Improving Drupal Taxonomy Editor

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Improving Drupal Taxonomy Editor

  1. 1. Improving the Drupal Taxonomy Editor for Biology Alexey Shipunov EOL [email_address]
  2. 2. Tasks <ul><li>Name editing, changing name strings </li></ul><ul><li>Classification editing, or manipulating the hierarchies in which organisms are arranged. </li></ul><ul><li>Reconciliation, or creation of name ontologies where we group together alternative names for the same species </li></ul>
  3. 3. Name editing <ul><li>There are 1,800,000 named species </li></ul><ul><li>Over 10,000,000 names in our compilation </li></ul><ul><li>100,000,000 names eventually </li></ul><ul><li>In hundreds of forever changing taxonomies </li></ul><ul><li>The name editor should allow: </li></ul><ul><li>To add new names manually and also a semi-automatic batch addition(s) </li></ul><ul><li>To change the misspelled name (add a lexical variant) </li></ul><ul><li>To delete the mistaken name entry (i.e., make name not visible) </li></ul>
  4. 4. Classification editing <ul><li>Allow changes in the classification: first of all, move branches </li></ul><ul><li>Allow changes to hierarchy level, i.e. rank </li></ul><ul><li>Allow changes to batches of multiple names </li></ul><ul><li>Delete children </li></ul><ul><li>To do it as easily as possible (see the next slide) </li></ul>
  5. 5. Reconciliation <ul><li>Reconciliation is a way to group different names for the same entity (taxon) together </li></ul><ul><li>The simplest example – name and its synonyms: </li></ul><ul><ul><li>Homo sapiens Linnaeus 1758 (scientific name, preferred name)* </li></ul></ul><ul><ul><li>Homo sapiens L. 1758 (scientific name) </li></ul></ul><ul><ul><li>Homo sapiens (scientific name, canonical name) </li></ul></ul><ul><ul><li>Human (vernacular name, English) </li></ul></ul><ul><ul><li>Homa sapiens (misspelled name) </li></ul></ul><ul><ul><li>Homo troglodytes L. (scientific name, subjective synonym) </li></ul></ul><ul><li>* The items in parentheses are flags that define the relationships among the names </li></ul>
  6. 6. Reconciliation 2 <ul><li>In biology, it is very important to retain all alternative names, even misspellings </li></ul><ul><li>Reconciliation is changeable: for example, if someone finds an earlier name for species, this name becomes the preferred name within the reconciliation group </li></ul>
  7. 7. <ul><li>Name editing </li></ul><ul><ul><li>Add </li></ul></ul><ul><ul><li>Delete </li></ul></ul><ul><ul><li>Edit </li></ul></ul><ul><ul><li>Flag </li></ul></ul><ul><ul><li>Assign rank </li></ul></ul><ul><ul><li>Batch functions </li></ul></ul><ul><li>Classification editing </li></ul><ul><ul><li>Change rank </li></ul></ul><ul><ul><li>Move branch: two windows, drag and drop interface </li></ul></ul><ul><li>Reconciliation editing </li></ul><ul><ul><li>Add, delete, change synonyms – ideally a two window drag and drop environment </li></ul></ul><ul><ul><li>Allow different kinds of synonyms </li></ul></ul><ul><ul><li>Allow flags </li></ul></ul><ul><ul><li>Merge and split reconciliation groups </li></ul></ul>The ideal editor
  8. 8. “ Union Editor prototype” <ul><li>Edit, add, delete </li></ul><ul><li>Move subtrees with 2 windows </li></ul><ul><li>Relatively fast </li></ul><ul><li>No synonyms </li></ul><ul><li>No merging </li></ul><ul><li>No ranks </li></ul><ul><li>No flags </li></ul>
  9. 9. Drupal Taxonomy Editor <ul><li>Edit, add, delete </li></ul><ul><li>Move subtrees with 1 window </li></ul><ul><li>Synonyms </li></ul><ul><li>Merging </li></ul><ul><li>No ranks </li></ul><ul><li>No flags </li></ul><ul><li>No different kinds of synonyms </li></ul><ul><li>Relatively slow </li></ul>
  10. 10. Things to implement <ul><li>Flags </li></ul><ul><li>Ranks </li></ul><ul><li>Two-windows interface </li></ul><ul><li>Different kinds of synonyms </li></ul><ul><li>Increase speeds </li></ul><ul><li>Or maybe it is better to create a new taxonomy editor especially for biology? </li></ul>

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