2 - Searching the CDE Browser

The CDE Browser provides several different ways to find CDEs. Which method is the best depends on what you are looking for.

If you are looking for an existing collection, such as a list of the CDEs used on a form, or you want to browse the CDEs associated with a context or classification, use the context Search Tree. Otherwise, you can search by keyword using either the Basic data element search or the Advanced Search form.

This chapter includes the following topics:

Using the Basic Search Form

The Basic Search form resides on the main page of the CDE Browser and consists of a Keyword text box along with Search Options radio buttons.

The Keyword search text box allows you to enter text or a number into the box and then search the caDSR database for CDEs with attributes that match the criteria entered. The Keyword search text box also allows you to use the asterisk as a wildcard. Details on how to use wildcards appears in the Using Wildcards section below.

Use the Search Options radio buttons to determine the scope of the search. You can select to search for the Exact Phrase, All of the words, or At least one of the words you entered into the Keyword search text box.

The Browser searches the following caDSR database fields:

• Public ID
• Long Name
• Preferred Name
• Document Text
• Definition
• Reference Documents
• Designations

CDE Browser searches are not case sensitive. Searches for "Gene" and "gene" return the same results.

To use the Basic Keyword search in CDE Browser:

1. Enter the term(s) or public ID number you want to search on in the Keyword search field. Use the asterisk as a wildcard if necessary.
2. Select the appropriate Search Option radio button: Exact Phrase, All the words, or At least one of the words.
3. Click Search (or press Enter).

The results of the search appear in the results list located below the Basic search form. If you result set is too large or too small, you may need to adjust your Search Options, change your Search Preferences, Search within the results to narrow the list, or use the Advanced Search form to better target your search.

Search Options

The radio buttons to the left of the Keyword search text box provide you with three options for conducting your keyword search: Exact Phrase, All of the words, and *At least one of the words. These search options function as follows:

• Exact Phrase – This search attempts to find the exact term or phrase entered into the Keyword Search text box.
• All the Words – This search returns only those CDEs where all of the terms entered appear in one or more of the searched fields. This is the same as performing a logical "AND" search operation.
• At least one of the words – This search returns those CDEs where any of the terms entered into the Search text box appear in one or more of the searched fields. This is the same as performing a logical "OR" search operation.

All of the search options take into account any wildcards entered with the search terms.

The Browser searches for terms in the Public ID, Long Name, Preferred Name, Document Text, Definition, Reference Documents, and Designations fields of the caDSR database.

Using Wildcards

If you are not sure of the exact term or phrase you are looking for, or if you want to broaden your search to include CDEs that contain a certain term, you can use the asterisk as a wildcard along with the text you enter into the Keyword search field. The wildcard character can be used more than once in the Keyword search field.

Tips on Using Wildcards

To search for a Data Element that contains the word "gene" somewhere in its name, definition, or in the title of attached reference documents, put a wildcard before and after the term.

To search for Data Elements that begin with the word "gene", put a wildcard after the term.

To search for matching phrases, use wildcards to bridge words. For example, using "gene*brother*" will return a match for items such as "Genetic Full Brother Count" and "Genetic Half Brother Count".

Search Preferences

You can use the Search Preferences page to restrict or expand your search results by selecting or de-selecting to exclude certain groups of CDEs from your results. By default, the CDE Browser excludes the following types of CDEs from search results:

• CDEs in the Test and Training contexts
• CDEs with a Workflow Status of CMTE Approved, Submitted, or Submitted Used,
• CDEs with a Workflow Status of RETIRED Archived, Phased Out, or Withdrawn.
• CDEs with a Registration Status of Retired

To open the search preferences page, click the Search Preferences link, located at the top of the search pane.

When it first appears, the Search Preferences page selections reflect the default settings enabled for all CDE Browser searches. By selecting or de-selecting the items on the page, you can reduce or expand the qualifying CDEs returned by your searches.

For the Workflow Status and Registration Status list boxes, hold down the CTRL or key when clicking list items in order to select or de-select mulitple items in the list. Holding down the CTRL key ensures that the existing selections are retained while you alter your preferences.

To clear all selections from the list, click the space above the top-listed item without holding the CTRL key.

When you are finished changing your preferences, click Save. Otherwise click Back to return to the main search page without making changes to your search preferences.

Using the Advanced Search Page

Advanced searches are performed using the Advanced Search form, which is accessed using the Advanced Search link located above the Basic search area.

The Advanced Search page gives you greater control over the search parameters. You can opt to search by Name, Public ID, Concept, Alternate Name, or other attributes. You can target your search to specific database fields. You can also use the form to limit your search to only Derived Data Elements.

The criteria you enter into the form work together to narrow the result set to only those items that match all of the search criteria. This allows you to combine criteria to create complex and very targeted searches.

All of the editable text fields in the Advanced Search form allow for the use of the asterisk as a wildcard.

The sections of the Advanced Search form include Search by Name, Search by Concept, and Search by Attributes. The bottom section of the form allows you select additional criteria for limiting your result set.

