tripal/legacy/tripal_feature/theme/templates/tripal_feature_help.tpl.php

<h3>Module Description:</h3>
<p>The Tripal Feature module provides a new feature content type and interface
    for genomic features. </p>

<h3>Setup Instructions:</h3>
<p>After installation of the feature module. The following tasks should be
    performed</p>
<ol>
    <li><p><b>Set Permissions</b>: By default only the site administrator
            account has access to create, edit, delete
            or administer features. Navigate to
            the <?php print l('permissions page', 'admin/user/permissions') ?>
            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.</p></li>

    <li><p><b>Loading of Ontologies</b>:
            Before loading genomic features you must also have several
            vocabularies loaded as well. Using the
        <?php print l('OGO loader', 'admin/tripal/loaders/chado_vocabs/obo_loader') ?>
            you should load the following
            ontologies:</p>
        <ul>
            <li>Sequence Ontology</li>
            <li>Gene Ontology (if loading GO terms for features)</li>
        </ul>
    </li>

    <li><p><b>Create Organisms</b>: Before adding feature data you must already
            have the
            organisms loaded in the database. See the
        <?php print l('Tripal Organism Admin Page', 'admin/tripal/tripal_organism') ?>
            for
            instructions for adding and Syncing organisms.</p></li>

    <li><p><b>Create an Analysis</b>: 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 <?php print l('create an analysis', 'node/add/chado-analysis') ?>
            for the data.</p></li>

    <li><p><b>Create Database Cross References</b>: If you would like to
            associate your feature data with an
            external database, check to ensure that
            the <?php print l('database already exists', 'admin/tripal/tripal_db/edit_db') ?>
            .
            If not you
            should <?php print l('add a new database record', 'admin/tripal/tripal_db/add_db') ?>
            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.</p></li>

    <li><p><b>Data Import</b>: 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
            <a href="http://gmod.org/wiki/Chado">distribution of Chado</a> or
            you can use
            the
            <a href="<?php print url('admin/tripal/tripal_feature/fasta_loader') ?>">FASTA
                loader</a> and
            <a href="<?php print url('admin/tripal/tripal_feature/gff3_load') ?>">GFF
                loader</a> 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.
        </p></li>

    <li><p><b>Sync Features</b>: 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 <a
                    href="<?php print url('admin/tripal/tripal_feature/configuration/sync') ?>">Feature
                Sync page</a>
            you can sync (or create pages) for the desired feature types. </p>
    </li>

    <li><p><b>Set Feature URL</b>: 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
            <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Feature
                Configuration page</a>
            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.</p></li>

</ol>


<h3>Features of this Module:</h3>
<p>Aside from data loading and feature page setup (as described in the Setup
    section above),
    The Tripal feature module also provides the following functionality</p>
<ul>
    <li><p><b>Retrieve Sequences</b>: A tool
            to <?php print l('retrieve sequences', 'find/sequences') ?> 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 <?php print l('organism_feature_count', 'admin/tripal/mviews') ?>
            and
        <?php print l('analysis_organism', 'admin/tripal/mviews') ?>
            materialized
            views must be populated before using this tool. Those views should
            be re-populated
            when new data is added. If you use
            the <?php print l('jquery_update module', 'http://drupal.org/project/jquery_update') ?>
            the tool may break. You will need to update the
            jquery_update/replace/jquery.form.js file with <?php
        print l('a more recent version', 'https://raw.github.com/malsup/form/master/jquery.form.js') ?>
            . </p></li>

    <li><p><b>Generic Feature URL</b>: 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
        <?php print l('Feature Configuration page', 'admin/tripal/tripal_feature/configuration') ?>
            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.</p></li>

    <li><p><b>Feature Browser:</b> 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
            <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Feature
                Configuration page</a></p></li>

    <li><p><b>Feature Summary Report:</b> 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
            <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Feature
                Configuration page</a></p></li>

    <li><p><b>Integration with Drupal Views</b>: <a
                    href="http://drupal.org/project/views">Drupal Views</a> 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 <a href="<?php print url('admin/build/views/') ?>">here</a>,
            as well as create your own. </p></li>

    <li><p><b>Simple Search Tool</b>:
            A <?php print l('simple search tool', 'chado/features') ?> is
            provided for
            finding features. This tool relies on Drupal Views. <a
                    href="http://drupal.org/project/views">Drupal Views</a>
            which must be installed to see the search tool. Look for it in the
            navigation menu under the item
            "Search Data". </p></li>

    <li><p><b>Delete Features</b>: You can <a
                    href="<?php print url('admin/tripal/tripal_feature/delete') ?>">bulk
                delete features</a>
            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.</p></li>
</ul>