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

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One of the most important tasks in creating a study in caIntegrator is in properly annotating the data. Each annotation has a definition you must identify. Because the process can be quite complex, you might want to review the following steps for working with annotations.

Annotation Workflow Summary

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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 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 containing annotations and starts the workflow for assigning uploaded data definitions. See Editing an Annotation Group, step 1.
   
   1. Edit the annotations. This step opens the Define Fields for Subject Data page. See 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 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 an Identifier or Annotation for more information about permissible values.
   5. Locate and verify the assignment as "identifier" for one annotation. See 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 an Identifier or Annotation.
      --Create or manage definitions manually. See Assigning an Identifier or Annotation.
      --Search for and use definitions existing in other caIntegrator studies. See Searching for Annotation Definitions.
      --Search for and use definitions from caDSR. See 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.

Adding an Annotation Group

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 existing annotation group, see Editing an Annotation Group.

An annotation group is a group of annotation definitions configured in a subject data source 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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1. On the Edit Study page for a study, Annotation Groups section, click the Add New button.
2. On the Edit Annotation Group page that opens, enter a name for the annotation group.
3. Enter a description (optional).
4. Browse for the Group Definition Source CSV file.
   The CSV file must include columns with these column headers in the first row: File Column Name, Field Type, Entity Type, CDE ID, CDE Version, Annotation Def Name, Data Type, Permissible, and Visible. Subsequent rows in the file define each subject annotation column in the subject annotation file.
   
   1. If a subject annotation is defined by a CDE Public ID, values for the following columns are required: File Column Name, Field Type, Entity Type, CDE ID, and Visible; a value for CDE Version is optional.
      OR
   2. If a subject annotation definition is not defined by a CDE Public ID, values for the following columns are required: File Column Name, Field Type, Entity Type, Annotation Def Name, Data Type (String, Date, Numeric), Permissible (Yes or No), and Visible (Yes or No).
5. Click Save. This uploads the file, whose name now displays on the Edit Study page under Annotation Groups.

When you open the Define Fields for Subject Data page, the annotation definitions in the file you uploaded display on the page, available for assignment in the study. Additionally, you can view the definitions by viewing the annotation group listed in the first column of the matrix.

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

To add subject annotation metadata on this page, follow these steps:

To add subject annotation metadata on this page, follow these steps:

1. In the Subject Annotation Data Sources section of the In the Subject Annotation Data Sources section of the page, click the Add New button. The page expands to reveal new fields for you to identify information about the annotation data sources.
2. Navigate to locate a subject annotation data file which is required for a study. Files must be in CSV file format.
3. Click the appropriate box if you want caIntegrator to Create an annotation definition if one is not found.
4. Click Upload Now to load the annotation source data.

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1. You can specify visibility of specified annotation data in the Visiblecolumn.
   • Select a checkbox for a row to make the corresponding data visible to all subscribers of the study or anonymous users if the study is made available to the public.
   • Clear a checkbox to hide the corresponding annotation from any subscriber or anonymous user of the study. Data continues to exist but does not show up in query fields nor in query results.
2. The Annotation Header from File column on the Define Fields for Subject (or Image) Data page (the figure shown above) displays column headers taken from the source CSV file. The Define Fields... page also displays data values in the file you have designated. You must map each column name to an existing column name in the caIntegrator database or in caDSR. If it doesn't yet exist, you can create a custom column name. The following figure is an example CSV file whose data you would be mapping in caIntegrator in the Define Fields page.
   Image Modified
3. To indicate the unique identifier of choice, on the row showing the column header (PatientID in the figure, but other examples are subject identifier, sample identifier, etc), click Change Assignment in the Annotation Definition column.

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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.
   Image Modified
   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 for Annotation Definitions.
   4. You can search for and use definitions found in caDSR. See 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 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 New button 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 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. Warning title Required values Note that for all annotations you want to appear, you MUST select the Permissible values. To do this, select Change Assignment, as described in step 3 and click the New button on the page that opens. As you are describing each annotation, be sure to add the permissible valudes and move them as described in this table cell. Click Save.

