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Querying the database

The website offers the possibility to users to perform queries about the whole content of the database. A query searches in the whole data set that a user is granted to access. Any parameter contained in the glossary can be used in a query and they can be combined using brackets and logical operator (and, or...). The query engine searches for matching records in the database and provides a summary view or a more detailed view according to the user's role.

  1. The query builder page

    • Concepts
      1. Query structure : a query is built of search criteria combined by logical and grouping operators. For instance, a query that retrieves "all male patients from Bergonié institute with a liposarcoma" would be built combining 3 criteria with the "and" operator.
      2. Parameter types : there are 4 distinct types of parameters in the database :
        1. Dates : in "dd/mm/yyyy" format (i.e. birth date)
        2. Numbers : using the "." as a decimal separator (i.e. size of primary tumour)
        3. Free text : alphanumerics (i.e. sample reference)
        4. Constrained values : most parameters can only have a value included in a set of predefined values (i.e. histotype)
      3. The N/A value : There is a special value that can be used to specify that the query should match records that do NOT have a particular parameter set. It can be used to retrieve cases for which some parameter has not been entered (very likely because it is not known)

    • Screenshot


    • 1) Grouping and logic column : to combine criteria
      2) Parameter to match : which parameter is concerned by the criteria
      3) Operator : whether the criteria should be equal, different, greater than...
      4) Value : the value to give to the selected criteria
      5) Grouping and logic column #2 : to combine criteria
      6) Save : to save the selected criteria before editing another criteria
      7) Delete : to delete the selected criteria from the query (can not be undone)
      8) Select criteria : to edit existing criteria, just click on their line
      9) Add criteria : to add new criteria to the query to narrow results
      10) Search : to run the query and display matching results
      11) Reset : to delete all criteria and start a new query
      12) Cancel : to exit the query builder


  2. The query results page
  3. Once the query is submitted, the query engine looks for all matching records in the data set the user is allowed to access (according to his role). A summary view is available, grouping matching results by centre. If the user's privileges are sufficient, a detailed view is also provided. The individual patient data are accessible by clicking on the corresponding line, provided the user is allowed to access it.

    • Summary view


    • Detailed view



  4. Show case
    • Introduction
    • In this part of the document we will build a complex query step by step to have an overview of how to use the query tool. The defined query has strictly no scientific interest but it gives a good catch on what can be done. Set the case you want to retrieve patient cases that are :

      1. Either males patient born after 1950 with a rhabdomyosarcoma diagnosis.
      2. Either patients with a primary tumour bigger than 3 cm who had a complete remission after treatment.
      3. But you are only interested in cases from Bergonié and UCBL.

    • Structure of the query
    • There are several ways to combine search criteria to obtain the data set described above but for our purpose we will write it as such :

      ( centre = Bergonié OR centre = UCBL)
      AND
      (
          ( sex = male AND birth date >= 01/01/1950 AND histotype = rhabdomyosarcoma )
      OR
          ( size of primary tumour >= 3 AND complete remission after treatment = yes )
      )

    • Building the query
      • First row
        1. Select "(" in "Logic" column.
        2. Select "Centre" in "Field" column.
        3. Select "=" in "Operator" column.
        4. Select "Bergonié" in "Value" column.
        5. The first row is done, press "Add a new line" to create the second one.
      • Row 2
        1. Select "or" in "Logic" column.
        2. Select "Centre" in "Field" column.
        3. Select "=" in "Operator" column.
        4. Select "UCBL" in "Value" column.
        5. Select ")" in the second "Logic" column.
        6. The second row is done, press "Add a new line" to create the third one.
      • Row 3
        1. Select "and ( (" in "Logic" column.
        2. Select "Sex" in "Field" column.
        3. Select "=" in "Operator" column.
        4. Select "Male" in "Value" column.
        5. This row is done, press "Add a new line" to create the next one.
      • Row 4
        1. Select "and" in "Logic" column.
        2. Select "Histotype" in "Field" column.
        3. Select "=" in "Operator" column.
        4. Select "rhabdomyosarcoma" in "Value" column.
        5. This row is done, press "Add a new line" to create the next one.
      • Row 5
        1. Select "and" in "Logic" column.
        2. Select "Birth date" in "Field" column.
        3. Select ">=" in "Operator" column.
        4. Select "01/01/1950" in "Value" column.
        5. Select ")" in the second "Logic" column.
        6. This row is done, press "Add a new line" to create the next one.
      • Row 6
        1. Select "or (" in "Logic" column.
        2. Select "Size of primary tumour" in "Field" column.
        3. Select ">=" in "Operator" column.
        4. Select "3" in "Value" column.
        5. This row is done, press "Add a new line" to create the next one.
      • Row 7
        1. Select "and" in "Logic" column.
        2. Select "Complete remission after treatment" in "Field" column.
        3. Select "=" in "Operator" column.
        4. Select "Yes" in "Value" column.
        5. This was the last row, press search to execute the query. Unless there are some errors in the query you should get the results view.

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