NIH | National Cancer Institute | NCI Wiki  

Error rendering macro 'rw-search'

null

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 4 Next »

This guide explains how to use caBIG® Annotation and Image Markup (AIM) to build templates that are compatible with the AIM information model. The intended audience for this guide is a biomedical researcher familiar with the AIM information model.

To Print the Guide

You can send this page to a printer or export it to PDF and HTML.

Contents of this Page

 

Getting Started with the ATB

The ATB allows you to generate a set of well-defined questions and answer choices to facilitate collecting information for a particular purpose, such as The Cancer Genome Atlas Glioblastoma (TCGA GBM) study. These questions and answers are contained in an AIM XML template file that you can import into an AIM-enabled application, such as NCI's implementation of AIM on the ClearCanvas open source workstation. Aided by the information in the XML file, users of the AIM-enabled application can then annotate medical images using a controlled vocabulary and standard template. This results in simple and constrained annotations that are reproducible and consistent. The AIM-enabled application captures answers and exports them as an AIM XML document or AIM Digital Imaging and Communications in Medicine (DICOM) Structured Reporting (SR) document. Users can then send the document to the AIM Data Service or DICOM storage Service Class Provider (SCP), respectively.

You use the ATB to design templates based on lexicons of standard and user-definable terms. You add anatomic entities, imaging observations, inferences, calculations, and markups as components to a template. Adding tags to a template helps you make them easier to find. You combine multiple templates into template groups.

You can search for shared templates and template groups using the AIM Template Service and then modify them in the ATB.

AIM templates are based on the AIM template XML schema:
Version 1, revision 18
Version 1, revision 23

The AIM template XML schemas are based on the AIM 3.0 model.


Return to top of page

Why Use the AIM Model?

Imaging reports contain both graphical drawings and medical knowledge in the form of annotations. These annotations are stored as unstructured text and separated from graphical drawings, which are typically in a proprietary format on an imaging system. Extracting this valuable medical information and combining it with drawings on another system is a time-consuming process that yields results that are cumbersome to filter and search. Also, existing vocabularies used to describe medical images contain thousands of terms. This makes it difficult for users to find these terms and then include them in their AIM annotations.

The AIM model begins to solve this problem by capturing the descriptive information of an image with user-generated graphical symbols placed on the image into a single common information source. AIM captures medical findings using standard vocabularies such as RadLex, SNOMED CT®, and DICOM, and user-defined terminology. Image information captured in the AIM model includes the anatomic entity and its characteristics, imaging observation and its characteristics, and inference.

Return to top of page

What is in an AIM Template?

An AIM template contains a collection of data collection items (questions) and possible values (answers) for each question. You create a template for each imaging study. You capture each item and value using a standardized vocabulary.

An AIM template has one or more components. Each component represents a study question that may have one or more answers. Template components can be any of the following: anatomic entity, imaging observation, inference, calculation, or geometric shape (markup).

Both anatomic entities and imaging observations are also described by their associated characteristics. Anatomic entity and imaging observation characteristics inherit the attributes of their respective component. Characteristics have annotator confidence that allows a user to enter a percentage that represents the level of user confidence in answering the question. A characteristic may also have a quantification value.

Return to top of page

Configuring ATB for Publishing

You must configure ATB so that it can find the AIM Template Service and include the appropriate user name in an AIM template. The AIM Template Service is web service that can be used to store, search, and retrieve AIM template XML documents.

This procedure only applies if you are using ATB 1.1.

  1. Open the conf/atb.properties file in an editor.
  2. Change the atsBaseURL value to the URL of the server where the AIM Template Service is located. If you are not hosting your own AIM Template Service instance, the URL is http://imaging.fsm.northwestern.edu.
  3. Change the caGridUsername to the user name that you want to include in the AIM template. This user name is also used to authenticate your use of the caGrid security service.
  4. Save the file.

Return to top of page

Working with Template Groups

A template group is a container that holds individual templates.

Adding a Template Group

  1. Click the Template Groups tab.
  2. Below the left panel, click New template group button.
    The Group Members panel expands to include a new template group panel.
  3. Enter the name of the new group and optionally a version number and description in the boxes provided. You can edit the author by editing the template group.
  4. Click Save.
    The new template group appears in the Groups panel.

