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- Filter by variableSet: Users might want to filter all the entities that have been annotated (have values) using one user-defined variableSet. * Follow Filtering by variableSet and annotationSet section defined below to see the supported operations.
- Filter by annotationSet: Users might want to filter all the entities that have been annotated (have values) for one particular annotationSet. * Follow Filtering by variableSet and annotationSet section defined below to see the supported operations.
- Filterby annotation: Users are also allowed to filter by any of the clinical data values. Example:
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The first option to search, though longer, should never fail as long as there exist a variableSet in the study containing the variables that are being queried. Basically, we are telling OpenCGA to look for any Individual matching those values but, at the same time, we are giving OpenCGA information of where the variables the user want to look for have been defined (the variableSet that defines those variables). A general way of seeing this query would have the following format: [[{annotationSetId}@]{variableSetId}:]{variable}{operator}{value}, where operator can be any of =, == or != for any data type, plus >, >=, <, <= for numeric variables.
However, OpenCGA also allows performing the query using the shorter way as seen in the second line in which users can omit specifying the variableSet where the variables were defined. In this case, OpenCGA will look for all the VariableSets that might have defined these variables and, as long as those variables have only been defined in one VariableSet, the query will be performed. Otherwise, OpenCGA will raise an error because it will not know the real scope of the query.
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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. |
Project the annotation fields to return
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