Build a cohort query

You can query on any combination of the following data:

• Patient Information
  
• Clinical Data
  
• Genomic Data
  

Patient Information

In this section;

• Demographics
  
• Consent
  
• Patient Group
  

Demographics

1. On the Home page, on the left, click the Cohort Query icon().
2. In the Cohort Query screen, on the left, click the Patient Information category, then click Demographics.
3. Either enter the Patient ID or click the search icon ().

   To search for a Patient ID:

   1. Select a condition and enter part of a patient ID.
   2. Click Search.
   3. Select the patient ID that you want to use from the left side and move it to the right side using the arrow ().
      Alternatively, multiple patent IDs can be specified by:

      • Pasting comma or new line separated values in the designated input box.
      • Uploading a text file containing multiple comma or new line separated values.

      After pasting the values or uploading the file, when you click the Search button the patient IDs found in the system are listed in the left side list and the remaining patient IDs are listed below the left side list.
   4. Click Submit.
4. Either enter the Patient Universally Unique Identifier (Patient UUID) or click the search icon ( ). To search for a Patient UUID:
   1. Select a condition and enter part of a Patient UUID.
   2. Click Search.
   3. Select the Patient UUID that you want to use from the left side and move it to the right side using the arrow ().
   4. Click Submit.
   Alternatively, multiple Patent UUIDs can be specified by:

   • Pasting comma or new line separated values in the designated input box.
   • Uploading a text file containing multiple comma or new line separated values.

   After pasting the values or uploading the file when the Search button is clicked, the Patient UUIDs found in the system are listed in the left side list and the remaining Patient UUIDs are listed below the left side list.
5. Set any other criteria that you want to use in your query:
   • Gender: Select the gender from the drop-down list.
   • Marital Status: Select the status from the drop-down list.
   • Age: Select a condition, and then add the age in years, as a single value or a range.
   • Date of Birth: Select condition, and then enter the date.
   • Deceased: Select this check box, if needed.
   • Last Contact Date: Select a condition, and then add the date as a single value or a range.
   • Ethnicity: Select the appropriate ethnicity.
   • If in the Subject context, specify Age at Study Start.

     Select a condition, then add the Age as a single value or a range and select the unit of measure of the age, that is, Year(s), Month(s), Week(s), or Day(s). To match the Subjects based on this criteria, Cohort Query uses the Cohort Data Mart's database column Age At Study Start in Days (W_EHA_SUBJECT_D.AGE_AT_STUDY_START_DAYS or AGE_AT_STUDY_START_DAYS_OBF, depending on the data access privileges of the logged in user). The value in the database column Age At Study Start in Days is automatically populated based on the values populated in the columns Age at Study Start (AGE_AT_STUDY_START) and Age at Study Start Unit Of Measure (AGE_AT_STUDY_START_UOM_WID) using the following calculations and the same calculations are also used for parsing the search criteria defined for Age at Study Start.

     If value of the database column Age at Study Start Unit Of Measure matches the parameterized value for:	Value of the database column Age At Study Start in Days:
     Day	= Age at Study Start
     Week	= Age at Study Start X 7
     Month	= Age at Study Start X 365/12
     Year	= Age at Study Start X 365
     Any other value	=Null

     Refer to the Oracle Healthcare Foundation Administrator's Guide for information on the Cohort Data Mart ETL's configurable parameters related to automatic population of the database column Age at Study Start in Days.

   • Race: Select the appropriate race.
   • Location: Enter either a city, state, zip code, county, or country.
   • Data Source: Enter or search for a Data Source.
6. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
7. Click Submit.

Consent

1. On the left, click the Patient Information category, then click Consent.
2. Enter a Consent Type or click the search icon ().

   To search for a Consent Type:

   Note:

   Follow the same steps for the Consent Code and Consent Status.
   1. In the Select Consent Type window, select a condition for Consent Type Name or Consent Type Code and enter part of the consent name or type.
   2. Click Search.
   3. Select the consent type or code that you want to use from the left side and move it to the right side using the arrow ().
   4. Click Submit.
3. Set any other criteria that you want to use in your query:
   • Consent Code: Enter or search for a Consent Code.
   • Consent Status: Enter a consent status, or follow steps from 2a to 2d, to search for a consent status.
   • Consent Start Date: Select a condition, and then add the date.
   • Consent End Date: Select a condition, and then add the date.
   • Data Source: Enter or search for a Data Source.

