Page History

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This chapter describes the processes for creating and managing studies in caIntegrator. Topics in this chapter include:

Creating a Study – Overview

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1. In the Study Management section of the left sidebar, click Create New Study.
2. In the Create New Study dialog box that opens, provide a name and description for the study you are creating.
3. Select the checkbox to specify if you want to allow public access to the study.
4. Click Save. Click Cancel to close the dialog without creating the study.
   When you save the study, an Edit Study page opens where you can add identify data files for your study. See #Creating Creating or Editing a Study.

Creating or Editing a Study

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1. Enter or change (if editing) the name and/or description.
2. Select or verify the checkbox to specify if you want to allow public access to the study.
3. For the study log feature, click View Log or Edit Log. See Study Log for details about the log.

4. Click Save.

   Tip
   title Tip
   You can save the study at any point in the process of creating it. You can resume the definition and deployment process later.

5. If you choose to add a logo for the study, click the Browse button corresponding to Logo File in the upper right of the Edit Study page. Navigate for the file, and click Browse. The file type displays above the Upload Now button.
   
6. Click the button to upload the logo. Once you save the study (or its edit), the logo displays in the center of the page. On the home page for the study, the logo displays in the upper left, above the sidebar.

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1. Add an annotation group. This optional step is for users who have a rigid data dictionary of all annotations relevant to the study. This step can also be helpful in cases where a study has many annotations. For more information, see #Adding Adding an Annotation Group.
2. Add subject annotation data. This consists of multiple sub-steps.
3. Add a new subject annotation data sources file. This step uploads the file and starts the workflow for assigning uploaded data definitions. See #Editing Editing an Annotation Group, step 1.
   1. Edit the annotations. This step opens the Define Fields for Subject Data page. See #Editing Editing an Annotation Group, step 2.
   2. In the Define Fields for Subject Data page, review possible definitions in the annotation group associated with this study. See Define Fields Page.
   3. Assign the visibility of each annotation definition. See #Editing Editing an Annotation Group, step 2.
   4. In the authorization column, select the annotation or annotations to be used to restrict data by subject for authorized groups. If authorization groups are to be used to restrict study data, at least one annotation authorization must be selected. If authorization groups are not to be used to restrict study data, selecting an annotation authorization is not necessary. Annotations used to restrict data by subject must contain permissible values. See #Assigning Assigning an Identifier or Annotation for more information about permissible values.
   5. Locate and verify the assignment as "identifier" for one annotation. See #Assigning Assigning an Identifier or Annotation.
   6. Review, verify and assign definitions for each annotation. You can do this in one of four ways:
      --Accept existing default definitions as described in the associated annotation group. See #Assigning Assigning an Identifier or Annotation.
      --Create or manage definitions manually. See #Assigning Assigning an Identifier or Annotation.
      --Search for and use definitions existing in other caIntegrator studies. See #Searching Searching for Annotation Definitions.
      --Search for and use definitions from caDSR. See #Searching Searching for Annotation Definitions.
4. Load the Subject Annotation Source. Up until this point, you can periodically save your work with the annotations, but before you can deploy the study, you must complete this step.
5. Deploy the study.

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This topic opens from both the Create Annotation Group page and the Edit Annotation Group page. If you plan to create a group, continue with this topic. If you plan to edit an annotation group, see #Editing Editing an Annotation Group.

An annotation group is a group of annotation definitions configured in a CSV file. This feature is primarily meant for the Study Manager who knows that they have tightly restricted vocabulary definitions that are relevant to a study. In this optional step, you can review the uploaded Group Definition Source file before assigning the appropriate definitions for your study.

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This topic opens from the Edit Annotation Group page. You may want to refer to #Adding Adding an Annotation Group if you are adding a group for the first time.

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1. You can change the Name and Description for the group.
2. A list of annotation definitions applied to the original annotation group displays on the Edit Annotation Group page.
   1. In the drop-down list, you can select a different annotation group for the annotation definition.
   2. You can change the visibility for the annotation definition.
   3. You can change the authorization for the annotation definition. Authorized annotations can be used to restrict data by subject for authorized groups. Annotations used to restrict data by subject must contain permissible data. See #Assigning Assigning an Identifier or Annotation for more information about permissible values.
   4. Click Change Assignment to modify the properties of the annotation definition.
3. Click Update Annotations to confirm your edits for the group.

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The Edit Study page, described in #Creating Creating or Editing a Study, opens after you save a new study or click to edit an existing study.

