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This page tree describes how to abstract and edit the scientific details of clinical trials.
About Scientific Data
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Abstracting Trial Descriptions
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Abstracting Interventional Trial Design
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Abstracting Non-Interventional Trial Design
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Abstracting Outcomes
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Abstracting Eligibility Criteria
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Abstracting Diseases and Conditions
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Abstracting Data Table 4 Anatomic Sites
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| MultiExcerptName | anatomicsite |
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You can select and record anatomic site terms that identify the anatomic cancer site(s) on which a trial or study is focused. These records are included in a Data Table 4 report. A trial can have multiple anatomic sites.
Adding Data Table 4 Anatomic Sites
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How to Add Data Table 4 Anatomic Sites
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Data Table 4 Anatomic Site. The Data Table 4 Anatomic Site page appears, with or without any anatomic records displayed.
Data Table 4 Anatomic Site Page - To add a site, click Add.
The Add Data Table 4 Anatomic Site page appears.
- Select the anatomic site from the drop-down list.
- Click Save.
- If applicable, repeat the steps above to record additional sites.
Deleting Data Table 4 Anatomic Sites
How to Delete Data Table 4 Anatomic Sites
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Data Table 4 Anatomic Site. The Data Table 4 Anatomic Site page appears.
- Do one of the following:
- To delete one or more sites, in the Delete column for the appropriate record(s), select the check box, and then click Delete.
- or - - To delete all records, click Select All, and then click Delete.
- To delete one or more sites, in the Delete column for the appropriate record(s), select the check box, and then click Delete.
Abstracting Biomarkers
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| MultiExcerptName | plannedmarker |
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The abstraction of biomarkers applies to Complete and Abbreviated trial categories. You can record biomarkers, their classification, and purpose. Biomarkers for a given study may be available from the study protocol documents. You can search caDSR for biomarkers. If you do not find the biomarker in the caDSR, you can create a placeholder entry for the biomarker named in the protocol.
Adding Biomarkers
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| MultiExcerptName | abstractmarker |
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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
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Search for and select the biomarker from the caDSR by following the instructions in Searching for Biomarkers in caDSR.
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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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Select the appropriate attributes. The following table describes the fields. An asterisk (*) indicates a required field.
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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. |
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Trial Description
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Instruction
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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.
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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. |
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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:
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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. |
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Biomarker Use* (CDE ID 2939411)
Select the value that describes the assay use. Valid values include:
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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:
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Specimen Type* (CDE ID 3111302)
Select the type(s) of sample. Valid values include:
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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. |
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Record Status
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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
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- Scroll to the top or bottom of the page, and click Save.
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- 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.
Searching for Biomarkers in caDSR
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- 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
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If you provide the marker's Public ID, you must enter it exactly, in its entirety. |
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
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How to Search for Markers in caDSR
- Follow Steps 1 and 2 in Adding Biomarkers.
- Next to the Name field, click caDSR
The Marker Search in caDSR window appears.
Enter all or part of the criteria for the search in the fields provided.
To restrict your search by case, next to Case-Sensitive Search, select Yes (the default is case-insensitive).
To highlight the term you searched for in the list of results, next to Highlight Query Text, select Yes.
Press the ENTER key on your keyboard, or click Search.
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).
- 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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| If you do not find the marker you are looking for in the caDSR database, you must create a placeholder. For instructions, see Requesting New Permissible Biomarker Values or Adding Markers from HUGO to the caDSR Database. |
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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
- Follow Steps 1 and 2 in Adding Biomarkers.
- Next to the Name field, click caDSR
The Marker Search in caDSR window appears.
- Click Create Biomarker Request.
The Create Permissible Value Request window appears, with your email address in the Sender's Email address field.
- 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. - 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.
- 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.
- 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.)
Editing Biomarkers
You can change recorded marker information or delete marker records from a trial.
How to Edit Marker Records
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Deleting Biomarkers
You can delete one or more marker records from a trial.
How to Delete Marker Records
- Do one of the following to select the markers you want to delete:
- 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 - - To delete all markers, click Select All.
The button changes to Deselect All.
- To delete a marker(s), select the check box in the Delete column for the appropriate marker record(s). You can select multiple records.
- Optionally, to clear all check boxes, click Deselect All.
- Click Delete, and then confirm that you want to delete the record.
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There is no way to recover a deleted record. If you delete a record accidentally, follow the instructions in Adding Biomarkers to add it back. |
Requesting New Permissible Values for Biomarkers
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How to Request New Permissible Values for Biomarkers
- Follow Steps 1 and 2 in Adding Biomarkers.
