal coding standards will be officially approved by the Tripal Developers Group. These modules will be listed on the Tripal website and will be available in the Drupal module repository for download. Anyone wishing to extend Tripal should take advantage of the resources listed previously for development.