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A trial can have multiple biomarker records. You can add them individually, or copy the marker records as you create them to enter variations of attributes (e.g., multiple assay types) for the same marker.

How to Abstract Markers

1. Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
2. On the Scientific Data menu, click Markers. The Markers page appears. It displays any markers that may have been recorded previously. 
   
3. Click Add.
   The Add Marker page appears.
   

4. Search for and select the biomarker from the caDSR by following the instructions in Searching for Biomarkers in caDSR.

    

   Tip
   title You can enter a biomarker name directly
   If you cannot find the biomarker indicated in the protocol document in caDSR, click Cancel to return to the Markers page, and enter the biomarker name directly in the Name field.

    

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5. Select the appropriate attributes. The following table describes the fields. An asterisk (*) indicates a required field.

   Info
   You can select multiple attributes for Evaluation Type, Assay Type, Biomarker Purpose, and Specimen Type. If you select Other as an attribute for Evaluation Type, Assay Type or Specimen Type, you must enter text in the Evaluation Type Other Text , Assay Type Other Text or Specimen Other Text fields respectively.

   Trial Description	Instruction
   Name* Anchor 6065 6065	Click caDSR and follow the instructions in Searching for Biomarkers in caDSR. If you cannot find the biomarker indicated in the protocol document in caDSR, enter the biomarker name directly in the Name field to create a placeholder value.
   Evaluation Type*	Select the type of evaluation. Valid values include: Include Page Marker Evaluation Types - Include v4.4 Marker Evaluation Types - Include v4.4 Note title Special instructions for "Other" text If you select "Other," copy and paste the exact name of the evaluation (as written in the protocol) into the Evaluation Type Other Text box.
   Assay Type* (CDE ID 64731)	Select the test type(s), the test name(s), or method(s) used to assess a specific marker. Valid values include: Include Page Marker Assay Types - Include v4.4 Marker Assay Types - Include v4.4 Note title Special instructions for "Other" text If you select "Other," copy and paste the exact name of the assay/method (as written in the protocol) into the Assay Type Other Text box.
   Biomarker Use* (CDE ID 2939411)	Select the value that describes the assay use. Valid values include: Include Page Marker Assay Use - Include v4.4 Marker Assay Use - Include v4.4
   Biomarker Purpose* (CDE ID 2939397)	Select the value(s) that describes the reason or intention of the assay in the clinical study. Valid values include: Include Page Marker Purpose - Include v4.4 Marker Purpose - Include v4.4
   Specimen Type* (CDE ID 3111302)	Select the type(s) of sample. Valid values include: Include Page Marker Specimen Type - Include v4.4 Marker Specimen Type - Include v4.4 Note title Special instructions for "Other" text If you select "Other," copy and paste the exact name of the specimen (as written in the protocol) into the Assay Type Other Text box.
   Record Status	This field is populated by the PA system. When you save the biomarker information, the system sets the marker status to one of the following: Pending - Indicates that a request for a new permissible value has been submitted Footnote The Pending status changes to Accepted once the Research Scientist enters corresponding Public ID  in the Pending Markers Report. For information about updating the status of a marker, see Processing New Marker Requests. Active - Indicates that the marker was listed in caDSR

   Footnotes Display

6. Do one of the following to save the record:

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• Scroll to the top or bottom of the page, and click Save.

- or -

• To create a new record for a different marker but with the same attribute selections, click Save & Retain Attributes. Then search for and select the biomarker from the caDSR, and save the record.

The Marker page displays the record(s) you created.

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Searching for Biomarkers in caDSR

The search feature enables you to search for biomarkers listed in caDSR. You can search for biomarkers by the following criteria:

• Search Term. Search for biomarkers meanings that contain the search term
• Search Scope. Search for biomarkers that contain the search term in their preferred permissible values only, in their synonyms (alternate names) only, or in both (the default).
  
• Public ID. Search for biomarkers by their Public IDs only
  

Additional search options include the following:

• Case-sensitivity. You can elect to make the search term case-sensitive or insensitive. Searches are case-insensitive by default.
• Highlighting search terms. Query text in search results is highlighted by default to make search terms easier to identify. You can turn on or off query text highlighting in the search results.

Most search results list primary terms followed by all possible synonyms in parenthesis in the following order:

• Exact matches for the Primary term
• Matches that contain the search term alone (i.e., the term is not part of a larger term)
• All other matches that contain the search term

How to Search for Markers in caDSR

1. Follow Steps 1 and 2 in Adding Biomarkers.
2. Next to the Name field, click caDSR
   The Marker Search in caDSR window appears.
   