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From this page you can initiate editing the annotations. In the Subject Annotation Data Sources section, click Edit Annotations corresponding to the subject annotations that have been uploaded for the study. This open the #Define Define Fields Page for Editing Annotations.

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The Define Fields for Subject Data page, shown in the following figure, opens when you click Edit Annotations in the Subject Annotation Data Sources or the Image Data Sources section of the Edit Study page. The exception to this is if you have not yet imported annotations for the imaging data for the study, In that case, when you click the Edit Annotations button in the Imaging Data Sources section, a page opens where you can identify and upload image annotation data. See #Adding Adding or Editing Image Annotations.

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• You MUST designate one column in the file as a unique "identifier" column type.
• You MUST review and define column annotation definitions for each column header in the file.
  Note the following regarding the list of annotations on this Define Fields... page:
• If caIntegrator "recognizes" the same column header in other files already in the system, a term, for example "age" or "survival", which is the current definition, appears in the Annotation Definition column above the blue Change Assignment link on the page.
• When the annotation definition has not been assigned, and the area above the blue Assign Annotation Definition link is blank on this page, no correlating term exists in the database. In this case, you must specify the field type, and then the term will populate the space. See #Assigning Assigning an Identifier or Annotation for more information.
• A field name that displays in red indicates an error in the annotation. Click the Change Assignment button for more information about the error.

The first column of the table on this page displays annotation groups that have been created for this study. For more information, see #Adding Adding an Annotation Group.

To add subject or image annotation metadata in this page, follow these steps:

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1. For the column that you choose to be the one and only Identifier column (in this case, PatientID), in the Column Type drop-down list, select Identifier. The following figure shows the dialog box rendering when "identifier" is selected in the Field Descriptor Type drop-down list.
   
2. Click Save to save the identifier. This returns you to the Define Fields for Subject Data page where the Identifier is noted in the Annotation Definition column.
3. After you have defined which field is the Identifier, you must ensure that ALL other data fields also have an annotation definition assignment. For those fields without an annotation definition assignment or for those whose annotation definition you want to review, click Change Assignment.
4. In the Assign Annotation Definition for Field Descriptor dialog box, shown in the following figure, select Annotation in the drop-down list.
   
   As you select the column type, you can work with column headers in one of four ways in this dialog box.
   1. You can accept existing default definitions (those that are inherent in the data file you selected). See Step 5.
   2. You can create and/or manage your own definitions manually. See Step 6.
   3. You can search for and use definitions in other caIntegrator studies. See #Searching Searching for Annotation Definitions.
   4. You can search for and use definitions found in caDSR. See #Searching Searching for Annotation Definitions.
5. Review the current annotation definition in the Assign Definition page, Current Annotation Definition section. Click Cancel to return to the Define Fields... page.
   You can still initiate a search for another annotation definition in the Search for an Annotation Definition section on the browser page if you choose to change the definition. See the bottom section of the preceding figure. See also #Searching Searching for Annotation Definitions. Click Save to retain any changes.

6. To enter a new name annotation, or any other information about the annotation definition, click the Newbutton and enter the information described in the following table.

   Annotation Field	Field Description
   Name	Enter the name for the annotation.
   Definition	Enter the term(s) that define the annotation.
   Keywords	Insert keyword(s) that could be used to find the annotation in a search, separated by commas.
   Data Type	Select a string (default), numeric, or date.
   Apply Max Number Mask	This field is available only for numeric-type annotations, or when a new definition is created. This feature is unavailable when permissible values are present. Select the box and enter a maximum number for the mask, such as "80" for age. When you query results above the value of the mask, then the system displays the mask and not the actual age. Tip title Tip If you enter masks of both "max number" and "range", caIntegrator applies both masks at the same time. The Data Dictionary page now has a Restrictions column that shows restrictions whenever a mask has been applied.
   Apply Numeric Range Mask	This field is available only for numeric-type annotations, or when a new definition is created. This feature is unavailable when permissible values are present. Select the box and enter a width of range for the mask, such as "5" representing blocks of 5 years. For example, if you enter a width of 5, the query only allows age blocks of 0-5, 6-10, 11-15, etc. When you query results above the value of the mask, then the system displays the mask and not the actual age ranges. Tip title Tip If you enter masks of both "max number" and "range", caIntegrator applies both masks at the same time. The Data Dictionary page now has a Restrictions column that shows restrictions whenever a mask has been applied.
   Permissible/Non-permissible Values	Tip title Tip The first time you load a file, before you assign annotation definitions, step #3 in #Assigning Assigning an Identifier or Annotation, these panels may be blank. If the column header for the data is already "recognizable" by caIntegrator, the system makes a "guess" about the data type and assigns the values to the data type in the newly uploaded file. They will display in the Non-permissible values sections initially. Use the Add and Remove buttons to move the values shown from one list to the other, as appropriate.

