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Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
Improving Drupal Taxonomy Editor
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Improving Drupal Taxonomy Editor


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