The Tripal Feature module provides a new feature content type and interface for genomic features.
After installation of the feature module. The following tasks should be performed
Set Permissions: By default only the site administrator account has access to create, edit, delete or administer features. Navigate to the and set the permissions under the 'tripal_feature' section as appropriate for your site. For a simple setup, allow anonymous users access to view content and create a special role for creating, editing and other administrative tasks.
Loading of Ontologies: Before loading genomic features you must also have several vocabularies loaded as well. Using the you should load the following ontologies:
Create Organisms: Before adding feature data you must already have the organisms loaded in the database. See the for instructions for adding and Syncing organisms.
Create an Analysis: Tripal requires that feature data loaded using the Tripal loaders be associated with an analyis. This provides a grouping for the feature data and can be used later to visualize data pipelines. Before loading feature data through the FASTA or GFF loaders you will need to for the data.
Create Database Cross References: If you would like to associate your feature data with an external database, check to ensure that the . If not you should before importing feature data. Be sure to set the URL and URL prefix for the database if you would like accessions (e.g. GO terms, NCBI accession) to link out to the external database.
Data Import: if you do not already have an existing Chado database with preloaded data then you will want to import data. You can do so using the Chado perl scripts that come with the normal distribution of Chado or you can use the FASTA loader and GFF loader provided here. If you created the Chado database using Tripal then you'll most likely want to use the Tripal loaders. If your data is not condusive for loading with these loaders and you can get your data into a tab-delimited format you can use Tripals' bulk loader.
Sync Features: After data is loaded you need to sync features. This process is what creates the pages for viewing online. Not all features need be synced. For instance, if you have loaded whole genome sequence with fully defined gene models with several features to define a gene and its products (e.g. gene, mRNA, CDS, 5\'UTR, 3\'UTR, etc) you probably only want to create pages for genes or genes and mRNA. You probably do not want a page for a 5\'UTR. Using the Feature Sync page you can sync (or create pages) for the desired feature types.
Set Feature URL: It is often convenient to have a simple URL for each feature page. For example, http://www.mygenomesite.org/[feature], where [feature] is a unique identifier for a feature page. With this, people can easily include links to feature pages of interest. Use the Feature Configuration page to specify whether to use the feature name, unique name or internal ID as the [feature] portion of the URL. Select the one that will guarantee a unique identifier for feature pages.
Aside from data loading and feature page setup (as described in the Setup section above), The Tripal feature module also provides the following functionality
Retrieve Sequences: A tool to is provided which allows end-users to download sequences in FASTA format. The site admin must first load sequence residues as well as alignments. The and materialized views must be populated before using this tool. Those views should be re-populated when new data is added. If you use the the tool may break. You will need to update the jquery_update/replace/jquery.form.js file with .
Generic Feature URL: As described in the setup instructions above, it is often convenient to have a simple URL for each feature page. For example, http://www.mygenomesite.org/[feature], where [feature] is a unique identifier for a feature page. The allows a site admin to generate unique URLs for all feature. The unique URL is necessary, however, sometimes it is easier to allow for links to the feature name without knowing the unique URL. This is possible using the URL: http://[site url]/feature/[feature name], where [site url] is the URL for the site and [feature name] is the name of the feature. If the feature name is not unique then a page will be presented listing all of the features with the same name and allow the user to choose which one to view. If the feature name is unique then the user will automatically be redirected to the unique URL for the feature.
Feature Browser: The feature browser is a tabular list of features with links to their feature pages which appears on the organism page. It was created to provide a mechanism to allow site visitors to quickly accesss feature pages when they do not know what to search for. For sites with large numbers of features, this method for finding a specific pages is inadequate, but may still be included to aid new site visitors. This browser can be toggled on or off using the Feature Configuration page
Feature Summary Report: The feature summary report is a pie chart that indicates the types and quantities of feature types (Sequence Ontology terms) that are loaded in the database. It appears on the organism page. The summary can be toggled on or off using the Feature Configuration page
Integration with Drupal Views: Drupal Views is a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content. It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database and create custom lists without PHP programming or customization of Tripal source code. Views can also be created to filter content that has not yet been synced with Druapl in order to protect access to non published data (only works if Chado was installed using Tripal). You can see a list of available pre-existing Views here, as well as create your own.
Simple Search Tool: A is provided for finding features. This tool relies on Drupal Views. Drupal Views which must be installed to see the search tool. Look for it in the navigation menu under the item "Search Data".
Delete Features: You can bulk delete features by providing a list of feature names, or for a specific organism or for a specific feature type. Be sure you have a full backup of your site before performing a bulk delete.