When you select or change annotation definitions by selecting matching definitions (described in #Searching Searching for Annotation Definitions), this may add (or change) the list of non-permissible values in this section.

If you leave all values for a field in the Non-permissible panel, then when you do a study search, you can enter free text in the query criteria for this field.

If there are items in the Permissible values list, then the values for this annotation are restricted to only those values. When you perform a study search, you will select from a list of these values when querying this field. If there are no items in the permissible values list then the field is considered free to contain any value.
To edit a field's permissible values, you must change the annotation definition. You can do this even after a study has been deployed.

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1. Enter search keyword(s) in the Search text box on the Assign Annotation Definition page (the preceding figure). Click Search or click Enter to launch the search. After a few moments, the search results display on the same page. An example of search results is shown in the following figure.
   

2. To view the definitions corresponding to any of the "Matching Annotation Definitions", which are those currently found in other caIntegrator studies, click the [term], such as "age", hypertext link. The definition then appears in the Current Annotation Definition segment of the page just above.

   Info
   title In Summary
   When you click the link for a definition, that assigns the definition to the Define Fields for Subject Data page, and it also closes the Annotation Definition page. You can modify any portion of the definition, as described in Step 6 in #Assigning Assigning an Identifier or Annotation.

3. The matches from caDSR display some of the details of the search results. To view more details of a match, such as permissible values, click View, which opens caDSR to the term. If you click Select, the caDSR definition automatically replaces the annotation definition for this field with which you are working.

   Note
   title Caution
   Take care before you add a caDSR definition that it says exactly what you want. caDSR definitions can have minor nuances that require specific and limited applications of their use.

4. Once you have settled on an appropriate field definition for the annotation, click Save. This returns you to the Define Fields for Subject Datapage.

   Info
   title Note
   If you have not clicked Select for alternate definitions in this dialog box, then click Save to return to the Define Field...dialog box without making any definition changes.

5. From the Define Fields for Subject Data page, be sure and designate the data types for each field in the file. Click Save on each page to save your entries or click New to clear the fields and start again. You will not be able to proceed until every field definition entry on the Fields for Subject Data screen has an entry, one as the unique Identifier and the remainder as annotations.
   The Data From File columns on the Define Fields... page display the column header values of the first three rows you designated as "annotations".

   Tip
   title Tip
   Saving your entries in this way saves the study by name and description, but does not deploy the study. See #Deploying Deploying the Study.

   The Edit Study page now displays a "Not Loaded" status for the file whose annotations (column headers) you have defined. An example of a file whose annotations have been defined but not yet loaded is shown in the following figure.
   Image Modified
   Status definitions:

   • Definition Incomplete – An annotation definition or definitions must be modified on the Define Fields for Subject Data page. This status may be displayed because an identifier has not been selected. See #Define Define Fields Page for Editing Annotations.
   • Not Loaded – The annotation definitions must be loaded before a study can be deployed. If an error appears after attempting to load a subject annotation source, cick the Edit Annotations button which takes you to the Define Fields for Subject Data page where the problematic annotations will appear in red. See #Define Define Fields Page for Editing Annotations.
   • Loaded – The annotation definitions are properly loaded.

6. Click the Load Subject Annotation Source button in the Action section to load the data file you have configured, The Deploy Studybutton, to this point has been unavailable, but this step activates the button.

   Tip
   title Adding Files
   You can add as many files as are necessary for a study. Patients 1-20 in first file, 21-40 in second file, or many patients in first file and annotations in second file, etc. As long as IDs are defined correctly, it works.

7. Click Deploy Study. caIntegrator now loads data from the file to the caIntegrator database, and the file status changes to "Loaded".

   Tip
   title Changing Assignments
   You can change assignments even after the study is deployed, using the Edit feature. For more information, see #Creating Creating or Editing a Study.

The Manage Studies page opens when the study is deployed. The Deployed status is indicated on the Manage Studies page as well as the Edit Study page. For more information, see Managing a Study.
You can continue to perform other tasks in caIntegrator while deployment is in process.

