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Subject Annotation Data Configuration

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The following subject annotation data configuration information is collected:

• Subject annotation Data Source (delimited text)
• Protocol Id (of study to import)

For delimited text, see #Delimited-Text Annotation Import. For subject annotation files, one field must be identified as the subject identifier.

See #Annotation Field Configuration for details on specification of visibility and browse configuration.

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• Annotation semantics: each annotation field (whether associated with a subject, image series, image or sample) must either:
  • be associated with an existing annotation definition known to the system,
  • be associated to an existing CDE in caDSR or
  • have sufficient semantic metadata recorded so that the field may be submitted for registration as a CDE in caDSR.
• Field authorization: Each field must be either declared publicly visible or restricted to a list of groups. The default will be the visibility settings given at the study level. For more information, see on page 21 Define Fields Page for Editing Annotations.
• Whether the field is to be included in the results list for a given entity type (i.e. Subject, Sample, Image Series or Array Data) when browsing data.
• Whether the field is to be included in simple single-input searches when browsing data.

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• Whether to import the data
• The visibility of the data; either public or restricted to a set of groups. Low-level genotyping data (raw data and normalized) will always have restricted visibility.

See also #Supplemental Files Configuration.

Supplemental Files Configuration

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The file itself is a tab-delimited text file. The file extension can be anything, though users typically use .txt. The name of each supplemental file must be unique within a caArray experiment.

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• Wiki Markup

  Affymetrix Expression Console – This software produces supplemental files. In Expression Console, use the "Export Result" function to create these files. Note that when you use an algorithm other than MAS5 to normalize the data (for example using RMA or Plier), Expression Console automatically creates a \[… {{summary.txt}}\] file that contains extra lines on top of the derived data results. The extra lines all start with a "#" to signify that it is a remark. These lines are ignored by caIntegrator parsing.

• Agilent GeneSpring GX – This software can export a results table in .txt format.

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Additional annotation for either images or image series can be imported using the delimited-text import functionality.