Return to top of page

Deleting a Template Group

Deleting a template group does not delete the templates within it.
  1. Click the Template Groups tab.
  2. Select the template group you want to delete by clicking it.
  3. Below the left panel, click Delete template group button.
    A message appears asking you to confirm the deletion.
  4. Click Delete.

Return to top of page

Editing a Template Group

You can edit the name, version, description, and author of a template group.
  1. Click the Template Groups tab.
  2. Below the left panel, click New template group button.
    The selected template group's description appears.
  3. Change the name of the group, version, description, and authors as needed.
  4. Optionally, add a tag to the group to make it easier to search for the template group in the future.
  5. Click Save.
    The edited template group appears in the Groups panel.

Return to top of page

Copying a Template Group

You can create a copy of a template group to make it easier for you to customize it.
  1. Click the Template Groups tab.
  2. Select the template group you want to copy.
  3. At the bottom of the Groups panel, click Copy template group button.
    A copy of the template with the name of Current Template Name copy appears in the Groups panel. You can now customize the copied template group.

Return to top of page

Searching for a Template Group

When you search the AIM Template Service for a template group that you want to modify in ATB, you import it at the same time. You do not have to take a separate step to download the template group. Once you find the template group in the search results, click it to begin using it in ATB.
  1. Click the Template Groups tab.
  2. Below the left panel, click Publish template group button and then select Search.
    The Template Group Search page appears.
    Template group search page of ATS. Options described in procedure.

  3. Narrow your search by entering information into the fields. If you do not enter any information into the fields, all template groups available in ATS appear, and it may take longer to see the results of your search. The following fields are available.

    Field

    Description

    Container Name

    Template group name

    Container Description

    Template group description

    Container Author

    Person who created the template group in the AIM-enabled application

    Disease

    Disease that is the topic of the templates in the template group

    Body Part

    Body part that is the topic of the templates in the template group

  4. Click Search.
    All template groups matching the search criteria you entered appear.
  5. Click the name link for a template group.
    The AIM template file opens in ATB. The template group name appears in your local template groups tab.

Return to top of page

Importing a Template Group

You can import a template group and use or customize it in AIM Template Builder.
  1. Click the Template Groups tab.
  2. Below the left panel, click Import Export button.
  3. Click Import.
    The Open dialog box appears.
  4. Search for an XML file that contains template group information in it. The AIM Template Builder only accepts template group files that have been validated by the AIM Template XML schema. This file could have been exported from the AIM Template Builder or it could have been created manually using the AIM template XML schema.

A message appears that notifies you if the file was successfully imported. A template group that is successfully imported also appears in the Template Group list. If the import was unsuccessful, a message appears that indicates the reason why.

No need to import template groups downloaded from the AIM Template Service

After you search for a template group in the AIM Template Service, you can open it and begin using it. It has already been imported to the AIM Template Builder. The import feature described in this procedure supports the importing of template files that are in XML format.

Return to top of page

Exporting a Template Group

You can export a template group you created in AIM Template Builder to use it in an AIM-enabled workstation. Template groups created in AIM Template Builder validate the AIM template schema and are in XML format.
  1. Click the Template Groups tab.
  2. Select the template group you want to export.
  3. Below the left panel, click Import Export button.
  4. Click Export.
    The Save dialog box appears.
  5. Select a location where you want to save the template group XML file.

Return to top of page

Publishing a Template Group

You can publish a template group that you created in AIM Template Builder to the AIM Template Service so that others can find it or so that you can import it into another application.
  1. Click the Template Groups tab.
  2. Select a template group from the Groups panel.
  3. Below the left panel, click Publish template group button.
  4. Click Publish.
    A window opens, prompting you to log in to the AIM Template Service.
  5. Enter your password or log in as a different user and then click Login. You must have a caGrid account to publish templates to the ATS.
    The steps that follow are unique to your configuration of the AIM Template Service.

Return to top of page

Working with Templates

When you design a template, it is helpful to keep the purpose in mind. A template structures how users will enter information into an imaging application. The following table may help make the connection between the AIM Template Builder and information entered into an imaging application.

AIM Template Builder Concept

Annotation Concept

Component

Item being annotated; for example, Tumor Location. A component can be anatomic entity, imaging observation, inference, calculation, and markup or geometric shape.

Characteristic

Descriptive element of that item; for example, Site of Tumor Center. Only anatomic entity and imaging observation can have characteristics associated with them.