     Note:

     The double asterisks next to the input label of an attribute indicate that at least one of such attributes is required for defining search criteria for the selected data (in this case, Consent). The same convention is used in all other search dialogs as well.
4. Under Insert As select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Note:

To define search criteria for Consent, the criteria must include at least one of the following attributes: Consent Type, Consent Code or Consent Status.

For more information, visit:

"Build a cohort query"

"Before you begin building your query"

Patient Group

1. In the Patient Context, on the left, click the Patient Information category, then click Patient Group.
2. Enter a Group Name or click the search icon ().

   To search for a Group Name:

   Note:

   Follow the same steps for the Responsible Party Number and Responsible Party Name.
   1. In the Select Group Name window, select a condition for Group Name and enter part of the Group Name.
   2. Click Search.
   3. Select the Group Name that you want to use from the left side and move it to the right side using the arrow ( ).
   4. Click Submit.
3. 3. Set any other criteria that you want to use in your query:
   1. Enter a Group Type or click the search icon.
      1. In the Select Group Type window, select a condition for Group Type Name or Group Type Code or Code System ID or Code System Name and enter part of the Type Name or Type Code or Code System ID or Code System Name.
      2. Click Search.
      3. Select the group type that you want to use from the left side and move it to the right side using the arrow.
      4. Click Submit.
   2. Group Start Date: Select a condition, and then add the date. This is the date when the Group was started or became active.
   3. Group End Date: Select a condition, and then add the date. This is the date when the Group was ended or became inactive.
   4. Participation Start Date: Select a condition, and then add the date. This is the date when a Patient became part of the Group.
   5. Participation End Date: Select a condition, and then add the date. This is the date when the participation of a Patient in the Group ended.
   6. Responsible Party Number: Enter or search for a Responsible Party Number (Identifier of the Party). Responsible Party for a Group can be an individual or organization party who is managing the Patient Group, such as an institutional review board (IRB).
   7. Responsible Party Name: Enter or search for a Responsible Party Name.
   8. Data Source: Enter or search for a Data Source.
4. 4. Under Insert As, select:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Clinical Data

In this section:

• Diagnosis
  
• Clinical Encounter
  
• Appointment
  
• Procedure
  
• Medication
  
• Patient History
  
• Test or Observation
  
• Specimen
  
• Study
  
• Relative Time Events
  

Diagnosis

1. On the left, click the Clinical Data category, then click Diagnosis.
2. Either enter the diagnosis or click the search icon ().

   To search for a Diagnosis:

   1. Select one of the Search Modes:
      • Classic Search. Select it to use more search conditions for Diagnosis Name, Code, and Code System.
      • Hierarchy Drill-in Search. Select it to search all of the codes in a hierarchy that are associated with a single Code System, and have only one parent code.

      Note:

      This feature does not support mixed hierarchy, meaning different levels of codes belonging to different Code Systems or multi-parent hierarchy, meaning one code having multiple parent codes.
   2. Select a condition for one or all: Diagnosis Name, Diagnosis Code, Code System ID or Code System Name.
   3. Click Search.
   4. Select the diagnosis codes that you want to use from the left side and move them to the right side using the arrow ().
   5. Click Submit.
3. Set any other criteria that you want to use in your query:
   • Concern Subtype: Enter or search for a Concern Subtype.
   • Diagnosis Status: Enter or search for a Diagnosis Status.
   • Diagnosis Severity: Enter or search for a Diagnosis Severity.
   • Onset Date: Select a condition, and enter a date.
   • Reported Date: Select a condition, and enter a date.
   • End Date: Select a condition, and enter a date.
   • Age At First Onset: Select a condition, and then add the age in years, as a single value or a range.
   • Anatomical Site: Enter or search for an anatomical site.

     See Sequence Variants for more details.

   • Hospital Acquired Concern: Select one or more values for Hospital Acquired status of the Concern/Diagnosis.
   • Cancer Grade: Enter or search for a Grade of diagnosis.
   • Cancer Stage: Enter or search for a Stage of diagnosis.
   • Staging System: Enter or search for a Staging System of the Stage.
   • Primary Tumor: Enter or search for a Primary Tumor value.
   • Node Extension: Enter or search for a Node Extension value.
   • Metastasis: Enter or search for a Metastasis value.
   • Clinical Encounter: In the section Clinical Encounter, search for clinical encounter by specifying search criteria for:
     • Visit ID: Enter or search for a Visit ID (Encounter Number). In the Select Visit ID dialog, select a condition for Visit ID to search for Visit IDs.
     • Encounter Type: Enter or search for an Encounter Type. In the Select Encounter Type dialog, select a condition for Encounter Type Name, Encounter Type Code, Code System ID or Code System Name to search for Encounter Types.
   • Data Source: Enter or search for a source of data.