- Next to the Name field, click caDSR
The Marker Search in caDSR window appears. Click Create Biomarker Request.
The Create Permissible Value Request window appears, with your email address in the Sender's Email address field.
- 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.
- 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.)
Abstracting Interventions
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| MultiExcerptName | interventionintro |
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You can search for, and select, interventions from a stored list of active intervention terms extracted from NCIt and link them to a trial. NCIt is an online database developed and maintained by the National Cancer Institute Enterprise Vocabulary Services. You can find more detailed information about NCIt at http://ncit.nci.nih.gov/.
Additionally, Protocol Abstraction provides a structure for describing drug, radiation, and surgical procedure details. It generates a description from values you provide for such parameters as dose, target site, frequency of administration, etc.
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Some intervention terms become obsolete over time. When you validate the trial, the system displays an error message if the abstraction contains an obsolete term. If this occurs, look up the intervention name and replace the obsolete term with the new one. |
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Before you begin abstracting or validating any trial, be sure you check it out first. Otherwise you will not be able to modify any trial data. |
Trials can have multiple intervention records. Each record displays the following information about the intervention:
Intervention data definitions
Column Name | Definition | |||||
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Name | Standard name used to refer to each intervention. For drugs, this is the generic name. For investigational new drugs that do not yet have a generic name, this may be the chemical name, company code, or serial number. | |||||
Other Names | Synonym or other name
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Description | For drug interventions, a summary of the drug’s chemical nature and (potential) mechanism of action, and/or details such as dosage form, dosage, frequency, and duration.
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Type | Mode of intervention, for example, drug or device. |
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Additionally, you can add, edit, reorder, and delete records.
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You can change the sort order (ascending/descending) of any column other than Edit and Delete by clicking the column name and selecting the up or down arrow that appears. |
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Adding Interventions
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| MultiExcerptName | addintervention |
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You can link interventions to a trial by searching for an intervention name from the current list of active records.
The terminology list is refreshed weekly.
How to Add Interventions
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Click Add. The Add intervention page appears.
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In the Intervention Name field, type part or all of the intervention name.
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- To include synonyms in your search in addition to preferred names, select the Include Synonym check box.
- To limit your search to exact matches only, select the Exact Match Only check box.
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Optionally, in the Intervention Description field, enter the name/description of the intervention.
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Although not displayed on the Interventions page, the system records the ClinicalTrials.gov code for the intervention. |
Generating Drug, Radiation, Procedure, and Surgery Descriptions
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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
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Interventions. The Interventions page appears, with or without any intervention records displayed.
- Click Add. The Add intervention page appears.
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.
- 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.
- In the Drug, Procedure, or Radiation Information section of the page, enter the values in the text fields provided.
- To provide values for the parameters that require harmonized terms (the gray fields), click Look Up.
The Search window appears .
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.
- In the search results list, locate the preferred item, and then click Select.
- Once you have provided information for all relevant fields, click Generate.
The information you provided is displayed in the Intervention Description field.
- Click Save.
Editing Interventions
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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
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Interventions. The Interventions page appears.
- In the Edit column for a given record, click the Edit (pencil) icon.
The Edit Intervention page appears.
- 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.
- To edit the intervention description and/or details of drugs, radiation, and procedures/surgeries, follow the instructions in Adding Interventions.
- Click Save.
Reordering Interventions
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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
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Deleting Interventions
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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
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Interventions. The Intervention page appears.
- 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.
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.
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- At the bottom of the Interventions page, click Manage NCIt Terms.
The Manage NCIt Terms menu contains options for managing intervention terms.
Follow the instructions in the following sections:
Abstracting Arms
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| MultiExcerptName | abstractarms |
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When adding arms to a trial, you assign to them the interventions currently abstracted for the trial.
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Before you begin abstracting or validating any trial, be sure you check it out first. Otherwise you will not be able to modify any trial data. |
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There must be at least one arm/group that implies that the entire study subject population receives the same intervention.
The number of arms/groups added to the trial must coincide with the number indicated in the trial’s Design Details. See Abstracting Interventional Trial Design Details.
- Every arm must have at least one assigned intervention (except for the arm type "no intervention").
- Every intervention must be assigned to at least one arm.
- There must be only one arm with the same combination of description and associated intervention.
- Arm details for single-arm trials are not required.
Trials can have multiple arm records. Each record displays the following arm information:
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Field
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Definition
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Label
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Short name used to identify the arm or comparison group.
