CAIS - Comparative Anatomy Information System for the Foundational Model of Anatomy (FMA) and the Mouse Anatomy Ontology (MOA)

User information: how-to guide

This is information about how to use the graphical interface of the application.

Mapping direction
The Mapping direction drop-down boxes allow a user to select a species as the subject (from) of the query and a species as the object (to) of the query. Initially, the subject of the query is the mouse, and the object of the query is the human. A user has the option to make a single-species query (human -> human, mouse -> mouse) or two-species queries (human -> mouse, mouse -> human).

Searching the hiearchies
After selecting the mapping direction, the user can search for an entity by using the search box or by browsing the hierarchy to find the anatomical entity he or she requires.

If the user searches with the exact name of an anatomical structure, the tree expands and the corresponding node is selected. If the user searches with word(s) that do not match a structure exactly, then the structures that contain those word(s) are displayed and the user can choose the correct structure. If the user searches with a string that is not found in the knowledge-base (it is not part of the name of any structure), a pop-up box saying 'No match was found' is displayed.

Browsing the trees
The anatomy of each species is displayed as a subclass hierarchy. The hierarchy consists of abstract and concrete classes; instances of abstract classes do not exist in the real world, whereas one can "point to" real instances of concrete classes. For example, the class "organ" is an abstract class, where as the "human prostate" (a concrete instance of an organ) is a concrete class. The abstract classes define the structure of the hierarchy but only concrete classes can be used in queries. The abstract classes have red 'A' icons and cannot be selected, whereas the concrete classes have green 'C' icons and the user can select them to use in a query.

Query buttons
The Query radio buttons allow the user to select the query relationship he or she is interested in finding between the subject and the object. The default selection is 'differs from'.

Recursion level box
The user is given the option to select the number of levels of the part-of hierarchy that the query searches. If the level is 0, only the subject and the object are compared and the results displayed. If the level is 1, the subject and object are compared with the specified relationship AND their parts are also compared using the relationship. The number of levels of the part hierarchy that the query can be performed on is 0 to 4, inclusive. We limit the number of levels because of performance reasons. If a number greater than 4 is entered, a message is displayed informing the user that it is not possible to search more than 4 levels deep, and the search defaults to 4 levels.

Query results
The query results panel contains a previous queries pane and the actual results display.

• Previous results
  Previous queries are saved and the results can be seen by clicking on the corresponding row in the "Previous queries" table. If the query is executed a second time by selecting its row, it does not get added to the table again. Each query has a single entry in the table, and even if it gets executed again, its place in the table does not change. As queries are executed, they are added to the bottom of the table.
  
  There are also two buttons, a "Delete Selected" button and a "Clear all" button so that the user can remove previous queries. Clicking the "Delete Selected" button removes the row of the table selected at that time, and clicking the "Clear all" button removes all entries from the table.
  
  
• Results display
  The display panel has three tabs - text, tree and graphics. The text tab displays results in a text format, the tree tab displays the results in a tree hierarchy and the graphics tab shows the results as a picture.
  
  Graphics tab
  As of September 2005, the graphics tab has not yet been implanted.
  
  Tree tab
  The tree display is useful when a user is interested in searching multiple levels of the part hierarchy, because the results are displayed in an intuitively hierarchical fashion.
  
  Text tab
  The text results are useful if the user would like to copy-and-paste the results in a different document. The text tab also displays all the error messages, and so it is the default tab. It is possible to switch between tabs by clicking on the tabs or by pressing Alt-1, Alt-2 or Alt-3, where:
  1 = text tab
  2 = tree tab
  3 = graphics tab
  

Additional information

• Mappings
A Mapping is a correspondence between a structure in the source (subject) species and a structure in the target (object) species. A mapping answers the question, "what is the structure in species1 that corresponds to a structure in species2?" For example "what is the structure in the human that corresponds to the set of prostates (mouse)?" The answer would be "prostate (human)" which means human prostate maps to set of mouse prostates.

A mapping is bidirectional i.e. if structure A in species A maps to structure B in species B, then necessarily structure B in species B maps to structure A in species A. This ensures that queries in which the subject and the object are swapped return the same result set as queries with the original subject and object (not swapped).


• Queries
Boolean queries
The Boolean query operators are is different? and is homologous?.


• Species1.anatomical-entity1 is different? species2.anatomical entity2
  Returns T if species1.anatomical-entity1 does not map to species2.anatomical-entity2, and F if the two entities map to each other.
  
  
• Species1.anatomical-entity1 is homologous? species2.anatomical entity2
  Returns F if species1.anatomical-entity1 does not map to species2.anatomical-entity2, and T if the two entities map to each other. This operation is the inverse of is different?


Non-Boolean queries
The non-Boolean operators are differs from, similar to, shared, not shared and union.


• Species1.anatomical-entity1 differs from species2.anatomical-entity2
  Returns the difference between anatomical-entity1 in species1 and anatomical-entity2 in species2.


• Species1.anatomical-entity1 similar to species2.anatomical-entity2
  Returns the similarities between anatomical-entity1 in species1 and anatomical-entity2 in species2.


• Species1.anatomical-entity1 shared species2.anatomical-entity2
  Returns the set of parts in anatomical-entity1 and anatomical-entity2 that map to each other.


• Species1.anatomical-entity1 not shared species2.anatomical-entity2
  Returns the set of parts in anatomical-entity1 and anatomical-entity2 that do not map to each other.


• Species1.anatomical-entity1 union species2.anatomical
  Returns what anatomical-entity1 maps to and what anatomical-entity2 maps to.


Differs-from and similar-to method
The following approach is taken when comparing two structures to find similarities or differences:

Mapping results
1. Check whether the structures map to each other. If they do, proceed to the next step. If they do not, inform the user what each structure does map to.

Attribute and relationship results
2. Compare the attributes and relationships of the subject and object. If the user is looking for similarities, the shared attributes and relationships are returned. If the user is looking for differences, attributes and relationships that only the subject has and that only the object has are displayed.

Attribute value and relationship value results
3. For the attributes and relationships that the structures share, check whether the values are the same. For example, if both the subject and the object have the attribute "has mass" compare the value of "has mass" i.e. true or false. If the user is looking for similarities, display the values that both structures share. If the user is looking for differences, display what value the subject has that the object doesn't and what value the object has that the subject doesn't.

Queries with "unknown" structures
When selecting a subject entity or object entity, the user has the option of selecting unknown for either one of the entities. A query that involves one known and one unknown entity returns what the known entity maps to. A query involving two unknowns returns an error message. For a query involving an unknown, the query type chosen does not make any difference.