   Note:

   To define search criteria for Diagnosis, the criteria must include at least one of the following attributes: Concern Subtype, Diagnosis, Diagnosis Severity, Diagnosis Status, Anatomical Site, or Hospital Acquired Concern.
4. Under Insert as select either:
   • Inclusion to include the criteria in the query
   • Exclusion to exclude the criteria from the query
5. Click Submit.

   Back to "Build a cohort query".

6. A Diagnosis search criteria can be linked to search criteria for Test or Observation, Procedure, Medication and Specimen to define advanced search criteria like “Diagnosis D1 with Test or Observation T1, with Procedure P1, with Medication M1, with Specimen S1" which allows searching for Patients who have:
   • Diagnosis D1 and Test or Observation T1 in association/linked to Diagnosis D1 and
   • Diagnosis D1 and Procedure P1 in association/linked to Diagnosis D1 and
   • Diagnosis D1 and Medication M1 in association/linked to Diagnosis D1 and
   • Diagnosis D1 and Specimen P1 in association/linked to Diagnosis D1

     In the above example the criteria D1, T1, P1 and M1 can be defined using multiple values of the selected data (for example: Diagnosis DA1 or DA2 or DA2…; Procedure PR1 or PR2 or PR3… and so on) and the criteria can include all of the attributes available for defining the search on a particular data (for example: Diagnosis, Diagnosis Status, Onset Date, Cancer Grade and so on)

   To define a criteria linked to Diagnosis search criteria:

   1. Define a criteria on Diagnosis via Clinical Data category Diagnosis dialog and Submit.
   2. On the query builder page, where the query criteria is displayed under the sections Inclusions and Exclusion, click the Link icon () displayed next to the Diagnosis search criteria. This action brings up the popup menu for selecting the clinical data for which search criteria is to be defined and linked to the Diagnosis search criteria. The menus has options to select the following clinical data: Procedure, Medication, Test or Observation, and Specimen.
   3. Click on the popup menu to select a clinical data. This action brings up the search dialog for the clinical data, which is similar to the search dialog invoked via Clinical Data menu on the left side of the screen. To indicate that this search dialog when submitted would create a linked criteria, a label ‘Add Linked <clinical event>', for example ‘Add Linked Procedure' is displayed in the search dialog.
   4. Define the search criteria for the selected clinical data and submit the search dialog for the clinical data. This action adds the search criteria for the linked clinical data to the query builder screen where the newly added criteria is displayed below the diagnosis search criteria and linked to it via the label ‘WITH'.

      For information on defining search criteria for a clinical data see section Clinical Data under Build a Cohort Query in this document.

   5. Similarly linked search criteria can be defined for the other clinical events.

A criteria defined using the Diagnosis dialog can be linked to criteria for Procedure, Medication, Test or Observation and Specimen to create a single set of linked criteria. Such linked set can be ANDed to any other criteria including another Diagnosis based linked set(s) or standalone criteria defined using any of the clinical or genomic data, for example:

Diagnosis (DA1 or DA2 or DA3…) OR (DB1 or DB2 or DB3…)

• WITH Procedure P1 or P2 or P3…
• WITH Medication M1 or M2 or M3…
• WITH Test or Observation T1 or T2 or T3…
• WITH Specimen S1 or S2 or S3…

AND

Diagnosis (DA2 or DA3 or DA4… ) OR (DB2 or DB3 or DB4…)

• WITH Procedure P3 or P4 or P5…
• WITH Medication M3 or M4 or M5…
• WITH Test or Observation T3 or T4 or T5…
• WITH Specimen S1 or S2 or S3…

AND

Diagnosis D7 or D8 or D9…

AND

Procedure P10 or P11 or P12…

AND

Medication M10 or M11 or M12…

AND

History H1 or H2 or H3…

AND

Specimen S1 or S2 or S3…

...