Each section of the Advanced Search form is discussed in more detail in the sections that follow.

Once the form is completed, click the Search button located at the bottom of the form.

Advanced Search by Name

The Search by Name section of the Advanced Search form works the same way as the Basic Keyword search, except that it provides the ability to limit your search to one or more specific database fields, or you can search all of the same fields as the Basic search.

Enter the term or number you want to search for, including wildcards if necessary, and then select the fields to search. You can select ALL to search all of the same fields as the basic search would, or you can select one or more of the other fields. Hold down the CTRL or SHIFT key while clicking an item to select multiple fields from the list.

Use the Search Options radio buttons to determine the scope of the search. You can select to search for the Exact Phrase, All of the words, or At least one of the words entered into the text box.

To limit the search to only derived data elements, enable the Search only Derived DEs checkbox.

Advanced Search by Concept

The Search by Concept section of the Advanced Search form provides additional semantic support to the data element search functionality. If you are familiar with the EVS concepts that provide the semantic interoperability for registered models, searching by concept can be a powerful way to find data elements.

Enter the Concept Name or Concept Code you want to find, including wildcards if necessary. The Browser searches object classes, properties, and value domains for matches to the information entered. If a match is found, the Browser returns all data elements whose components are associated with the concept criteria entered.

Advanced Search by Attributes

CDEs are represented in the caDSR database using the ISO/IEC 11179 standard. The Search by Attributes section of the Advanced Search form lets you search for data elements using ISO/IEC 11179-based attributes.

The flashlight icons located to the right of the fields in this section of the form provide a Keyword search capability for the attribute with which they appear. This allows you to perform a search for a particular attribute, and then select that attribute to populate the field in the Advanced Search form. This helps more accurately complete the form to target your search.

The Keyword search for the attributes also allows you to select whether to limit the attribute search to only the current context or to search across contexts for the item.

The fields in the Search By Attributes section of the Advanced Search form include:

Public ID
To return a list of data elements based on or limited to a Public ID, enter a valid Public ID into the field, using wildcards to broaden the search if necessary.

Data Element Concept
To search for only data elements that contain a specific data element concept (DEC), click the flashlight icon. Complete the keyword search in the popup window and select a DEC from the result set. The DEC you select appears in the search criteria box.

Classification
To search for only data elements that are associated with a particular classification, click the flashlight icon. Complete the keyword search in the popup window and select a classification from the result set. The classification you select appears in the search criteria box.

Value Domain
To search for only data elements that are contain a specific value domain, click the flashlight icon. Complete the keyword search in the popup window and select a value domain from the result set. The value domain you select appears in the search criteria box.

Value Domain Type
Use these radio buttons to limit your search results to those data elements with either enumerated or non-enumerated value domains. All value domains (Both) are included by default.

Permissible Value
To return a list of data elements based on or limited to certain permissible value(s), enter a value into the field, using wildcards to broaden the search if necessary. The Permissible Value text field also provides Search Options radio buttons. This allows you to determine the scope of the search for the terms Permissible Value text box.

Alternate Name
A data element may have multiple alternate names in multiple contexts. Use this field, in conjunction with Alternate Name Type(s) selection list to search for data elements based on their alternate name. Enter a term into the field using wildcards to broaden the search if necessary.

Alternate Name Type(s)
If you entered an Alternate Name to search for, you must also specify an alternate name type for the search. Hold down the Ctrl or Shift key while clicking an item to select multiple types from the list.

Object Class
To return a list of data elements that contain only certain object classes, enter a keyword into the field, using wildcards to broaden the search if necessary.

Property
To return a list of data elements that contain only certain properties, enter a keyword into the field, using wildcards to broaden the search if necessary.

Advanced Search Result Set Filters

The bottom section of the Advanced Search form allows you to limit your result set based on a number of optional filters.

The filtering selections are defined as follows:

Version
Data Elements are assigned version numbers by the Context administrator. To filter data elements based on their version, select the Latest Version or All Versions radio button.

Workflow Status
The Workflow Status is the administrative status of the data element. In most cases you will want to search for data elements with a status of RELEASED, but any status is available as a search criterion. Use the Workflow Status list to filter your results based on workflow status. Hold down the Ctrl or Shift key to select multiple items from the list.

Context Use
Data elements are "owned by" the context that has administrative authority to edit and update them. In addition to the owning context however, a data element can be "designated" for use by another non-owning context. Selecting a particular Context Use from the drop-down list allows you to return only those data elements that are Used, Owned, or Owned By/Used By the current context. Owned By/Used By is the default setting.

Registration Status
Use the Registration Status list to filter your results based on data element registration status. Hold down the Ctrl or Shift key to select multiple items from the list.

Using the Context Search Tree

The context search tree lists the names of the different contexts in caDSR and uses a hierarchical structure to display the various groupings of DEs within each context.