Allowed Term

Represents a possible answer choice. It is used to describe the descriptive element of a component or characteristic. For example, Frontal Lobe is an answer choice for anatomic entity.

Return to top of page

Creating a Template

  1. Click the Templates tab.
  2. Below the left panel, click New template button.
    The new template window appears.
  3. Enter a name, description, and version for the template. The UID is also a required field but the AIM Template Builder supplies it automatically. Optionally, select values for Modality and Preceding Annotation.
  4. Click Save.
    The new template appears in the Templates panel. You may see warnings depicted by yellow triangles in the template. For example, if you have not yet assigned the required metadata, you are notified that it is missing. The Description section below the Template Components panel shows the list of warnings. Click to locate the problem location and fix it.
    A template with three warnings on it.
  5. Add a tag (also called a code) to the template. Tags can either be string values or lexicon terms. A template must have a code assigned to it. The assigned code describes the purpose of the template.
  6. Add one or more components to the template. Components can be anatomic entity, imaging observation, inference, calculation, and markup or geometric shape.
  7. Add one or more characteristics to each template component you add, as applicable (Inference and Calculation components do not have associated characteristics).

  8. Specify the allowed termsfor each characteristic (for Anatomic Entity and Image Observation components) or component (for Inference and Calculation components).

    Expanding and collapsing

    Above the Template Components panel, click the plus or minus buttons (plus and minus buttons) to expand or collapse the template components, respectively. When you expand a template component, you see all of its characteristics. In the template component tree, double-click a component or characteristic to expose additional detail about its metadata.

Return to top of page

Adding a Template Component

  1. Click the Templates tab.
  2. In the Templates panel, select the template to which you want to add a component.
  3. In the Template Components panel, right-click the template name and select Create Template Component. You can also find this option in the toolbar (Create template component button). A new panel appears on the right and the toolbar below the Template Components panel changes to provide options for template components.
    New template component panel before any options have been selected.

  4. Specify the attributes of the template component, as described in the following table.

    Field

    Description

    Label

    Double-click this field to add a label. A label becomes a heading in the image annotation form that users complete once the template is imported into an imaging application. For example, "Lesion".

    Explanatory Text

    Description of the component; for example, "Select the type of lesion".

    Cardinality

    The minimum and maximum number of times the template will allow users to select this term when they annotate an image. Click Unlimited if users are not limited in how many times they may select this term.

    Should Display

    Select this box to display this component in the template.

    Authors

    The AIM Template Builder user who created this component

    Group Label

    Any text that you want to associate with one or more template components and thereby group them together

  5. Click Save.

  6. Right-click the new template component to add the AIM elements of question, anatomic entity, imaging observation, inference, calculation, geometric shape, and allowed terms.

    Click Move Up or Move Down to change the order in which template components appear in the template.

Return to top of page

Creating a Question

AIM templates include a set of questions and one or more answer choices for each question.
  1. Add a template component.
  2. Right-click the template component and select Create Question. You can also find this option in the toolbar (Create a question button).
    A new panel appears on the right and the toolbar below the Template Components panel changes to provide options for question, which are to add or delete a question (delete button).

  3. Provide information about the question.

    Field

    Description

    Code Meaning

    The lexicon term you want to use in the question

    Code Value

    The value of the lexicon term

    Schema Designator

    The organization that created the schema

    Schema Version

    The version of the schema you are using

    In this version of ATB, a question is defined as a concept code. This means that you will have to select a concept code from a list of existing lexicons from your local ATB. If you don’t have a concept code defined, which you probably don’t have in your local ATB, you will have to create your private lexicon that consists of your set of questions.

    Example

    You may want to create the following question: Where is a tumor located?
    You may define the question as follows.

    1. Create a lexicon called My private questions.
      1. Select the Lexicon tab.
      2. Click add button to add a new lexicon.
      3. Enter the metadata as follows:
        Name: My Private Lexicon
        Schema Designator: MPL
        Schema Version: 1.0
        Description: My private lexicon
        Authors: NCI
      4. Click Save.
    2. Click small add button next to each Allowed Terms entry row. to add a new term.
    3. Enter the metadata as follows:
      Code Meaning: Where is the tumor?
      Description: Identify where the tumor is on the image or images.
      Code Value: MPL-0001
    4. Click Save. You can now use this question concept code.
  4. Click Save.
  5. Add valid terms to the question. Valid terms are lexicon entries that you want to reference in a question in the template.