See also #Deploying Deploying the Study.

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1. On the Edit Study page, click Edit Survival Values. This opens the Survival Value Definitions dialog box, shown in the following figure.
   
2. Click New to enter new survival value definitions.
   OR
   Click Edit to edit existing survival value definitions.
   The dialog box extends, now displaying radio buttons and three drop-down lists that show column headers for date metadata in the spreadsheet you have uploaded. If survival value ranges have already been added to a study, they display on the page. The dialog box is shown in the following figure.
   
3. Survival values can be defined by Date or by Length of time in the study. Select the radio button for the category that defines the data.

4. In the drop-down lists, select the appropriate survival value definitions for each field listed. You might want to refer to the column headers in the data file itself. Because dates covered by the definitions are already in the data set, you cannot enter specific dates.

   Field Type	Description
   Survival Definition Type	Select whether the survival time is defined by dates or length of time subject was in the study.
   Name	Enter a unique name that adequately describes the survival values you are defining here. Example: Survival from Enrollment Date or Survival from Treatment Start. The name you enter displays later when you are selecting survivals to create the K-M plot.
   Survival Length Units	Select the appropriate units for this data.
   Survival Start Date	Select the column header for this data.
   Death Date	Select the column header for this data.
   Last Followup Date	Select the column header for this data.

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To add genomic data to your caIntegrator study, follow these steps:

1. On the Edit Study page where you have selected and added the subject annotation data, click the Add New button under Genomic Data Sources. You can upload genomic data only from caArray.
   This opens the Edit Genomic Data Source dialog box. Enter the appropriate information in the fields, shown in the following figure and described below.
   Image Modified|| Field Types || Field Description ||

   caArray Web URL	Enter the URL for the caArray instance to be used for the genomic data sources. This will enable a user to link to the referenced caArray experiment from the study summary page.
   caArray Host Name	Enter the hostname for your local installation or for the CBIIT installation of caArray. If you misspell it, you will receive an error message.
   caArray JNDI Port	Enter the appropriate server port. See your administrator for more information. Example: For the CBIIT installation of caArray, enter 8080 .
   caArray Username and caArray Password	If the data is private, you must enter your caArray account user name and password; you must have permissions in caArray for the experiment. If the data is public, you can leave these fields blank.
   caArray Experiment ID	Enter the caArray Experiment ID which you know corresponds with the subject annotation data you uploaded. Example: Public experiment "beer-00196" on the CBIIT installation of caArray (array.nci.nih.gov). If you misspell your entry, you will receive an error message.
   Vendor	Select either Agilent or Affymetrix.
   Data Type	Select Expression or Copy Number.
   Platform	If appropriate, select the Agilent or Affymetrix platform. Info title Multiple platforms Because you can add more than one set of genomic data to a study, a study can also have multiple platforms, one for each set of genomic data.
   Central Tendency for Technical Replicates	If more than one hybridization is found for the reporter, the hybridizations will be represented by this method.
   Indicate if technical replicates have high statistical variability	If more than one hybridization is found, checking this box will display a ** in the genomic search results when a reporter value has high statistical variability.
   Standard Deviation Type	When the checkbox for indicating if technical replicates have high statistical variability is checked, this parameter becomes available. Select in the drop-down the calculation to be used to determine whether or not to display a ** (see previous bullet point). --Relative calculates the Relative Standard Deviation in percentage value --Normal calculates the Standard Deviation in numeric value
   Standard Deviation Threshold	When the checkbox for indicating if technical replicates have high statistical variability is checked, this parameter becomes available. This is the threshold at which the Standard Deviation Type is exceeded and the reporter is marked with a **.

2. Click Save.

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1. Start with the 6-column mapping file template, described as follows:
   • All platforms – Raw (level 1) data cannot be mapped; only normalized, processed (level 2) data is acceptable.
   • The required six-column file format uses the following columns:
     • Subject ID
     • Sample ID
     • Name of supplemental file (if appropriate, as attached to the experiment in caArray)
     • Probe Header – Name of column header (in the supplemental file) which contains the probe IDs.
     • Value Header – Name of column header (in the supplemental file) which holds the level 2 data.

     • Sample Header– Name of column header (in the supplemental file) which holds the level 2 data.

       Info
       title Last two columns
       Only one of the last 2 columns is used: a single sample per file uses the Value Header column; multiple samples per file used Sample Header column. Unused columns are blank.

