Clinical data is supported in File, Sample, Cohort, Individual and Family in a field called annotationSets. Any of these entities will be able to perform the same operations described below apart from their own particular features.
In this document, we will be referring to annotationSets and annotations (the field names used in OpenCGA to store any clinical data or any other user-defined free data model).
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Individual 3: { C, D }
Individual 4: { }
The operators supported to perform queries and know which Individuals have been or have not been annotated with a concrete AnnotationSet or VariableSet are:In this case, the operators =, == and != are also supported, though they might give unexpected results to the user. For this reason, we have also added === and !== operators to support any possible query operation. An example containing the results that would be obtained is shown in the table below:
| Operator | Value looked for | Individuals returned | Explanation | |
|---|---|---|---|---|
| =, == | B | 1, 2 | Fetch all the individuals containing annotationSet or variableSet B | |
| === | B | 2 | Fetch all the individuals that only contains annotationSet or variableSet B | |
| != | B | 1, 3, 4 | Fetch all the individuals that doesn't only contain annotationSet or variableSet B. Individuals containing B plus any other annotationSet or variableSet will be returned. | |
| !== | B | 3, 4 | Fetch all the individuals that have never been annotated using annotationSet or variableSet B. |
- All the annotationset webservices have been deprecated.
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