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Type
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Description
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Brief description of the arm or comparison group to distinguish it from other arms/groups in the trial.
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Assigned Interventions
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Intervention(s) assigned to a given arm.
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Interventions imported from ClinicalTrials.gov may not match CTRP terminology. |
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Adding Arms
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You can add one or more arms to a trial according to the trial’s design details.
How to Add Arms
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In the drop-down lists and text fields, select or enter the appropriate information. The following table describes the fields. An asterisk (*) indicates a required field.
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Trial Description
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Instruction
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Label*
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Type the descriptive name of the arm.
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Type*
Select the appropriate arm function. Valid values are as follows:
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Arm Description
Type a brief description of the arm.
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Assignment
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For arm types other than No Intervention, select the check box in the column for the intervention assigned to the current arm.
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Editing Arms
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You can edit arm records as necessary.
How to Edit Arm Records
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Deleting Arms
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When you delete arms from a trial, you delete them from the system, and can not recover them.
How to Delete Arms
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Arms. The Arms page appears.
In the Delete column for the appropriate record, click the Delete icon.
Warning There is no way to recover a deleted record. If you delete a record accidentally, follow the instructions in Adding Arms to add it back.
Abstracting Groups and Cohorts
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| MultiExcerptName | abstractcohort |
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Group/cohort information pertains to Complete non-interventional trials only. In non-interventional studies, cohorts are groups of individuals, initially defined and composed, with common characteristics (e.g., condition, birth year), who are examined or traced over a given time period.
When adding groups to a trial, you assign to them the interventions currently abstracted for the trial.
| Info | ||
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Before you begin abstracting or validating any trial, be sure you check it out first. Otherwise you will not be able to modify any trial data. |
The following rules apply to each trial:
There must be at least one group/cohort that implies that the entire study subject population receives the same intervention.
The number of groups/cohorts added to the trial must coincide with the number indicated in the trial’s Design Details. See Abstracting Non-Interventional Trial Design Details .
- Every group/cohort must have at least one assigned intervention.
- Every intervention must be assigned to at least one group/cohort.
- A trial must have only one group with the same combination of description and associated intervention.
Trials can have multiple group/cohort records. Each record displays the following group information:
| Field | Definition |
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Label | Short name used to identify the group |
Description | Explanation of the nature of the study group (e.g., those with a condition and those without a condition; those with an exposure and those without an exposure). |
Assigned Interventions | Intervention assigned to a given group |
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Adding Groups
You can add one or more groups to a trial according to the number specified in the trial’s design details. See Abstracting Non-Interventional Trial Design Details .
How to Add Groups
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Field | Instruction/Description |
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Label* | Enter the descriptive name of the group. |
Description* | Enter a brief description of the group. |
Assignment | Select the check box(s) in the column for the intervention(s) assigned to the current group. |
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Editing Groups
You can edit group records as necessary.
How to Edit Group Records
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Deleting Groups
When you delete groups from a trial, you delete them from the system, and can not recover them. If you delete a record accidentally, follow the instructions in Adding Groups to add it back.
How to Delete Groups
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Groups/Cohorts. The Groups page appears.
- In the Delete column, select the check box for the appropriate record(s), and then click Delete.
- To delete all groups, click Select All, and then click Delete.
Abstracting Sub-Groups
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| MultiExcerptName | abstractsubgroups |
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Trials can have multiple sub-group records. Each record displays the following information about the disease or conditions:
Field | Definition |
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Code | Characters, or phrase used to identify the sub-group |
Description | Stratification criteria |
| Info | ||
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Before you begin abstracting or validating any trial, be sure you check it out first. Otherwise you will not be able to modify any trial data. |
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Adding Subgroups
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You can add one or more sub-groups to a trial according to the trial’s design details.
How to Add Sub-groups
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Editing Subgroups
You can edit sub-group records as necessary.
How to Edit Sub-group Records
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Sub-groups. The Sub-groups page appears.
- In the Edit column for a given record, click the Edit icon. The Add/Edit Sub-group Information page appears.
- Modify the sub-group details according to instructions in Adding Sub-Groups.
- Click Save.
Deleting Subgroups
When you delete groups from a trial, you delete them from the system, and can not recover them. If you delete a record accidentally, follow the instructions in Adding Sub-Groups to add it back.
How to Delete Sub-groups
- Search for the trial of interest. In the search results, click the NCI Trial Identifier link for that trial.
- On the Scientific Data menu, click Sub-groups. The Sub-group page appears.
- In the Delete column for the appropriate record, click the Delete icon.