Return to top of page

Creating an Anatomic Entity

  1. Click the Templates tab.
  2. In the Templates panel, select the template to which you want to add an anatomic entity.
  3. In the Template Components panel, right-click the template name and select Create Anatomic Entity. You can also find this option in the toolbar (Create an anatomic entity button).
    A new panel appears on the right and the toolbar below the Template Components panel changes to provide options for anatomic entities, which are to add or delete an anatomic entity.(delete button).
  4. In the panel on the right, select the button that describes your display preference for Annotator Confidence.
  5. Click Save.
  6. Add one or more characteristics to the anatomic entity.
    For example, to describe a screen that is ruptured, the AIM template captures an anatomic entity of spleen and an anatomic entity characteristic of ruptured.

Return to top of page

Creating an Imaging Observation

  1. Click the Templates tab.
  2. In the Templates panel, select the template to which you want to add an imaging observation.
  3. In the Template Components panel, right-click the template name and select Create Imaging Observation. You can also find this option in the toolbar (Create an imaging observation button).
    A new panel appears on the right and the toolbar below the Template Components panel changes to provide options for imaging observations, which are to add or delete an imaging observation (delete button).
  4. In the panel on the right, select Annotator Confidence, if that attribute applies to the imaging observation.
  5. Click Save.
  6. Add one or more characteristics to the imaging observation.
    For example, to describe an image showing a cystic mass, the AIM template captures an imaging observation of mass and an imaging observation characteristic of cystic.

Return to top of page

Creating an Inference

  1. Click the Templates tab.
  2. In the Templates panel, select the template to which you want to add an inference.
  3. In the Template Components panel, right-click the template name and select Create Inference. You can also find this option in the toolbar (Create an imaging observation button).
    A new panel appears on the right and the toolbar below the Template Components panel changes to provide options for inferences, which are to add or delete an inference (delete button).
  4. In the panel on the right, select Annotator Confidence, if that attribute applies to the inference.
  5. Click Save.
  6. Add one or more questions to the inference.

Return to top of page

Creating a Calculation

  1. Click the Templates tab.
  2. In the Templates panel, select the template to which you want to add a calculation.
  3. In the Template Components panel, right-click the template name and select Create Calculation. You can also find this option in the toolbar (Create a calculation button).
    The toolbar below the Template Components panel changes to provide options for calculations, which are to add or delete a calculation (delete button).
  4. Right-click the calculation and select Create Calculation Type. You can also find this option in the toolbar (Create a Calculation Type button).
    The toolbar below the Template Components panel changes to provide options for calculation types, which are to Add Valid Terms, Create Algorithm Type, and Delete Calculation Type (delete button).

Return to top of page

Creating an Algorithm Type

Algorithms are types of calculations that you can add to an AIM template.
  1. Create a Calculation.
  2. Click create algorithm type button to add an algorithm type to the calculation type.
    A new panel appears on the right for algorithm attributes.
    new panel of algorithm attributes

  3. Provide attributes for the algorithm type.

    Field

    Description

    Description

    Explanatory text about the component

    Unique Identifier

    Any string that uniquely identifies this algorithm

    Algorithm Name

    Algorithm name

    Algorithm Version

    Algorithm version

    MathML

    An optional mathML representation of the calculation

  4. Click Save.

Return to top of page

Creating a Geometric Shape

Geometric shapes, which are equivalent to markups, describe a user's region of interest on an image and are patterned after DICOM SR graphical types. Combinations of these shapes can be used to represent graphical drawings placed on images.
  1. Click the Templates tab.
  2. In the Templates panel, select the template to which you want to add a geometric shape.
  3. In the Template Components panel, right-click the template name and select Create Geometric Shape. You can also find this option in the toolbar (Create a geometric shape button).
    A new panel appears on the right and the toolbar below the Template Components panel changes to provide the option for geometric shapes, which is to delete a geometric shape (delete button).
  4. In the panel on the right, select the shape type. Options include Point, Circle, Polyline, Ellipse, and MultiPoint.