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

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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.
   Image Modified

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 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 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.
   
   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 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 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 or Editing a Study.

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Survival value is the length of time a patient lived. If you plan to analyze your caIntegrator data to create a Kaplan-Meier (K-M) Plot, then during the Annotation Definition process described above in #Assigning Assigning an Identifier or Annotation, you should do one of two things:

1. Make sure that you have defined at least three fields set to the "date" Data Type. These will be matched to the following three properties during Survival Value definition.
   • Survival Start Date
   • Death Date
   • Last Followup Date
2. It is also possible to generate KM plots if an Annotation Field Descriptor such as DAYSTODEATH has been set to Data Type 'numeric'. See #Assigning Assigning an Identifier or Annotation.

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Once you have loaded subject annotation data and identified subject IDs, you can add one or more sets of array genomic sample data from caArray to the study. caIntegrator maps the data by sample IDs to the subject IDs in the subject annotation data, covered in this section, or you can load imaging files from NBIA, also mapped by IDs to the subject data. This is discussed in #Working Working with Imaging Data. You can also edit genomic data information that you have already added to the study. Genomic sample data and imaging data are independent of each other, so neither is required before loading the other.

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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.
   || Field Types || Field Description ||

   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.

caIntegrator goes to caArray, validates the information you have entered here, finds the experiment and retrieves all the sample IDs in the experiment. Once this finishes, the experiment information displays on the caIntegrator Edit Study page under the Genomic Data Sources section, as shown in the following figure. caIntegrator refreshes carray data on an hourly basis. The status of caArray data updates displays on the Manage Studies page and on the Edit Sample Mappings page.
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You, as the caIntegrator study manager, must create a Subject to Sample mapping file and then import it into caIntegrator before following the actual mapping steps. This file provides caIntegrator with the information for mapping patients to caArray samples.

1. Start with the 6-column mapping file template, If you are starting with parsed data, the mapping file will have 2 columns. If you are working with unparsed data, the mapping file will have 6-column columns. See step 3 below for more information. The six columns that may be part of your file are 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.

       Image Modified
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 from caArray is "imported and parsed" or "supplemental". These are the 'Loading Types' referred to in Step 4 3 of #Steps Steps for Mapping Genomic Data. Fill in the 2-column or 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 columnsThis mapping file for parsed data has only two columns, Subject ID and Sample ID, without a header.

   • Supplemental– Supplemental data files 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.

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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.
   Image Modified

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 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 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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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.
   

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	{multi-excerpt-include: Enter the URL for the grid segmentation service used to access the caCGHcall service. For more information, see CGHcall
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   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

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   Control for selecting the URL which hosts the caDNACopy grid service. For more information, see DNAcopy

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   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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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.
   || Fields || Description ||

   Field	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.
   Image Modified
4. Once the data is uploaded, you can add image annotations. For more information, see #Adding Adding or Editing Image Annotations.

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After you have configured an image data source with an NBIA Grid service and uploaded the image data, described in #Adding Adding or Editing Imaging Data Files from NBIA, you can load image annotations into caIntegrator from a file in CSV format or through an Annotations and Image Markup (AIM) service.

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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 Define Fields Page for Editing Annotations.

   

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

   

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

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Using either method, the image annotations are uploaded to caIntegrator. After this occurs, when you click the Edit Annotations button, the system opens to the Define Fields for Imaging Data page where you can edit the annotations. This is the same page (with a customized title) as that described in #Define Define Fields Page for Editing Annotations. You must assign identifiers and annotations to the data in the same way you did with the subject annotation data. For more information, see #Assigning Assigning an Identifier or Annotation and #Searching Searching for Annotation Definitions.

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Click an external link to open a page that displays appropriately formatted web page links; an example is shown in the following figure.
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Deploying the Study

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Note that you can continue to work in caIntegrator while the study is being deployed.

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