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Optima User Guide

User Interface Layout

Visualizers: Optima has 2 visualizers, one for each of the ontologies. Optima uses welkin platform as starting point.

Statistics: On the bottom of each of the visualizer, the following information is displayed

  • numbers of nodes in the ontology
  • numbers of edges in the ontology
  • matches tell us the number of matched node after the alignment
  • elapsed time tells us the time it took to complete the alignment process

Predicates: Each predicate contained in the loaded RDF model is shown, grouped by their URIs common prefixes.

Resources: This area of the tool is used to focus on the resources themselves. This is the panel that allows that. Two widgets perform actions on the relative URI:

  • a checkbox - turns on/off the visualization of the nodes (and the properties that were connected to it) associated to this resource. This is useful to restrict the model to only those resources that belong to a particular ontology or namespace.
  • a slider - changes the color of the nodes associated to this resource. This is useful to color-code different resources and isolate ontologies based on the information contained in the URI.

Charts: There are three graph-theoretical properties of a node

  • In Degree - the number of edges that point to the node.
  • Out Degree - the number of edges that start from the node.
  • Clustering Coefficient - the proportion of edges between the nodes within its neighbourhood divided by the number of nodes that could possibly exist between them.

Tree structure visualization: Optima has the option of visualizing ontologies in a tree format. It uses the breadth-first search graph traversal algorithm. If an ontology has no root, Optima adds a virtual root node called "Top" to the ontology. It traverses all nodes starting from the root to specify its position in the tree structure. Apart from the other forms of visualization, this provides a visualization of the hierarchial structure of the ontology.

Load ontology: The load ontology button on the tool performs the following actions:

  1. Loads the source ontology
  2. Loads the target ontology
  3. Provides options to enter the alignment parameters and seed-map (Details are specified in the seed-map and parameter sections below)

Clear: The clear button in the tool is used to clears the visualizers and optima can be used to load different set of ontologies.

Align Button: The align button is used to start the alignment process.


The commands are divided in three tabs:

  • Drawing - contains the main commands that drive the activity and the drawing properties of the graph pane. Here is a list of the commands and their effect:
    • Active- turns on/off the activity of the graph pane.
    • Circle- resets the position of all the nodes in a circle centered inside the graph pane.
    • Scramble- resets the position of all the nodes randomly around the graph pane.
    • Shake - add a random shift from the current position. This is useful to "give the graph a kick" because there are cases where the energy minimization algorithm encounters a local minimum and not a global one. By shaking the nodes, you might force the graph to reach the global minimum, thus a more meaningful representation of the clusters.
    • Nodes- turns on/off the drawing of nodes.
    • Edges - turns on/off the drawing of edges. This is very useful to speed up the calculations since normally a lot of time is spent in drawing the edges. For large graphs it's useful to start the graph without edges and then turn them on once the graph has reached a more stable state.
    • Antialias- turns antialiasing on/off. In some platforms, antialiasing can be very expensive, just like edges above you can achieve a faster drawing performance by disabling it during graph processing and re-enable it when the graph reaches a more stable state.
    • Background - turns background drawing for the graph panel on/off. On some platforms, disabling this gains a little time too.
  • Highlight - drives the search and highlight of nodes that have literals or URIs that match particular substrings. The nodes that match get their labels turned on.
  • Parameters - fine tune parameters for the graph activity algorithm.

Seed-map: To facilitate or steer the alignment, users may initially enter the seed matches by selecting pairs of nodes from the ontologies.

The user is given an option to choose between specifying a seed-map and using a default seed-map.

How do default values work?

The general idea behind the default values is to generate the seed-map without the user worrying about it.

The algorithm used for generating default seed-map is to generate the map based on the string similarity between the nodes of the two ontologies. If a node name of source ontology has a 100% string match with a node name of target ontology, then those two nodes are added into the default seed-map for alignment.

How do you choose a seed-map?

Clicking: A single click on the node will display the node name, that goes off when the button is released.

Double-clicking: Double clicking the node highlights the node name of the ontology. The node name stays until a double click occurs again.

After loading the ontologies, user should do the following:

  1. Double click a node from the source ontology and double click a node from the target ontology to add it into the seedmap. Continue this process until the complete seed map is selected.
  2. Clicking OK in the status bar will have the seed map accepted and it is later used in alignment.
  3. If the user is not satisfied with the selected seed-map and wants to go with the default, he can do so by clicking the default seedmap button.

Parameters: Parameters control the alignment process.

How are parameters set?

There are 2 parameters that can be set to run the alignment algorithm.

  1. Samples: The number of mixture model samples that should be generated at each iteration. A portion of these are generated by heuristics and some randomly.
  2. Iterations: The number of iterations the algorithm should be run to obtain the results of the alignment.

The user can then click the OK button to accept the values and use them in the algorithm or can go with the default values by clicking the default values button.

What are the default values?

The default values for the samples and iterations are 3 and 2 respectively.

Status bar: The status bar is present above the visualizers and beside the load and align buttons. The status bar provides status of the tool at any particular time.
  1. Loading Ontologies: This status is displayed when the load button is clicked and the user is in the process of loading the ontologies.
  2. Seed-map and parameter status: After clicking the submit button in the load dialog box, status box displays the user choice of seed-map and parameters the status bar.
  3. Alignment completed: This status is displayed after the alignment is finished.

Alignment Dialog: After starting the alignment of ontologies, the alignment dialog is displayed which shows the user a progress of alignment. After the alignment completes the dialog disappears.

Clicking: A single click on the node will display the node name, that goes off when the button is released.

Double-clicking: Double clicking the node highlights the node name of the ontology. The node name stays until a double click occurs again.

Save Alignment: The align button turns into save alignment button after the alignment is completed. The user can save the alignment based on the Ontology Alignment Evaluation Initiative (OAEI) XML format.

Viewing the alignment: The aligned nodes are shown in blue in each of the visualizers. User can double click the aligned node of one ontology, and the corresponding matched node name in the ontology can be visualized. The node names disappear in both the visualizer if a highlighted node name is double-clicked again. We don't show all the names simultaneously as the names might become clustered.