Semantic Integration Workbench

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The Semantic Integration Workbench must be run to as part of the caBIG Compatibility Review.

An outdated tutorial hosted by Claire Wolfe on November 15, 2006 has been recorded. The tutorial itself is outdated, but if you would like to listen to this original recording you can download the avi file (to view on the Windows Media Player) from here. You'll need to install Camtasia to get the codec required to view the video. You can download this from here.

SIW Steps

Errors to Look For

If you see the parsing error, address it. One error is that you cannot have "unbounded" in your model (to represent and array in EA). Instead, use -1. For more information on arrays and EA, see Enterprise Architect.

  • For each attribute of every class, you will want to map the attribute to a CDE. To do this, do the following:
    • Highlight the attribute in the project explorer of the SIW (on the left).
    • Click "Map to DE".
    • Click "Search Data Element".
    • Select "Search By Public Id" from the drop down. You will fill in the "Search" field with a public id. You can find the public id for each data element in the CDE browser at: http://cdebrowser.nci.nih.gov/CDEBrowser/. Click "Search".
    • Once the search is done (takes a few seconds), double click on the result and then hit "Apply".

Please note that the Java wrapper classes in the java packages (java.lang, java.util, etc.) will be included as part of your model and will show up in SIW. These classes do not need to be annotated or defined in order to load your model successfully. Therefore, you can ignore “missing concept” errors and “missing description” warnings for these classes only.

  • Classes and attributes are mapped correctly.
    • concepts are semantically correct.
    • order of concepts makes semantic sense (concepts appear in the SIW ordered as qualifierN, qualifierN-1, qualifierN-2, ..., qualifier1, primary concept).
  • Class/attribute definitions are correct and complete.
  • Attributes reusing an existing CDE have been mapped to that CDE.
  • Check the SIW error log for any errors the parser found.
    • Errors marked with red circles are errors that will prevent the UML Loader from running; these errors must be resolved.
    • Errors marked with yellow squares will not prevent the UML Loader from running; however we highly recommend you resolve these issues. Some of these issues could prevent your model from attaining caBIG Silver Compatibility.
  • Class associations are complete.
    • Source and/or target role names are required to fully specify the association. If a required role name is missing, an error will appear in the error log.
    • If you do not specify the directionality of the association, the association will be ignored by the SIW and by the UML Loader. Make sure all associations appear in the SIW.
  • Class generalizations are complete and correct.
  • Value Domains specified in your model must be accurate.
  • Make sure nothing is missing. For example, if you have a class that has no attributes and no associations, this class will not appear in the SIW, nor will it be loaded to UML Loader. You must include at least one association or one attribute in each class.

One of the most common errors is invalid data types. There are a set of default Value Domains that have been created for the UML Loader to map to the Java primitives and Java wrapper classes that are most commonly used as data types in Domain Models. Any data type that the UML Loader will not recognize will show up as an invalid data type error. If the data type is not recognized by the SIW, check the current list of mappable Value Domains (available from App Support). If the data type is not on this list, then you must specify a new Value Domain in your model, or reuse an existing Value Domain for that attribute.

As you verify each class/attribute in SIW, check the Human Verified box to indicate that you approve the concept/CDE mapping.

Any changes to the concept/CDE/Value Domain mapping can be made directly in the SIW. We recommend you discuss with the EVS team any concepts you want to change/add/remove. After you have made all your changes, verified your model and checked everything as human verified, then save your model using the File->Save/Save as option.

Any other changes (e.g., changes to definitions, changes to class or attribute names, adding/deleting classes or attributes, adding new Value Domains, etc.) must be made to the UML Model using EA. Before making changes to an annotated model, you must first import the annotated XMI file to EA to ensure that your model contains all annotations. Once imported, you can then make the changes to the model, export the model to an XMI file and run the Fix XMI task in SIW to create a final updated annotated fixed XMI file.

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