Page History

...

1. Select the Manage Studies button and select Edit for the study you wish to remap.
2. On the Edit Study page, select Edit under the Genomic Data Sources header.
3. Without altering any information, select Save. When the warning box appears, select OK.
4. Select ConfigureCopyNumberData.
5. Enter the new mapping file in the Subject and Sample Mapping File field. Select Save Segmentation Data Calculation configuration.
6. Select Deploy Study.

...

Working with Imaging Data

study:working with imaging data;imaging data:working withOnce Once you have loaded subject annotation data and identified patient IDs, you can add either array genomic sample data from caArray which caIntegrator maps by sample IDs to the patient IDs in the subject annotation data, or you can upload image data from NBIA, also mapped by IDs to the subject data. Once you have configured an NBIA image data source for adding images, then you can import image annotation data for the images. Genomic sample data and imaging data are independent of each other, so neither is required before loading the other.

It is essential that you are well acquainted with the data you are working with--the subject annotation data, and the corresponding imaging data in NBIA.

Adding or Editing Imaging Data Files from NBIA

study:adding imaging data;imaging data:adding to study;adding:imaging data;NBIA:adding files to caIntegrator;editing imaging files;imaging data:editing NBIA images sourcesTo 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 New button.

   Info
   title Note
   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 imaging data source in the fields (). Asterisks indicate required fields.. Image Modified
   • 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 Select Mapping File Type* field description.

    Info
    title Note
    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.

1. Click Save to upload the data from NBIA to caIntegrator.

...

1. The imaging data displays on the Edit Study page under the Imaging Data Sources section

...

1. , as shown in the following figure. Image Modified
2. Once the data is uploaded, you can add image annotations. For more information, see #Adding or Editing Image Annotations.

Adding or Editing Image Annotations

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

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

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

   Info
   title Note
   If you have not yet imported annotations, clicking this button opens the page from which you can import image annotations

...

1. , 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 . Image Modified Select the radio button Upload Annotation File. Click Browse to select an annotation CSV file for upload. Info title Note An image annotation CSV file must include an Image Series ID column. See the highlighted column in the following figure.

   Image Modified
2. Check the box for Create a new Annotation Definition if one is not found (if appropriate).
3. Click Add.

To load image annotations through an AIM service, follow these steps:

1. On the Edit Study page, click the Edit Annotations link under the Image Data Sources section.
2. Select the radio button Use AIM Data Service.
3. Select an AIM Server Grid URL.
4. Click Add.

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. For more information, see . You must assign identifiers and annotations to the data in the same way you did with the subject annotation data. For more information, see and .

Adding External Links

external links, adding for a studyThis This feature on the Edit Study page, described in , allows you to configure a CSV file with URLs to be used as external links relevant to a study. This allows you to easily share or configure references.

To add an external link, follow these steps:

1. As a study manager, you can configure a CSV file with URLs to be used as external links.
2. On the Edit Study page, click the Add button under External Links section. External links can be any URL(s) to resources that are hosted external to caIntegrator but are relevant to the study being deployed.
3. Assign a name to the external link.
4. Add a description for the link, if appropriate.
5. Browse for the CSV file containing URLs (HTTP linked) to resources outside of caIntegrator.
6. Click Upload Now. caIntegrator does not validate any links in the file being uploaded.

Once you have created external links for a study, when the study is open, an External Links section showing the link(s) displays on the left sidebar of the page, shown in the following figure ().

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

Deploying the Study

When you are ready to deploy the study, click the Deploy Study button on the Edit Study page. caIntegrator retrieves the selected data from the data service(s) you defined and makes the study available to a study manager or to anyone else who may want to analyze the study's data. Using the Manage Studies feature, you can then configure and share data queries and data lists with all investigators who access the study.

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

Managing a Study

Once you have started to create a study or have deployed it, you can update an existing study in the following ways:

...

To update, edit or delete a study, follow these steps:

1. On the left sidebar, click Manage Studies. The Manage Studies page appears

...

1. , shown in the following figure. Image Modified
   All of the "in process" or "completed" studies display on this page, with associated metadata. Note that whoever edited or updated the study last is shown in the Last Modified Column, indicated as the Study Manager.
2. Click the Edit link corresponding to your study of choice to open the Edit Studies page

...

1. , shown in the following figure. Image Modified
   On this page you can edit any details such as adding or deleting files, survival values, and so forth. For information about working with the Edit Study feature, see .
2. Click the Delete link to delete the corresponding study.

Managing Platforms

Integrator supports a limited number of array platforms, all of which originate from Agilent or Affymetrix. While they do not represent all of the platforms supported by caArray, caIntegrator must have array definitions loaded for the platforms it supports, and be able to properly load the data from caArray and parse it.

You can create a study without genomic data, but you cannot add genomic data to a caIntegrator study without a corresponding supported array platform. If you add more than one set of genomic data to the study, you can specify more than one platform for the study.

On the Manage Platforms page, you can identify, add or remove supported platforms.

To manage platforms in caIntegrator, follow these steps:

1. Click Manage Platforms on the left sidebar.
   The Manage Platforms page that opens lists the platforms caIntegrator currently supports, those that the system can pull from caArray

...

1. . See the following figure. You can also add a new platform by entering information in the fields in the Create a New Platform section. Image Modified
2. To add a platform, in the Platform Type field, select the appropriate platform type from the drop down list.
3. Click Browse to navigate for the Affymetrix or Agilent file you want to add.

   Info
   title Note
   Tab-delimited .txt or .tsv Agilent platform annotation files must contain the following column headers: ProbeId, GeneSymbol, GeneName and Accessions.

4. Enter a Platform Name if the file is a NON-GEML.xml file.
   Depending on the Platform Type you select, there may be other parameters to provide here as well, such as Platform Channel Type for an Agilent platform.

• Click the Browse button to browse for the appropriate annotation file. When you have located it, click Open in the Upload File dialog box. The system displays the annotation file you select in the Annotation File box.

1. Once all parameters have been entered, click Create Platform.

The platform deployment can be time-consuming. If the platform takes more than 12 hours to deploy, caIntegrator displays a "timed out" message. At that point, you can delete the platform, even if it has not loaded to the system.