Many of the items listed in the left navigation tree are active links. Selecting a link in the tree instructs the CDE Browser to return all of the CDEs associated with the selected item. Clicking the plus sign to the left of an item expands the tree to show sub-nodes for the selected node. For example, clicking the plus sign to the left of the caBIG context expands it to show three sub-nodes: Classifications, Protocol Forms, and Catalogue of Published Forms.

Clicking the plus sign to the left of the Classifications node expands it to show all of the classification schemes (CS) that have been loaded to that context (in this case, caBIG).

As with the contexts, each of the CS listed is an active link. Selecting a CS in the tree instructs the CDE Browser to return all of the CDEs associated with the CS. Clicking the plus sign to the left of a CS expands it to show all Classification Scheme Items (CSI) registered for the selected CS. Each CSI is also an active link that when clicked, returns all of the CDEs for that CSI.

Context Search Tree Groupings

The search tree contains multiple contexts. Within each context may reside any of four nodes for the context, depending on which of these categories of items exists for the context: Classifications, Protocol Form Templates, Protocol Form, and Catalogue of Published Forms. Some classifications also contain other specialized groupings of CDEs.

These categories are defined as follows:

Classifications
A Classification or Classification Scheme (CS) is simply a collection of related Classification Scheme Items (CSI), or in other words, a mini-hierarchy within the tree. Data elements, in turn, can be assigned to one or more CSIs. The actual classification assignments are managed by the context administrator.

Hovering the mouse over a CS in the Search Tree displays the definition for the classification.

Protocol Form Templates
Data elements can be used on a form. For clinical trials, this will be a case report form or CRF. Many of these forms have been generalized into form templates that can be re-used. For the Cancer Therapy Evaluation Program (CTEP) context, these templates have been grouped by Phase and Disease. Within these two groupings, the templates are further grouped by type of template. Clicking on a template form name in the tree returns a list of the data elements used on that form.

Protocol Forms
This node lists clinical report forms (CRFs) that are or have been used in a clinical trial. Clicking on a Protocol Form will generate a search for all CDEs used on the selected form.

Specialized Groupings
Other types of groupings can be found in the tree as well. For example, the CTEP context groups data elements into "core" and "non-core" categories, based on CDE disease committee decisions. These categories can be found in the tree under each type of disease classification.

Finding a Form using the Context Search Tree

To find forms and templates and their associated DEs in the CDE Browser, you need to use the search tree. There are two different ways to search for forms and templates using the context search tree: expanding and browsing the Forms Catalogue, and browsing for forms within a specific context.

Browse the Forms Catalogue

If you don't know the context to which the form or template you want belongs, or if you simply want to see a list of all the forms and templates that are available across all contexts, we recommend that you begin your search in the Forms Catalogue folder on the Search Tree. The Forms Catalogue is a central directory that lists all forms and templates that have been published through Form Builder. Forms and templates are listed alphabetically and (if applicable) by protocol.

The Catalogue of Published Forms folder resides as a sub-node of the caBIG context node.

Browse a Specific Context for a Form

If a form or template has not been added to the Forms Catalogue yet, you can browse for it within a specific context. However, since each context organizes it forms using different classification schemes, you may need to explore the sub-folders within each context before you find what you are looking for.

Remember, use the plus and minus signs located to the left of each node in the Search Tree to expand and collapse the nodes. When you find the form you want, click the form link in the tree to generate a search for all CDEs used on the selected form.

Breadcrumbs appear at the top of the screen that indicate, in a hierarchical display, what node you clicked to generate the current set of search results.

Finding a Protocol Form Template Using the Search Tree

In the same way that the CDEs used on forms can be found using the search tree, you can also use the search tree to find the CDEs used on any Protocol Form Templates listed for a context. In addition, when browsing Protocol Form Templates (as opposed to Protocol Forms), you may be able to preview and download the Template file in addition to viewing the CDEs used on the template.

The steps below provide an example of how to find, review, and if available, download a Protocol Form Template through CDE Browser. These steps access the Advanced Bladder Cancer Follow-up protocol form template owned by the CTEP Context.

1. Click the plus sign to the left of the folder icon for Cancer Therapy Evaluation Program context to expand the folder.
2. Click the plus sign to the left of the folder icon for Protocol Form Templates to expand it.
3. From the sub-nodes of the Protocol Form Templates folder, expand the Disease folder.
4. Under the Disease folder, find and expand the Bladder folder. The expanded Bladder folder lists all of the template types associated with that catalogue (i.e. follow-up, on-study, etc.).

5. Expand the Follow-Up folder to see the templates available for that type.
6. Click the name of one of the templates listed. The Search Results show all of the CDEs associated with the selected template.

After clicking on the link for a Protocol Form Template, notice that there is a Download Template link located above the search results table. If there is a file attached to the form template, clicking this link will open that file (typically a PDF) in a new browser window or tab. From there you can use your browser commands to save the attached template file.

Be advised that there are a few templates that do not have an image file loaded. If you select Download Template for any of these templates, you will receive a message stating that no document is found.