• All the annotationset webservices have been deprecated.

Querying annotation sets

• Querying by annotation sets is only possible through sample|individual|family|cohort/search. variableSet and annotationSetName parametesrs have been deprecated. Instead, all the queries should be done through the annotation query param. The annotation query param will be able to contain a ; separated string following any combination of the following:
  • Filtering by an annotation: Considering a.b is the variable of a nested object we want to query for from the variableSet "tumor", it would be supported "a.b=4" or "tumor:a.b=4". As long as the variable is only valid in one of the variable sets defined for the study, the variableSet part can be omitted. 
  • Filtering by a variableSet: 
    • "variableSet=tumor" will return all the objects that have been annotated with that variableSet
    • "variableSet!=tumor" will return all the object that have not been annotated with that variableSet
  • Filtering by annotation set name:
    • "annotationSet=pepe" will return all the objects that have an AnnotationSet with the name "pepe".
    • "annotationSet!=pepe" will return all the objects that don't have an AnnotationSet with the name "pepe".
• Projections of annotationSets can be done using the typical include/exclude query params. In this case, we have special words to only include/exclude some concrete things:
  • Projecting annotations: "annotationSets.annotations.a.b" and "annotation.a.b" will project the result of a.b annotations only !
  • Projecting whole AnnotationSets: "annotationSets.name.pepe" or "annotationSet.pepe" will project the result of the whole AnnotationSet with name pepe
  • Projecting AnnotationSets from VariableSets: "annotationSets.variableSet.tumor" or "variableSet.tumor" will project all the existing AnnotationSets annotating the VariableSet tumor.
• The boolean "flattenAnnotations" will be used to flatten the annotations in one single level (true) or leave it as nested objects (default - false)

Creating or modifying annotationSets

• AnnotationSets can be created when the entry that will contain it is being created or by calling to the /entry/{entry}/update webservice
• AnnotationSets can be updated by calling the /entry/{entry}/update webservice

Deleting annotationSets

• AnnotationSets can be deleted by using the /entry/{entry}/update webservice using the new deleteAnnotationSet parameter

Deleting annotations

• Single annotations can be deleted by using the /entry/{entry}/update webservice using the new deleteAnnotation parameter

GroupBy

• We can put something like the following the 'fields' field: annotation:29:pedigreeAnnotation:Population to group by Population