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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:
- 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
- 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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- 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.
- 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.
- Determine whether your data in caArray is "imported and parsed" or "supplemental". These are the 'Loading Types' referred to in Step 4 of #Steps 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.
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- On the Edit Study page, click the Map Samples button. This opens the Edit Sample Mappings page, shown in the following figure.
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.
- Enter the Loading Type of the data file you plan to map. (File types are described in #Creating Creating a Mapping File).
- 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.
- 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. 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.
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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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.
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 ||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.
- 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.
- 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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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.
- Select the radio button Upload Annotation File.
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 
- Check the box for Create a new Annotation Definition if one is not found (if appropriate).
- 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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