AND

Criteria defined on Genomic data

Have you checked "Before you begin building your query" yet?

Clinical Encounter

1. On the left, click the Clinical Data category, then click Clinical Encounter.
2. Either enter the Encounter Type or click the search icon ().
   To search for an Encounter Type:
   1. In the Select Encounter Type window, select a condition for Encounter Name or Encounter Code and enter part of the encounter name or code.
   2. Select the consent encounter codes and names that you want to use from the left side and move them into the right side using the arrow ().
   3. Click Submit.
3. Set any other criteria that you want to use in your query: Location, Time or Data Source.
   • Location: Enter or search for a location.
   • Time: Select a condition, and then enter a time in days or in the form of a date.
   • Data Source: Enter or search for a source of data.
4. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Back to "Build a cohort query".

Have you checked "Before you begin building your query" yet?

Appointment

1. In the Patient Context, on the left, click the Clinical Data category, then click Appointment.
2. Enter an Appointment Number or click the search icon ().

   To search for an Appointment Number:

   1. In the Select Appointment Number window, select a condition for Appointment Number and enter part of the Appointment Number.
   2. Click Search.
   3. Select the Appointment Number that you want to use from the left side and move it to the right side using the arrow ().
   4. Click Submit.
3. Set any other criteria that you want to use in your query:
   • Appointment Start Date: Select a condition, and then add the date.
   • Appointment End Date: Select a condition, and then add the date.
   • Facility: Enter a Facility or click the search icon.

     To search for a Facility:

     1. In the Select Facility window, select a condition for Facility Number or Facility Name or Facility Type Code or Facility Type Name or Code System ID or Code System Name and enter part of the Facility Number or Facility Name or Type Code or Type Name or Code System ID or Code System Name.
     2. Click Search.
     3. Select the Facility that you want to use from the left side and move it to the right side using the arrow.
     4. Click Submit.
   • Service Provider: Enter a Service Provider or click the search icon.

     To search for a Service Provider:

     1. In the Select Service Provider window, select a condition for Service Provider Identifier or Service Provider Name or Service Provider Type Code or Service Provider Type Name or Code System ID or Code System Name and enter part of the Service Provider Identifier or Service Provider Name or Type Code or Type Name or Code System ID or Code System Name.
     2. Click Search.
     3. Select the Service Provider that you want to use from the left side and move it to the right side using the arrow.
     4. Click Submit.
   • Data Source: Enter or search for a source of data.
4. Under Insert as select:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Back to Build a cohort query.

Have you checked Before you begin building your query yet?

Procedure

1. On the left, click the Clinical Data category, then click Procedure.
2. Either enter the Procedure and Procedure Type or click the search icon ().
   To search for a Procedure and Procedure Type:
   1. In the new window, select a condition for Procedure Name, Procedure Code or Code System and enter part of the procedure name, code or code system.
   2. Click Search.
   3. Select the procedure code, name and code system that you want to use from the left side and move them into the right side using the arrow ().
   4. Click Submit.
3. Set any other criteria that you want to use in your query: Procedure Start Date, Procedure End Date, Anatomical Site, Procedure Outcome or Data Source.
   • Procedure Start Date: Select a condition, and enter the date.
   • Procedure End Date: Select a condition, and enter the date.
   • Anatomical Site: Enter or search for an anatomical site.

     See Sequence Variants for search details.

   • Procedure Outcome: Enter or search for a procedure outcome.
   • Clinical Encounter: In the section Clinical Encounter, search for clinical encounter by specifying search criteria for:
     • Visit ID: Enter or search for a Visit ID (Encounter Number). In the Select Visit ID dialog, select a condition for Visit ID to search for Visit IDs.
     • Encounter Type: Enter or search for an Encounter Type. In the Select Encounter Type dialog, select a condition for Encounter Type Name, Encounter Type Code, Code System ID, or Code System Name to search for Encounter Types.

       See Diagnosis for search details.

   • Data Source: Enter or search for a data source.

     Note:

     To define search criteria for Procedure, the criteria must include at least one of the following attributes: Procedure, Procedure Type, Anatomical Site, or Procedure Outcome.
4. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Back to Build a cohort query.

Have you checked Before you begin building your query yet?