3. Enter all or part of the criteria for the search in the fields provided.

4. To restrict your search by case, next to Case-Sensitive Search, select Yes (the default is case-insensitive).

5. To highlight the term you searched for in the list of results, next to Highlight Query Text, select Yes.

6. Press the ENTER key on your keyboard, or click Search.

7. The results of your search are listed in a table with their permissible values

   Footnote
   The TSR document associated with a trial includes both the permissible value and alternates (synonyms).

   .
   

8. In the row that contains the appropriate marker, click Select.
   You are returned to the Add Marker page. The Marker Name field is populated with information from the marker you selected.

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Adding Biomarkers from HUGO to the caDSR Database

If you did not find a given biomarker in caDSR, The Research Scientist must review the term to determine if a request must be sent to caDSR. If the marker is a gene, the Research Scientist should access HUGO (via the link in the request form). The HGNC-approved symbol should be requested as the primary term, followed by any appropriate synonym from the protocol in parenthesis. The HGNC ID number should also be included in the request after selecting the Found in Hugo? check box.

How to Request Markers from HUGO for Addition to the caDSR Database

1. Follow Steps 1 and 2 in Adding Biomarkers.
2. Next to the Name field, click caDSR
   The Marker Search in caDSR window appears.
   
3. Click Create Biomarker Request.
   The Create Permissible Value Request window appears, with your email address in the Sender's Email address field.
   
4. Select the Found in HUGO? check box, and then click the HUGO link.
   The window displays a new field for the HUGO marker code, and the HGNC database is launched in a new browser window.
5. Search for the marker in the HGNC database, and then enter the HGNC ID number for the appropriate record into the Hugo Marker Code field. This field is displayed only when you select the Found in HUGO? check box.
6. In the Text of marker as written in the protocol field, copy and paste, or enter, the information about the marker as it appears in the protocol.
7. Click Send Email.
   Your request is sent to the caDSR for processing. The value you requested is listed on the Pending Markers Report with the Pending status. You can return to the Pending Markers report later to enter the Public ID number once caDSR has sent notification to the Research Scientist that the new term was created. (See Processing New Biomarker Requests.)

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Editing Biomarkers

You can change recorded marker information or delete marker records from a trial.

How to Edit Marker Records

1. Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
2. On the Scientific Data menu, click Markers. The Markers page appears.
   
3. To edit a marker, in the Edit column, click the Edit (pencil) icon.
   The Edit Marker page appears.

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4. Follow the instructions for selecting and saving attributes in Adding Biomarkers to change the recorded information.

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Deleting Biomarkers

You can delete one or more marker records from a trial.

How to Delete Marker Records

1. Do one of the following to select the markers you want to delete:
   
   1. To delete a marker(s), select the check box in the Delete column for the appropriate marker record(s). You can select multiple records.
      - or -
   2. To delete all markers, click Select All.
      The button changes to Deselect All.
2. Optionally, to clear all check boxes, click Deselect All.
3. Click Delete, and then confirm that you want to delete the record.

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Requesting New Permissible Values for Biomarkers

How to Request New Permissible Values for Biomarkers

1. Follow Steps 1 and 2 in Adding Biomarkers.
2. Next to the Name field, click caDSR
   The Marker Search in caDSR window appears.

3. Click Create Biomarker Request.

   The Create Permissible Value Request window appears, with your email address in the Sender's Email address field.

   
4. In the Marker Name field, enter the most appropriate biomarker name followed by the name as it appears in the protocol in parenthesis if the two are not identical.
5. In the Text of marker as written in the protocol field, copy and paste, or type, the information about the marker as it appears in the protocol.
   Click Send Email.
   Your request is sent to the caDSR for processing. The value you requested is listed on the Pending Markers Report with the Pending status. You can return to the trial later to accept it once it has been processed. (See Processing New Biomarker Requests.)

How to Add Interventions

1. Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
2. On the Scientific Data menu, click Interventions. The Interventions page appears, with or without any intervention records displayed.

3. Click Add. The Add intervention page appears.
   

4. From the Intervention Type drop-down list, select the means of intervention for the trial. Valid intervention types are as follows.
   
   • Drug
   • Device (including sham)
   • Biological/Vaccine
   • Procedure/Surgery
   • Radiation
   • Behavioral (for example, Psychotherapy, Lifestyle Counseling)
   • Genetic (including gene transfer, stem cell, and recombinant DNA)
   • Dietary Supplement (for example, vitamins, minerals)

   • Other
     

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     searchIntervention searchIntervention

5. To search for the name of the intervention, click Look Up.
   The Search Intervention window appears.
   
   

6. In the Intervention Name field, type part or all of the intervention name.

   Tip
   title Tip
   Include Page Wildcards - Include v4.4 Wildcards - Include v4.4

   1. To include synonyms in your search in addition to preferred names, select the Include Synonym check box.
   2. To limit your search to exact matches only, select the Exact Match Only check box.
7. Click Search.
   The system searches for the intervention from both preferred names and synonyms (if selected) in the database, and returns a list of results.
   
