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- <h3>Module Description:</h3>
- <p>The Tripal DB Module provides the ability to add database cross reference to
- the
- data in your Tripal Website. Typically an external database (such as NCBI
- Genbank, Gene Ontology (GO),
- stocks database) contains a collection of objects (genomic sequences,
- vocabulary terms, stocks) that are
- uniquely identified using an accession number (or identifier). Data loaded
- into Tripal can be a
- associated with these objects in remote databases, and links can appear on
- pages allowing site visitors
- to view the associated objects on the remote database\'s website </p>
- <h3>Setup Instructions:</h3>
- <ol>
- <li><p><b>Set Permissions</b>: By default only the site administrator
- account has access to
- or administer databases. Navigate to
- the <?php print l('permissions page', 'admin/user/permissions') ?>
- and set the
- permissions under the 'tripal_db' 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>Adding or Editing an External Databases</b>. Many resources such
- as NCBI nr or ExPASy SwissProt (to name a few)
- come pre-loaded with Chado. However, you can add new entries or edit
- existing entries. Also, when loading
- ontologies (controlled vocabularies) using the Tripal CV module new
- databases are added automaticaly for
- each ontology. To enable linking of accession on a page to the page
- for that accession on the external
- database, simply add the URL and the URL prefix when adding or
- editing a database.</p></li>
- <li><p><b>Associate Data with Accessions</b>. The Tripal loaders (e.g. GFF,
- OBO) can associate accessions from
- remote data to genomic features and controlled vocabularies
- automatically. Use the loaders to load genomic
- features and controlled vocabularies respectively. Additionally, the
- bulk loader can be used to create
- loading templates for associating external database accessions.
- </p></li>
- </ol>
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