Medication

1. In the Cohort Query screen, click the Clinical Data category, then click Medication.
2. Either enter the medication or click the search icon ().
   To search for Medication:
   1. Medication Status: Select one or more medication status values.
   2. Select one of the Search Modes:
      • Classic Search. More search conditions are available.
      • Hierarchy Drill-in Search. Select it to search all of the codes in a hierarchy that are associated with a single Code System, and have only one parent code.

      Note:

      This feature does not support mixed hierarchy, meaning different levels of codes belonging to different Code Systems or multi-parent hierarchy, meaning one code having multiple parent codes.
   3. Search for a medication either by Medication Name, Medication Code, Code System ID, or Code System Name and click Search.
   4. Select the medication codes that you want to use from the left side and move them into the right side using the arrow ().
   5. Click Submit.
3. Set any other criteria that you want to use in your query:
   • Medication Start Date: Select a condition and enter a date.
   • Medication End Date: Select a condition and enter a date.
   • Dosage: Select a condition and enter a date.
   • Dosage Units: Enter or search for dosage units.
   • Medication Outcome: Select a condition and enter a date.
   • Order Details: In the section Order Details (available only Patient context), search for an order by specifying search criteria for:
     • Order Number: Enter or search for an Order Number. In the Select Order Number dialog, select a condition for Order Number to search for order numbers.
     • Orderable Item: Enter or search for an Orderable Item. In the Select Orderable Item dialog, select a condition for Orderable Item Name, Orderable Item Code, Code System ID, or Code System Name to search for orderable items.
     • Order Date: Select a condition and enter a date or date range.
   • Clinical Encounter: In the section Clinical Encounter, search for clinical encounter by specifying search criteria for:
     • Visit ID: Enter or search for a Visit ID (Encounter Number). In the Select Visit ID dialog, select a condition for Visit ID to search for Visit IDs.
     • Encounter Type: Enter or search for an Encounter Type. In the Select Encounter Type dialog, select a condition for Encounter Type Name, Encounter Type Code, Code System ID, or Code System Name to search for Encounter Types.

       See Diagnosis for search details.

   • Data Source: Enter or search for a data source.

     Note:

     To define search criteria for Medication, the criteria must include at least one of the following attributes: Medication or Medication Outcome.
4. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Back to "Build a cohort query".

Have you checked "Before you begin building your query" yet?

Patient History

1. In the Cohort Query screen, click the Clinical Data category, then click Patient History.
2. Either enter the Patient History code or click the search icon ().
   To search for Patient History:
   1. In the Select Patient History window, select a condition for History Name, History Code, History Type, Code System ID, or Code System Name and enter part of the History Code or History name.
   2. Select the history code, name, type, and code system that you want to use from the left side and move them into the right side using the arrow ().
   3. Click Submit.
3. Set any other criteria that you want to use in your query:
   • Patient History Start Date: Select a condition and enter a date.
   • Patient History End Date: Select a condition and enter a date.
   • Amount: Select a condition and enter a numeric value.
   • Amount Units: Enter or search for the amount units.
   • Frequency: Select a condition and enter a numeric value.
   • Frequency Units: Enter or search for frequency units.
   • Patient History Value: Enter or search for a patient history value.
   • History Applicable To: Then select whom is it applicable to.
   • Data Source: Enter or search for a data source.

     Note:

     To define search criteria for Patient History, the criteria must include the attribute Patient History.
4. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Back to "Build a cohort query".

Have you checked "Before you begin building your query" yet?

Test or Observation

1. In the Cohort Query screen, click the Clinical Data category, then click Test or Observation.
2. Either enter the test or observation code or click the search icon ().

   To search for a Test or Observation:

   1. In the Select Test or Observation window, select a condition for Test or Observation Name, Test or Observation Code, Test or Observation Type, Code System ID, or Code System Name and enter part of either the code, the name or enter the Test or Observation Type.
   2. Select the test or observation code, name and type that you want to use from the left side and move them into the right side using the arrow ().

      Note:

      When in Patient Context in the Patient Observation table, if an Observation Code is used with more than one Observation Subtype, then the Observation Code is repeated as set of multiple identical rows in the left slide list, one for each Observation Subtype. When any one of such rows is selected in the left side list then all of the rows in above set are highlighted. In this case, when the arrow button is used to move the selected row to the right side list, the application ensures that only one row is used in the building the query criteria.
   3. Click Submit.

