tripal_db_help.tpl.php 2.3 KB

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  1. <h3>Module Description:</h3>
  2. <p>The Tripal DB Module provides the ability to add database cross reference to
  3. the
  4. data in your Tripal Website. Typically an external database (such as NCBI
  5. Genbank, Gene Ontology (GO),
  6. stocks database) contains a collection of objects (genomic sequences,
  7. vocabulary terms, stocks) that are
  8. uniquely identified using an accession number (or identifier). Data loaded
  9. into Tripal can be a
  10. associated with these objects in remote databases, and links can appear on
  11. pages allowing site visitors
  12. to view the associated objects on the remote database\'s website </p>
  13. <h3>Setup Instructions:</h3>
  14. <ol>
  15. <li><p><b>Set Permissions</b>: By default only the site administrator
  16. account has access to
  17. or administer databases. Navigate to
  18. the <?php print l('permissions page', 'admin/user/permissions') ?>
  19. and set the
  20. permissions under the 'tripal_db' section as appropriate for your
  21. site. For a simple setup, allow anonymous
  22. users access to view content and create a special role for creating,
  23. editing and other administrative tasks.</p></li>
  24. <li><p><b>Adding or Editing an External Databases</b>. Many resources such
  25. as NCBI nr or ExPASy SwissProt (to name a few)
  26. come pre-loaded with Chado. However, you can add new entries or edit
  27. existing entries. Also, when loading
  28. ontologies (controlled vocabularies) using the Tripal CV module new
  29. databases are added automaticaly for
  30. each ontology. To enable linking of accession on a page to the page
  31. for that accession on the external
  32. database, simply add the URL and the URL prefix when adding or
  33. editing a database.</p></li>
  34. <li><p><b>Associate Data with Accessions</b>. The Tripal loaders (e.g. GFF,
  35. OBO) can associate accessions from
  36. remote data to genomic features and controlled vocabularies
  37. automatically. Use the loaders to load genomic
  38. features and controlled vocabularies respectively. Additionally, the
  39. bulk loader can be used to create
  40. loading templates for associating external database accessions.
  41. </p></li>
  42. </ol>