  5. Click Save.
    The geometric shapes available are as follows.

    Shape

    Description

    Point

    A single pixel denoted by a single (column,row) pair

    Multipoint

    Multiple pixels each denoted by an (column,row) pair

    Polyline

    A series of connected line segments with ordered vertices denoted by (column,row) pairs. If the first and last vertices are the same, it is a closed polygon.

    Circle

    A circle defined by two (column,row) pairs. The first point is the central pixel. The second point is a pixel on the perimeter of the circle.

    Ellipse

    An ellipse defined by four pixel (column,row) pairs. The first two points specify the endpoints of the major axis and the second two points specify the endpoints of the minor axis of an ellipse.



Return to top of page

Adding Allowed Terms

When users of your AIM template answer template questions, you can offer a list of standardized terms for their answers. You can associate allowed terms with Anatomic Entity, Imaging Observation, and Inference components, and Anatomic Entity and Imaging Observation characteristics.

Once you create an allowed term, you can add more allowed terms under it hierarchically. This allows you to create new concepts from existing allowed terms.

  1. Click small add button next to each Allowed Terms entry row..
    The Lexicon Search dialog box appears.
  2. Select an allowed term from a lexicon you have created.
    1. From the list in the center of the page, select at least one lexicon where you believe the term you are searching for is located.
    2. From the list that is furthest to the left on the page, enter the term you want to search for. You can also enter only part of the term, such as "Tum" for "Tumor".
    3. Click Search term button. All lexicon entries containing the word you entered appear in the search results.
    4. Select a term in the search results.
    5. Click Add allowed term to characteristic button.
      The allowed term appears in the Allowed Terms list in the right panel.

    6. Click OK.

      Showing and hiding panels

      Adjust your view of the information in multiple panels by clicking and dragging the border between them.

  3. Click OK.

Return to top of page

Modifying Allowed Terms

  1. Select an allowed term belonging to a template component.
    The metadata associated with that term appears in the right panel.
  2. Below that metadata, click Select Term.
    The Lexicon Search dialog box appears. The term you selected appears in the Lexicon Term panel on the right.
  3. From the list in the center of the page, select at least one lexicon.
  4. From the list that is furthest to the left on the page, enter the term you want to search for. You can also enter only part of the term, such as "Tum" for "Tumor".
  5. Click Search term button. All lexicon entries containing the word you entered appear in the search results.
  6. Select a term in the search results.
    The selected term replaces your original term in the Lexicon Term panel.
  7. Click OK.
    The Templates tab appears.
  8. Click Save.

Return to top of page

Adding a Characteristic to a Template Component

When you add an anatomic entity or imaging observation component to your template, you may add one or more characteristics to it. When you import a template into an imaging application, each template component becomes a heading and the template component's characteristics describe the component. For example, the component might be "Lesion" while some of its characteristics might be "Enhancement Quality", "Proportion Enhancing", "Proportion nCET", and "Proportion Necrosis".

Anatomic entity characteristics and imaging observation characteristics can be quantifiable or non-quantifiable. A quantifiable value can be scale, quantile (such as quartile, percentile, or n-tile), numerical like a decimal number in a UCUM (Unified Code for Units of Measurement) unit, and interval. Examples of non-quantifiable are present, absent, and not applicable.

  1. Add a template component of the Anatomic Entity or Imaging Observation AIM class.
  2. Right-click the component and select Create Anatomic Entity Characteristic (anatomic entity characteristic button) or Create Imaging Observation Characteristic (imaging observation characteristic).

  3. Specify information describing the characteristic, as follows.

    Field

    Description

    Label

    Double-click this field to add a label. A label becomes a heading in the image annotation form that users complete once the template is imported into an imaging application. For example, "Lesion".

    Explanatory Text

    Description of the component; for example, "Select the type of lesion".

    Cardinality

    The minimum and maximum number of times the users may select this term when they annotate an image. Click Unlimited if users are not limited in how many times they may select this term.

    Should Display

    Select this box to display this component in the template. In certain situations, information in a component is known and will not be changed.

    Authors

    Describes the AIM Template Builder user who created this component.

    Group Label

    Describes any text that you want to associate with one or more template components and thereby group them together for display purposes.

