Trees in Specify 7

Specify 7 visually presents some data types in hierarchical tree displays. These data types include the information in the Taxon, Geography, (Specimen) Storage, Chronostratigraphy and Lithostratigraphy tables. These data types, or tables, are also included in the form system, but the tree displays offers a more convenient single-screen view of the data. And some data tasks are more intuitive when performed in tree displays as compared to data forms.

The Taxon, Geography, Chronostratigraphy and Lithostratigraphy trees (and tables) are scoped at the Discipline level, meaning that all collections within a Discipline share the same tree. Collection Objects in a particular collection though, that are associated with the nodes on what might be a shared tree across two or more collections, will only see the Collection Objects in that particular collection. (Linked Collection Objects can be seen by right-clicking on a tree node and choosing Associated Collection Objects from the pop-up context menu.) Associated Collection Objects from the ensuing context menu.)

The Storage tree is scoped at the Institution level, but as with the other trees only collection objects for the current collection will be shown when right-clicking on the node and choosing Associated Collection Objects from the context menu.

Specify Tree Terminology

The various Trees show relationships in a hierarchical structure. The hierarchies are composed of levels or ranks represented by columns in the display. Data values (e.g. taxa) are referred to as "nodes", and nodes are related to one another in "parent-child" relationships. Nodes within the next rank lower in the hierarchy are referred to as "children" And every node, except the basal root node, has one "parent" node.

Ranks are shown in columns on the tree. tree column colors can be set in Preferences > Tree. See also Preferences.

Specify 6 Tree Setup

Building Ranks

Each tree is visually displayed as hierarchical ranks. Ranks must first be defined in a tree definition, then nodes (data values) can be added. Ranks are defined through the use of either the Specify 6 Setup Wizard and the Add a Discipline Wizard. Ranks are edited, enforced in the Tree Definition tool. The full name is also configured in the tree definition tool.

Building Trees

All Trees can be defined and loaded into Specify through either the Specify Setup Wizard or the Add a Discipline Wizard. Data in these trees include:

  • Converted Taxon authority files for each of the Disciplines from the Catalog of Life.
  • Converted Geographic authority files from online website of the World Gazetteer, which includes Continent, Country, and States throughout the world as well as County data for the United States.
  • Chronostratigraphy authority files for five ranks in the North American System as converted from the Geological Society of America.
  • Four predefined ranks for Lithostratigraphy.
  • Ranks for the Storage tree.

Users who do not wish to build their trees through a Specify Wizard may build their own trees in the following ways:

  • Manually by adding one record at a time. This will be necessary for the Storage tree, as it is unique to each Institution and Collection.
  • In a batch operation from an existing user database. This may include a conversion from another database, which the Specify team can help with, or by a data import through the WorkBench.
  • n a batch process, by downloading and importing an authority file from an authority source.

Using Trees

You can navigate to the Tree interface by clicking the Trees button in the navigation bar.

Deleting Nodes

Nodes on specific trees can only be deleted if the following trees are not used in the specified ways:

Tree

Use

Taxon

  • not used in a Determination.
  • not included in a Taxon citation.
  • not a parent node of a Hybrid.
  • not a preferred name of a Synonym.
  • not a parent Node.

Geography

  • not used in a Locality.
  • not a preferred name of a Synonym.
  • not a parent Node.

Storage

  • not used in a Preparation.
  • not a preferred name of a Synonym.
  • not a parent Node.

Chronostratigraphy

  • not used in a Paleo Context.
  • not a preferred name of a Synonym.
  • not a parent Node.

Lithostratigraphy

  • not used in a Paleo Context.
  • not a preferred name of a Synonym.
  • not a parent Node.

If deletions are required, the condition or conditions preventing the deletion must first be eliminated. For example, open the related Collection Object record and delete the determination before deleting the tree node.

It is important to remember that the Institution tree is shared by all collections in an Institution and all other trees are shared by all collections within a single Discipline. Nodes that are not being used by your collection may have associations in other collections and therefore can not be deleted.