   Note:

   In the Search Test or Observation window, the Test or Observation Type by default uses the Equals operator and lists the first 100 types only. If there are more than 100 Test or Observation type values in your data, you can search using other operators like “Starts with", “Contains", and so on.
3. Set any other criteria that you want to use in your query:
   • Test or Observation Subtype: Enter or search for a Test or Observation Subtype. In the Select Test or Observation Subtype dialog, select a condition for Subtype Name, Subtype Code, Code System ID, or Code System Name to search for Test or Observation Subtypes.
   • Test Date: Select a condition, and enter a date.
   • Effective Start Date: Select a condition, and enter a date as a single value or a range.
   • Effective End Date: Select a condition, and enter a date as a single value or a range.
   • Result (Numeric) Search: For Based on absolute values, select an Operator, and enter the units. For Based on Reference Range select an Operator, and an option for the Compare field.
   • Coded Result: Enter or search for a Coded Result. In the Select Coded Result dialog, select a condition for Result Name, Result Code, Code System ID, or Code System Name to search for Coded Results.

     Note:

     In the earlier versions of the product the attribute Coded Result was labeled as Result String across all of the user interface.
   • Text Result: Enter or search for a Text Result.
   • Batch Number: Enter or search for a Batch Number.
   • Anatomical Site: Enter or search for an Anatomical Site.

     See Sequence Variants for search details.

   • Medication: Enter or search for a Medication. In the Select Medication dialog, select the mode to perform Classic Search or Hierarchy Drill-in Search, then select a condition for Medication Name, Medication Code, Code System ID, or Code System Name to search for Medication. The Select Medication dialog functions identically to the one available under Medication under the Select Medication dialog.
   • Order Details: In the section Order Details (available only in Patient context), search for Order by specifying search criteria for:
     • Order Number: Enter or search for an Order Number. In the Select Order Number dialog, select a condition for Order Number to search for order numbers.
     • Orderable Item: Enter or search for an Orderable Item. In the Select Orderable Item dialog, select a condition for Orderable Item Name, Orderable Item Code, Code System ID, or Code System Name to search for orderable items.
     • Order Date: Select a condition and enter a date or date range.
   • Panel: In the section Panel specify search criteria for:
     • Diagnostic Panel Set: Enter or search for a Diagnostic Panel Set. In the Select Diagnostic Panel Set dialog, select a condition for Diagnostic Panel Set Name, Diagnostic Panel Set Code, Code System ID, or Code System Name to search for Diagnostic Panel Sets.
     • Diagnostic Panel: Enter or search for a Diagnostic Panel. In the Select Diagnostic Panel dialog, select a condition for Diagnostic Panel Name, Diagnostic Panel Code, Code System ID, or Code System Name to search for Diagnostic Panels.
     • Observation Category: Enter or search for a Observation Category. In the Select Observation Category dialog, select a condition for Observation Category Name, Observation Category Code, Code System ID, or Code System Name to search for Observation Categories.
   • Clinical Encounter: In the section Clinical Encounter, search for clinical encounter by specifying search criteria for:
     • Visit ID: Enter or search for a Visit ID (Encounter Number). In the Select Visit ID dialog, select a condition for Visit ID to search for Visit IDs.
     • Encounter Type: Enter or search for an Encounter Type. In the Select Encounter Type dialog, select a condition for Encounter Type Name, Encounter Type Code, Code System ID, or Code System Name to search for Encounter Types.

       See Diagnosis for search details.

   • Data Source: Enter or search for a data source.

     Note:

     To define search criteria for Test or Observation, the criteria must include at least one of the following attributes: Test or Observation Subtype, Test or Observation, Anatomical Site, or Medication.
4. Under Insert as select:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Back to Build a cohort query.

Have you checked Before you begin building your query yet?

Specimen

1. In the Cohort Query screen, click the Clinical Data category, then click Specimen.
2. Either enter the codes in the mandatory fields (marked with a double asterisk) or click the search icon ().

   To search for a Specimen Type:

   1. In the Select Specimen Type window, select a condition for the Specimen Type Name, Specimen Type Code, Code System ID, or Code System Name and enter part of either the Name, Code, Code System ID, or Code System Name.
   2. Select the specimen code, name and code system that you want to use from the left side and move them into the right side using the arrow ().
   3. Click Submit.

      Note:

      Repeat the same steps when searching for a Specimen Number and Specimen Vendor Number.
3. Set any other criteria that you want to use in your query:
   • Specimen Number: Enter or search for a Specimen Number.
   • Specimen Vendor Number: Enter or search for a Specimen Vendor Number.
   • Anatomical Site: Enter or search for an anatomical site.