  4. Click Save.
  5. Add an allowed term to the characteristic.
  6. Create a characteristic quantification.

Return to top of page

  1. Add a template component of the Imaging Observation or Anatomic Entity type.
  2. Add a characteristic to a template component of the Imaging Observation or Anatomic Entity type.
  3. Add an allowed term to the characteristic.
  4. Right-click the allowed term and select Create Characteristic Quantification (Create Characteristic Quantification button).
  5. In the panel on the right, enter a name for the characteristic and select Annotator Confidence, if that attribute applies to the template component.
  6. Click Save.

  7. Create a characteristic quantification type. The options include Non Quantifiable, Scale, Numerical, Quantile, and Interval. Except for the Non Quantifiable type, which can always be added, you cannot create more than one type for a single allowed term.

    Note

    Delete any quantification from an allowed term by right-clicking it and selecting delete button.

Return to top of page

  1. Add a characteristic to the component.
  2. Add an allowed term.
  3. Right-click the allowed term and select Create Non Quantifiable (create a non quantifiable button).
  4. Search for the lexicon term you want to use to describe the non quantifiable.
    1. Click Select Term.
      The Lexicon Search dialog box appears.
    2. From the list in the center of the page, select at least one lexicon where you believe the term you are searching for is located.
    3. From the list that is furthest to the left on the page, enter the term you want to search for. You can also enter only part of the term, such as "Non" for "None", and then select RadLex from the lexicon list.
    4. Click Search term button.
      All lexicon entries containing the word you entered appear in the search results.
    5. Select a term in the search results.
    6. Click OK.
      The metadata for the lexicon term you selected populates the Code Meaning, Code Value, Schema Designator, and Schema Version fields.
  5. Click Save.

Return to top of page

  1. Add a characteristic to the component.
  2. Add an allowed term.
  3. Right-click the allowed term and select Create Scale (create a non quantifiable button).
  4. Add a description of the scale and additional comment, if needed.
  5. Click Save.
  6. Right-click the scale and select Create Ordinal Level (create ordinal level button).
  7. Provide a value for the ordinal level by typing in a number or using the arrow keys to reach the desired number.
  8. Optionally, describe the ordinal level.
  9. Click Save.
  10. Return to step 3 to create additional ordinal levels.

Return to top of page

  1. Add a characteristic to the component.
  2. Add an allowed term.
  3. Right-click the allowed term and select Create Numerical (create a numerical button).
  4. Provide a value and UCUM string for the numerical (required).
  5. Select an operator from the list (optional).
  6. Click Save.

Return to top of page

  1. Add a characteristic to the component.
  2. Add an allowed term.
  3. Right-click the allowed term and select Create Quantile (create a quantile button).
  4. Enter a value into the Bins field.
    For example, if your range is 100, you could create 5 bins containing 20 units each. Your Bin number would be 5 in this case.
  5. Click Save.

Return to top of page

Creating an Interval

  1. Add a characteristic to the component.
  2. Add an allowed term.
  3. Right-click the allowed term and select Create Interval (create an interval button).
  4. Specify Min Value, Max Value, Min Operator, Max Operator, and UCUM Value for an interval.
  5. Click Save.
  6. Return to step 3 to create additional intervals.

Return to top of page

Adding Tags to a Template

Associating one or more tags with a template makes it easier for you to find and others to discover a template that you created. Tags are composed of a name and a value. The tag name must be a lexicon term. The tag value can be a string you enter or a lexicon term.
  1. Click the Templates tab.
  2. Select a template.
    The template components appear in the center panel.
  3. In the Template Components panel, right-click the template name.
  4. From the menu that appears, select .
    A new tag appears in the Template Components panel.
    New tag in the template components tree for the selected template
  5. Provide the tag name and value.
    • To provide the tag name, click Select Term in the Lexicon Term (Tag Name) panel in the top right. A tag must contain at least three characters.
    • To provide the tag value, enter your own or select a term from the lexicon. To enter your own value, click Use String Value and then enter a value in the String Value box.
  6. Click Save.

Return to top of page

Searching for a Template

Unable to render {include} The included page could not be found.

Return to top of page

Editing a Template

  1. Click the Templates tab.
  2. Select the template you want to edit. The template information appears in the right panel.
  3. Edit any of the information about the template that you want to change.
  4. Click Save.

Return to top of page

Deleting a Template

  1. Click the Templates tab.
  2. Select the template you want to delete by clicking it.
  3. Below the left panel, click Delete template button.
    A message appears prompting you to confirm the deletion.
  4. Click Delete.
    The template is no longer in the Templates panel.