       The following figure shows an example multiple sample mapping file in CSV format.

       
2. When you use the mapping file, make sure you use the subject ID for mapping. If the file is human data, the subject ID is the patient ID.
3. Determine whether your data in caArray is "imported and parsed" or "supplemental". These are the 'Loading Types' referred to in Step 4 of #Steps for Mapping Genomic Data. Fill in the 6-column mapping file according to the following standard:
   • Imported and parsed – Complete only the first two columns of the 6-column mapping file as described above. You can ignore the remaining columns.

   • Supplemental– Supplemental data comes in two types: "single sample per file" and "multiple samples per file". In either case, only one of the last two columns is used. If the supplemental data format is, single sample per file, the column named "Sample_Header" can be left empty. If the supplemental data format is multiple samples per file, the column named "Value_Header" can be left empty.

     Info
     title Configuring supplemental files
     Supplemental files from caArray for mapping data must be configured appropriately. For information, see Supplemental Files Configuration.

     The following steps use data of either type.

Steps for Mapping Genomic Data

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1. On the Edit Study page, click the Map Samples button. This opens the Edit Sample Mappings page, shown in the following figure.
   

2. The first two caArray fields may be populated with the information for the instance of caArray to which you have access. You can, however, enter the caArray information described in the following table, if you prefer.

   Field	Description
   caArray Host Name	Enter the hostname for your local installation or for the CBIIT installation of caArray. If you misspell it, you will receive an error message.
   caArray JNDI Port	Enter the appropriate server port. See your administrator for more information. Example: For the CBIIT installation of caArray, enter 8080 .
   caArray Username	Enter your caArray account user name and password; you must have permissions in caArray for the experiment if it is private. If the data is public, you can leave this field blank.
   caArray Experiment ID	Enter the caArray Experiment ID which you know corresponds with the subject annotation data you uploaded. Example: Public experiment "beer-00196" on the CBIIT installation of caArray (array.nci.nih.gov). If you misspell your entry, you will receive an error message.

3. Enter the Loading Type of the data file you plan to map. (File types are described in #Creating a Mapping File).
4. In the Subject to Sample Mapping File section, click Browse to navigate for the Sample Mapping CSV file that you created (described in #Creating a Mapping File). This provides caIntegrator with the information for mapping patients to caArray samples.
5. Click the Map Samples button.
   If the caArray data you have identified is imported and parsed, when you click the Map Samples button, the mapping takes place as the data is uploaded into caIntegrator. If the caArray data is supplemental, the mapping does not occur until the study is deployed.

6. Mapped samples are listed in the Samples Mapped to Subjects section; scroll down the page to view them (see the following figure). caIntegrator refreshes caArray data hourly; once samples are mapped, a column on this page displays the status of the data in caArray (noted in the figure). Unmapped samples show at the top of the caIntegrator page. They were loaded from caArray, but they are not in the mapping file. These are not used for integration.
   Image Modified

   Info
   title Mapped or unmapped?
   If you have already mapped samples, when you first open this page they are listed in the Samples Mapped to Subjects section. If you have not already mapped samples, all of the samples in the caArray experiment you selected are listed as unmapped, because caIntegrator does not know how these sample names correlate to the patient data in the subject annotation file until you upload the subject to sample mapping file.

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To add copy number data relating to the genomic data you are adding, follow these steps:

1. In the Genomic Data Sources section of the Edit Study page, for the data you have already added, click Configure Copy Number Databutton.

   Info
   title Uploaded copy number data?
   This link is available only if you have uploaded copy number data and you are configuring a Copy Number data type (as indicated by the Data Type column on the Edit Study page).

   The Edit Copy Number page, shown in the following figure, opens.
   Image Modified

2. Browse for and enter appropriate information to identify and retrieve the copy number mapping file. The fields are described in the following table. An asterisk indicates a required field.

