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Let's imagine that for the above described Individual data model, we want to look for any Individual whose gender has been defined as FEMALE, older than 30 and living in London. To do this query, we would need to write something like:
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1. annotation: individual_private_details:age>30;individual_private_details:gender=FEMALE;individual_private_details:address.city=London
or
2. annotation: age>30;gender=FEMALE;address.city=London
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: {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.
Anchor variableSetQueries variableSetQueries Filtering by variableSet and annotationSet
Filtering by any of these fields can be a bit tricky depending on the amount of annotationSets stored for a particular entry. This can be better explained with an example. Let's say we have only 4 Individuals stored in OpenCGA, and they contain the following
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