Return to top of page

Adding a Template to a Template Group

You can combine any number of templates in a template group. You may want to do this, for example, to make it easier for you to reference your data during a certain time in a longitudinal study.

This procedure assumes that you have already created both templates and template groups.

  1. Click the Template Groups tab.
  2. Select the template group that you want to populate with one or more templates.
  3. In the Group Memberships panel on the right side of the screen, click the boxes next to the templates you want to add to the selected template group.
    AIM Template Builder with Template Group 1 selected and the boxes next to Template 1 and Template 2 selected.
  4. Below the Group Memberships panel, click Button below the Group Memberships panel that you click to include the selected template.
    The templates appear in the Group Members panel.
    AIM Template Builder showing Template 1 and Template 2 as part of Template Group 1

Return to top of page

Removing a Template from a Template Group

  1. If you are not already on the Template Groups tab, click it to select it.
  2. In the Group Memberships panel on the right side of the screen, click the box next to the template you want to remove from the template group.
  3. Click Button below the Group Memberships panel that you click to include the selected template.
    The page refreshes and the Group Members panel no longer shows the template in the template group.

Return to top of page

Building a Lexicon

A lexicon organizes the vocabulary that may appear in an AIM template. When you build a template, you can select terms from a lexicon that users of the template will be able to select as answers to template questions. For example, if an AIM template imported into an appropriate application prompts the user to specify the location of a lesion's geographic center, the template could restrict answers to certain allowed terms from the lexicon.

You must first create a lexicon, then add lexicon entries to it. Those lexicon entries become the allowed terms that you add to a template.

The ATB contains preselected terms from RadLex, caDSR (cancer Data Standards Registry and Repository) designed for a particular imaging study such as LIDC (Lung Image Database Consortium), and VASARI (Visually Accessible Rembrandt Images) vocabularies.

Return to top of page

Creating a Lexicon

  1. Click the Lexicons tab.
  2. In the toolbar at the bottom of the page, select Add a template button.
    A panel for information about the new lexicon appears.
    Window with one field labeled Lexicon Name.
  3. Enter information about the lexicon. Lexicon name and Scheme Designator are required. Schema Version and Description are optional. You can change the Authors from what appears by default, which is the user who is currently logged in.
  4. Click Save. The lexicon appears in the Lexicon panel.

Return to top of page

Deleting a Lexicon

  1. Click the Lexicons tab.
  2. Select the lexicon you want to delete by clicking it.
  3. At the bottom of the Lexicon panel, click Delete lexicon button.
    A confirmation message appears.
  4. Click Delete. The lexicon is no longer in the Lexicon panel.

Return to top of page

Creating a Lexicon Entry

  1. Click the Lexicons tab.
  2. Select the lexicon that you want to contain your new lexicon entry.
  3. Right-click the lexicon and select Create Lexicon Entry, or click Add Allowed Term button in the toolbar.
    A panel for the new lexicon entry appears.

  4. Complete the fields to describe the lexicon entry.
    An explanation of the purpose of each field is shown in the table below.

    Field

    Description

    Code Meaning

    The name of the term you want to use as the lexicon entry

    Description

    A description of the term

    Code Value

    The value assigned by the coding scheme designator

  5. Click Save.

Return to top of page

Deleting a Lexicon Entry

  1. Click the Lexicons tab.
  2. Select the lexicon that contains the term you want to delete.
  3. Click the term you want to delete to select it.
  4. Click Delete lexicon entry button.
    A confirmation message appears.
  5. Click Delete. The lexicon entry no longer appears in the Lexicon Terms panel.

Return to top of page

Searching for a Term

  1. Click the Lexicons tab.
  2. At the bottom of the Lexicon Terms panel, click Search term button.
    The Lexicon Search window appears.
  3. In the list in the top middle of the page, select at least one lexicon where you believe the term you are searching for is located. Click and hold the Shift or Ctrl key to select multiple lexicons.
  4. In the list at top left of the page, enter the term you want to search for. Click Whole word if you are entering the whole word and want to restrict your search to it. You can also enter only part of the term, such as "Tum" for "Tumor".
  5. Click Search term button.
    All lexicon entries containing the word you entered appear in the search results.
  6. Select a term from the search results.
  7. Click OK.

Return to top of page

  • No labels