One of the first steps on clinical trials is the selection of the candidate individuals for the study. The rules that an individual must match in order to be elected as a candidate usually involve complex queries combining clinical metadata and variants data, expressed as a list of filters with intersections (AND), unions (OR) and complementary (NOT).

Complex query

A complex query can be defined as a tree where each node is either a query or the intersection or union of a list of queries

To resolve the query, the tree has to be explored, resolve the leaves from the tree, and then join the results.

Query leaf node

Standard variant query. Can be combined with sample and individual catalog query prepending the query params with sample. or individual. respectively.

{
  "type" : QUERY,
  "query" : {
    "<query param 1>" : "<value>",
    "<query param 2>" : "<value>",
    ...
    "<query param n>" : "<value>",
  }
}

Complement node (NOT)

{
  "type" : COMPLEMENT 
  "nodes" : [ <node> ] 
}

Union node (OR)

{
   "type" : UNION
   "nodes" : [ <node1>, <node2>, ... ]
}

Intersection node (AND)

{
   "type" : INTERSECTION
  "nodes" : [ <node1>, <node2>, ... ]
}

Example

Plain text

Get all samples that have (a lof mutation in gene A and with HPO X) or ((a missense_variant mutation on gene B) and (a missense_variant on gene C) but not (a missense_variant on gene D))

This can be divided into 3 queries:

• Q1
  • gene : A
  • ct : lof
  • hpo : X
• Q2
  • gene : B
  • ct : missense_variant
• Q3
  • gene : C
  • ct : missense_variant
• Q4
  • gene : D
  • ct : missense_variant

These queries are combined with AND/OR like this:
Q1 OR (Q2 AND Q3 AND (NOT Q4))

Structured

This can be expressed in a JSON query like this:

{
  "type" : UNION
  "nodes" : [
    {
      "type" : QUERY,
      "query" : Q1
    } , {
      "type" : INTERSECTION
      "nodes" : [
        {
          "type" : QUERY
          "query" : Q2
        }, {
        {
          "type" : QUERY
          "query" : Q3
        }, {
          "type" : COMPLEMENT
          "nodes" : [{
            "type" : QUERY
            "query" : Q4
          }]
        },
      ]
    }
  ]
}

Implementation

Implementation details at opencga#1474.

Input

Parameters

Output

Files