Take Actions (Move, Synonymize or Merge nodes)

After selecting a node in a tree, you will see the following in the top right of the tree interface become interactable:

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Move

Move a node (and its child nodes) to a new parent. This is useful when a data entry error has occurred, or a new node has been introduced while uploading from the WorkBench. Nodes may be moved between ranks, but enforced ranks may not be skipped.

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Synonymize

Synonymize the node (in the Geography and Taxon trees only). The node that is selected first a synonym of the second node selected. This new preferred node is called the accepting, or target node.

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In this instance, I first selected Spatularia, then selected Proceros. After clicking Synonymize, I confirmed this node synonymization. Now, the node Spatularia is in red and references are now synonymized with Proceros. The target node is then the Preferred node. Changes in taxon are reelected in fields in the Determinations table. Collection object determinations are captured in the Taxon and Preferred Taxon fields. When a taxon is not a synonymy these fields will both refer to the same taxon (A). If taxon (A) becomes a synonymy of taxon (B) the Taxon field will still reflect Taxon (A) but the Preferred Taxon will change to Taxon (B).

Child nodes can not be added to a synonymized node and, in the same instance, parent nodes can not be synonymized unless their child nodes are first synonymized.

In the Taxon tree, nodes at the species level and below can be synonymized within and between ranks, but any node higher than species can only be synonymized within the same rank. In other words, a family level node may only be synonymized to another family level node.

Synonyms are differentiated from non-synonyms by their text color (by default, red). Synonyms also show as a tool tip on the node. Tool tips are displayed by holding the mouse over a rank.

To undo a synonymy, select the node, then click Undo Synonymy in the menu bar.

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Note: When taxa are synonymized in the Taxon tree, the Preferred Taxon field on the determination form is updated.

Synonymized node item colors are set in the User Preferences.

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Merge

Merge parts of the tree. This is typically performed to correct parts of the tree that are duplicated. For instance; if the country of the United States of America were entered as both "United States" and "U.S." and both included a large number of children (presumably U.S. states), a correction would require many distinct actions.

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Specify’s Tree Merge function however allows users to combine all the child information and choose the accepted form of a parent. The children of the node being dragged (unwanted node) will merge with those included in the node being targeted (remaining node) and the unwanted node will disappear. For example, if in the example above the “United States” included the states of Ohio and Oregon and the “U.S.” included the states of California and Hawaii and the user dragged the “U.S.” node and dropped it onto the “United States” node the tree will then have only the United States as a country (parent) with the states (children) California, Hawaii, Ohio and Oregon. If both nodes originally contain Ohio with various children of that rank (in this case U.S. Counties) t will be combined into a single node and all Counties would be accumulated or merged if they were previously redundant.

Once the node is dropped onto the accepting node a dialog will appear asking if the user would like to perform the appropriate task; i.e. synonymize the node (when applicable), move the node (when applicable) or merge the node and children (when applicable).

Select Cancel on the dialog to place the node back in its original position.

Collection Object Counts

Counts are displayed next to the Node as two numbers (X,Y):

  • X represents the number of Collection Objects for the Node only.
  • Y represents the number of Collection Objects for the Rank and all nodes beneath it.

The last node on the tree will only show the X value, as there are no nodes beneath it.

Find

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To find a node on the tree, you can use the Search Tree function in the top-left of the tree view.

By default, Specify places a wildcard at the end of a search term. Specify will also recognize an astrisk (*) as a wildcard when typing a search term when typed in front of, or in the middle of each search term. For instance, Joh*n could be used to search for Johnson County in the Geography tree.

Click the Next button to find the next usage of the term in the tree. For instance, if Johnson is the name of a county in different states, typing the term in the find text box and clicking the Find button will find the first instance of Johnson in the tree. Clicking the Find button a second time will find the next instance of 'Johnson' in the Geography tree.