   Field	Description
   caArray Service Host Name	Enter the hostname for your local installation or for the CBIIT installation of caArray. If you misspell it, you will receive an error message.
   caArray Experiment ID	Enter the caArray Experiment ID which you know corresponds with the copy number data.
   Loading Type	Enter the Loading Type of the data file you plan to map.
   Subject and Sample Mapping File	Browse for the appropriate CN mapping file. The file must be a CSV file with 3 column format for mapping data files (format: subject id, sample id, file name). Supplemental data uses 6 column-files.
   Bioconductor Service Type	This is the type of bioconductor module that will be used for segmentation. Select between the two options: DNAcopy or CGHcall.
   caCGHcall Service URL	Enter the URL for the grid segmentation service used to access the caCGHcall service. For more information, see CGHcall Wiki Markup {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true} .
   Call Level	An input parameter to CGHcall. This is the number of discrete values used to represent the copy number level. Select between two options: 3 (consisting of discrete values of -1, 0, 1) or 4 (consisting of discrete values -1, 0, 1, 2)
   caDNACopy Service URL	Control for selecting the URL which hosts the caDNACopy grid service. For more information, see DNAcopy Wiki Markup {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer.|nopanel=true}	.
   Change Point Significance Level	Significance levels for the test to accept change-points
   Early Stopping Criterion	The sequential boundary used to stop and declare a change
   Permutation Replicates	The number of permutations used for p-value computation
   Random Number Seed	The segmentation procedure uses a permutation reference distribution. This should be used if you plan to reproduce the results.

3. Click Save Segmentation Data Calculation Configurationfor a genomic data source. On the screen upload a copy number mapping file and configure the parameters to be sent when computing segmentation data.

   Note
   title Be Careful
   After a study has been deployed and the genomic source has been loaded, you cannot change these copy number parameters without reloading the data from caArray first.

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To add images from NBIA to the study you are creating, follow these steps:

1. On the Edit Study page under the Imaging Data Sources section, click the Add Newbutton.

   Info
   title Imaging data source
   If you have already provided an imaging data source, it is listed in this section of the Edit Study page. To edit the imaging data source, click the Edit button which opens the same dialog box described in the following steps.

2. In the Edit Imaging Data Source dialog box, configure the appropriate imaging data source information in the fields as shown in the selected area of the following figure and described below. Fields with an asterisk are required.
   Image Modified|| Fields || Description ||

   NBIA Server Grid URL*	Enter the URL for the grid connection to NBIA.
   NBIA Web URL	Enter the URL of the web interface of the NBIA installation.
   NBIA Username and NBIA Password	This information is not required, as currently all data in the NBIA grid is Public data.
   Collection Name	Enter the name/source for the collection you want to retrieve.
   Current Mapping	If a mapping file has already been uploaded to the study to map imaging data, the file name displays here.
   Select Mapping File Type	Click to select the file type: --Auto – No file is required. Selecting this takes all subject annotation subject IDs and attempts to map them to the corresponding ID in the collection in NBIA. If the ID does not exist in NBIA, then no mapping is made for that ID. --By Subject – Requires a mapping file to be uploaded. The "subject annotation to imaging mapping file" must be in CSV format with two columns that map the caIntegrator subject annotation subject ID to the NBIA subject ID. --By Image Series – Requires a file to be uploaded. The subject annotation to imaging mapping file needs to be a two column mapping (CSV) from the caIntegrator subject annotation subject ID to the NBIA study instance UID.
   Subject to Imaging Mapping File	Click Browse to navigate to the appropriate subject annotation to imaging mapping file. See the Select Mapping File Type* field description.

   Info
   title Mapping files uploaded?
   If mapping files have already been uploaded for the data sources you are editing, the Image Mapping tables of the dialog box show the mapping from NBIA Image Series Identifier to caIntegrator Subject Identifier.

3. Click Save to upload the data from NBIA to caIntegrator. The imaging data displays on the Edit Study page under the Imaging Data Sources section, as shown in the following figure.
   
4. Once the data is uploaded, you can add image annotations. For more information, see #Adding or Editing Image Annotations.

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To add image annotations from a file, follow these steps:

1. On the Edit Study page, click the Edit Annotationsbutton under the Image Data Sources section.

   Info
   title Options for this button
   If you have not yet imported annotations, clicking this button opens the page from which you can import image annotations, shown in the following figure. Continue with the steps in this section. If you are editing annotations, clicking this button opens the Define Fields for Image Annotations dialog box where you can edit annotations; see #Define Fields Page for Editing Annotations.

   Image Modified

2. Select the radio button Upload Annotation File.

3. Click Browse to select an annotation CSV file for upload.
   {{tip:title=Tip} An image annotation CSV file must include an Image Series ID column. See the highlighted column in the following figure.

   Tip

   Image Modified

4. Check the box for Create a new Annotation Definition if one is not found (if appropriate).
5. Click Add.

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