Trees

Tree_big Trees in Specify

Specify 6 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.

The default permissions that Specify ships with allow Guest users to View the trees, but not modify them in any way. By default, all other types of users can perform all read/write/update operations on data in tree displays.

 

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.

 

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 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

Trees are available through a tree button on the task bar. The task bar is configurable in Preferences. Users that do not have the tree button included on their task bar can add it by clicking Edit > Preferences > Task Bar on Windows, or Specify > Preferences > Task Bar on the Mac, then checking the Trees box.

Tree and Task Bar preferences are only available to users with permission to use the trees.

Click  Trees on the task bar to open the tree tool. Trees are grouped by their task on the side bar.

View Tree lists the Trees available to view. Click on a tree to open it in View mode in the work space.

Edit Tree lists the Trees available for the collection. Click a tree to open it in the work space.

Open Tree Definition lists the Definitions for each tree. This tool defines the ranks available in a tree as well as with how these ranks are enforced in data entry and used in aggregating the full name. Before adding nodes to an empty tree, the tree Definition must be completed. Please refer to Tree Definitions.

Unlock a Tree is only available to users with appropriate permission.

Simultaneous editing of a tree or tree definition and the corresponding form is not allowed for the same user. Multiple users can edit tree data in a data form, but a tree display, and the corresponding data table form may not be open at the same time. Trees are available for viewing, searching or querying simultaneously, but not editing. A second user may only edit a tree or tree definition after the first user closes their tree edit tab.

If your project requires multiple users to add data to a Geography, Taxon, Storage, Lithostratigraphy or Chronostratigraphy table, they must use the related form for those data types and not the tree displays.

When a tree is being edited by a user (A) and another user (B) opens the tree, a prompt will notify user (B) that the tree is in use by user (A) and will open in view mode. Then the tree will open to view.

In the event that a tree becomes locked and the user of that tree cannot be located, (which may occur due to uncontrolled shutdown of the application, or someone leaving their desk for a long period without closing a tree), the tree can be unlocked, by clicking it under the 'Unlock a Tree' heading if you have been granted the necessary permissions. This action will remove the original user from the tree and close his activities there.

 

Tree Tools

Expand a Node

Click the forward (expand) icon to expand nodes on the tree.

Expand a Tree Column

  1. Mouse over the header column until a crossbar appears.
  2. Right-click and drag to expand the column.

 

Toolbar Buttons

Button

Definition

Result

left

Move Column Left Shifts the entire tree to the left, closing the highest rank.

ExpandParent20

Move Column Right Shifts the entire tree to the right, opening the highest rank.

reparent_20

Select Parent Walks up the tree selecting the parent node.

Split Screen Creates two simultaneous mirror images of the tree. This allows different sections of the tree to be viewed and edited, which is useful when trees are large. Changes made to one of the Trees will be updated in the second tree.

Single Screen Reverts the tree display to a single screen.

edit

Edit Node Opens a form for editing the node.

add

Add Child Opens a form for adding a child to the selected parent.

delete

Delete Child Deletes the child. The table below shows the instances in which nodes may not be deleted.

sync view

Sync Split Screens Syncs the split screen views to display the same section of the tree on each screen.

 

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.

Note: Any edits/additions to large trees may take several minutes to save.

 

Dragging and Dropping to Move, Synonymize or Merge nodes in a Tree

Nodes can be dragged and dropped onto other nodes within a tree. When the screen is split, nodes can be dragged and dropped within the same screen or into the opposite screen. While dragging a node a highlight box will appear around any nodes that can accept the node being dragged (the hightlight will appear when the node being dragged is over the top of the accepting node). Dragging and dropping is used to:

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. Moves may only occur when a node Does Not have any children.

Synonymize the node (in the Geography and Taxon trees only). The node that is dragged and dropped becomes a synonym of the accepting, or target node. 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. Synonym text color can be set in Preferences. 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, right-click on the node, then click Undo Synonymy in the resulting Context Menu.

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

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. 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 of collection objects associated with each node can be enabled for all trees. This feature requires data processing and therefore is not enabled by default. Enable Collection Object Counts on a tree by choosing Preferences > Tree. See also Preferences.

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.

 

More Options (Context Menu)

A right-mouse click on the node offers the following choices:

Option

Result

Move columns left

Shifts the entire tree to the left, closing the highest rank.

Find Next

Finds the next usage of the exact name. For instance, Johnson may be used as the name of a county in different states. This would find the next 'Johnson' in the Geography tree.

Edit ... (View)

Opens the taxon form for the node. When editing the tree, the Edit option will appear, when viewing the tree, the View option will appear.

Delete

Deletes the node. See the table above for deletion requirements.

Add Child

Opens a form for adding a child.

Undo Synonymy

Restores the node as a preferred taxon name. This is only available on the Geography and Taxon trees.

Associated Collection Objects

Opens any associated Collection Objects in Collection Object forms for the active collection only.

 

Find

Click Cntl + F to open the Find tool (which opens under the tree Workspace). This is particularly useful to expand the tree to the end Nodes.

Button

Result

Find Searches for the search term.
Next Searches for the next use of the search term.

up

Searches the upper tree.

down

Searches the lower tree.

downup

Searches both trees.
check_boxExact Checking this box will allow Specify to search the exact search term as entered. Specify by default uses a wildcard at the end of a search term. Checking this box will terminate the wildcard and search only the term as entered into the search text box.

The arrow icons refer to the view that is appropriate for the search when using a split screen. When using a single screen simply use the up (Upper) button.

Find and select a node by typing a few letters in a single term, or a single term, into the Find text box and clicking the Find button. Full taxon names are not accepted, so enter a name from a single rank, such as genus.

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.