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• Subject Annotation – Subject annotation data refers to pre-subject annotation, phenotypic, subject annotation, pathology or any other annotations associated with a subject.The subject annotation data should be available in CSV files, with a unique patient subject identifier in one column, one patient subject per row. Note that if you are using human data, the subject will probably be a "patient". Other relevant data can be supplied in other columns to be identified as annotations in the file from within caIntegrator. You, as the study creator, must have access to the subject annotation data file, as the file does not come from a caBIG^® repository.
• Genomic – To use caIntegrator to integrate array data, the data should be imported into caArray, either locally or in the CBIIT installation, using that system's data file import functionality. You must also have a mapping file in CSV format. This file indicates correlations between array files and the subjects in the subject annotation data files.
• Imaging – Imaging data should have been submitted to the NBIA grid node as public data, either locally or as part of the CBIIT NBIA installation. Image annotations, which include information about images provided by radiologists or other researchers can include such information as tumor size, tumor location, etc. It must be in CSV format, with unique image series IDs in one column (required) and annotation IDs in the second column. caIntegrator can map the images automatically, or alternatively you can upload an image mapping file in CSV format. This file indicates correlations between subject annotation subjects or images in NBIA and subjects in the subject annotation data files.

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Creating/Editing a Study

The Edit Study page, as shown in the following figure, displays the Name and Description that you entered for a new study, or for an existing study that you are editing.
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To continue creating a study or to modify a study, on the Edit Study page complete these steps:

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1. Click View Log on the Edit Study page to simply review an existing log. The log records all steps comprising activity in the study, with the most recent displaying at the top of the log.
2. To edit a log, click Edit Log on the Edit Study page.
3. Add an appropriate description/annotations to the individual log entries.
4. Check the Update box next to the description, then click Save to save the edits. The descriptions will now be available when any user views the log.

See also #Study Log.

Working with Annotations

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One of the most important factors 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.

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