8.  Scroll through the list to locate the intervention, and click Select.

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   selectIntervention selectIntervention

   
   The selected intervention and any other names are displayed on the Add Intervention page.
   

9. Optionally, in the Intervention Description field, enter the name/description of the intervention. 

10. Click Save.
    The record is added to the trial and displayed on the Interventions page.

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Generating Drug, Radiation, Procedure, and Surgery Descriptions

Protocol Abstraction provides a structure for abstracting detailed descriptions of drug, radiation, and procedure/surgery interventions.

How to Generate Drug, Radiation, and Procedure/Surgery Descriptions

1. Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
2. On the Scientific Data menu, click Interventions. The Interventions page appears, with or without any intervention records displayed.
3. Click Add. The Add intervention page appears.

4. From the Intervention Type field, select Drug, Radiation, or Procedure/Surgery as appropriate.

   Tip
   title Tip
   Do not type an intervention description at this point. The system automatically populates the Intervention Description from information you provide in the next steps.

5. Follow the steps in Adding Interventions for instructions for searching for, and selecting, interventions.
   The Interventions page expands to display a Drug Information, Radiation, or Procedure Information section, depending on your selection.
   
   
   
   
6. In the Drug, Procedure, or Radiation Information section of the page, enter the values in the text fields provided.
7. To provide values for the parameters that require harmonized terms (the gray fields), click Look Up.
   The Search window appears .
   
   

8. Type your search criteria in the field(s) provided, and then click Search. If the information you are abstracting includes a range, for example, dose range, you can provide the lower limit without providing the upper limit. However, do not provide the upper limit of a range unless you also include a lower limit.

   Info
   You must type at least one character in any of the search fields.

   The Search window displays the result(s) of your search.
   

9. In the search results list, locate the preferred item, and then click Select.
10. Once you have provided information for all relevant fields, click Generate.
    The information you provided is displayed in the Intervention Description field.
    
11. Click Save.

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Editing Interventions

You can edit trial descriptions. However, if you need to change the intervention type or name, you must delete the record and create a new one with the correct information. See Deleting Interventions.

How to Edit Intervention Records

1. Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
2. On the Scientific Data menu, click Interventions. The Interventions page appears.
   
3. In the Edit column for a given record, click the Edit (pencil) icon.
   The Edit Intervention page appears.
   
4. Edit or enter the intervention description, and then click Save.
   If you edit a drug, radiology, or procedure intervention, the Edit Intervention page displays the original form for the record.
    
   
5. To edit the intervention description and/or details of drugs, radiation, and procedures/surgeries, follow the instructions in Adding Interventions.
6. Click Save.

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Reordering Interventions

You can change the order in which the interventions are displayed in the interventions table and in the TSR/XML documents.

How to Re-Order Intervention Criteria

1. Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
2. On the Scientific Data menu, click Interventions. The Interventions page appears, displaying all other interventions currently abstracted.
   
   
3. In any column other than  Edit or Delete, click and drag the record you want to move to a new location in the Interventions table. The record background changes color as you move the record.
   
   

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Deleting Interventions

When you delete interventions from a trial, you delete them from view, and can not recover them. If you delete a record accidentally, follow the instructions in Adding Interventions to add it back.

How to Delete Interventions

1. Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
2. On the Scientific Data menu, click Interventions. The Intervention page appears.
3. In the Delete column, select the check box for each record you want to delete, then click Delete. To delete all records, click Select All, and then click Delete.

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Managing Intervention Terms

You can import NCIt terms on demand if the term you require for abstraction does not exist in the CTRP database. Once imported, CTRP syncs the term with in the NCIt database automatically.

If a term does not exist (i.e., has not been published yet) in the NCIt, you can request the term directly from EVS. Once EVS curators have responded to your request, you can enter new term details when abstracting trials. Later EVS publishes the new term in the NCIt. Refer to Managing Disease and Intervention Terminologies.

How to Manage NCIt Intervention Terminology

1. At the bottom of the Interventions page, click Manage NCIt Terms.
   The Manage NCIt Terms menu contains options for managing intervention terms.
   

2. Follow the instructions in the following sections:

• Importing Intervention Terms

• Synchronizing Intervention Terms

• Requesting New Intervention Terms

• Entering Intervention Terms