     See Sequence Variants for more details.

   • Specimen Collection Date: Select a condition and enter a date.
   • Specimen Amount: Select a condition and a numeric value.
   • Units: Enter or search for units.
   • Specimen Alias: Enter the Specimen Aliases in the input box or click the search icon () to invoke the Select Specimen Alias dialog.
     • In the dialog select a condition for Specimen Alias, Service Provider ID or Service Provider Name (Service Provider being the issuer of the Specimen Alias) and click the Search button.
     • Select the Specimen Alias(es) that you want to use from the left side and move them to the right side using the arrow icon ().
     • Click Submit.
   • Specimen Context: Enter or search for a Specimen Context.
   • Data Source: Enter or search for a data source.

     Note:

     To define search criteria for Specimen, the criteria must include at least one of the following attributes: Specimen Type, Specimen Number, Specimen Vendor Number, Anatomical Site, Specimen Alias, or Specimen Context.
4. Under Insert as select:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

   Back to "Build a cohort query".

6. A Specimen search criteria can be linked to search criteria for Test or Observation to define advanced search criteria like Specimen S1 with Test or Observation T1 which allows searching for Patients who have Specimen S1 and Test or Observation T1 in association/linked to the Specimen S1.

   In the above example, the criteria S1 and T1 can be defined using multiple values of the selected data (for example: Specimen S1 or S2 or S3…; Test or Observation T1 or T2 or T3… and so on) and the criteria can include all of the attributes available for defining the search on a particular data (for example: Specimen Type, Specimen Number, Specimen Vendor Number, Specimen Anatomical Site and so on).

   To define a criteria linked to Specimen search criteria:

   1. Define a criteria on Specimen via Clinical Data category Specimen dialog and Submit.
   2. On the query builder page, where the query criteria is displayed under the sections Inclusions and Exclusion, click the Link icon () displayed next to the Specimen search criteria. This action brings up the popup menu for selecting the clinical data for which search criteria is to be defined and linked to the Diagnosis search criteria, in this case, Test or Observation.
   3. Click on the popup menu to select Test or Observation. This action brings up the search dialog for Test or Observation, which is similar to the search dialog invoked via Clinical Data menu on the left side of the screen. To indicate that this search dialog when submitted would create a linked criteria, a label 'Add Linked Test or Observation' is displayed in the search dialog.

   Define the search criteria for Test or Observation and submit the search dialog. This action adds the search criteria for the linked Test or Observation to the query builder screen where the newly added criteria is displayed below the Specimen search criteria and linked to it via the label 'WITH'.

Have you checked "Before you begin building your query" yet?

Study

1. In the Cohort Query screen, click the Clinical Data category, then click Study.
2. Either enter the code for a study or click the search icon ()

   To search for a Study:

   1. In the Select Study window, select a condition for Study Name or Study Identifier and enter part of the name or identifier.
   2. Select the study identifier and study name that you want to use from the left side and move them into the right side using the arrow ().
   3. Click Submit.
3. Set any other criteria that you want to use in your query:
   • Study Start Date: Select a condition and enter a date.
   • Study End Date: Select a condition and enter a date.
   • Data Source: Enter or search for a data source.
4. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
5. Click Submit.

Back to Build a cohort query.

Have you checked Before you begin building your query yet?

Relative Time Events

You can search for patients who have a particular diagnosis, procedure, or medication combination in a particular chronological order. For example, you can search for patients who:

• Received a diagnosis of X disease any time after starting medication A.
• Had procedure K 30 days or more after receiving a diagnosis of Y.
• Started medication B at the same time as having procedure M.

1. In the Cohort Query screen, click the Clinical Data category, then click Relative Time Events.
2. Under “Select Patients who have, Step 1" select Diagnosis, Procedure, Medication, Test or Observation, or Genomic Variant.
3. Specify how the events in Step 1 and Step 3 are time-related: “at any time while" or specify a condition.
4. Under Step 3, specify the related event: having Diagnosis, undergoing Procedure, or taking Medication.
5. Under Insert as selec eithert:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
6. Click Submit.

Back to "Build a cohort query".

Have you checked "Before you begin building your query" yet?

Genomic Data

Topics in this section:

• Sequence Variants
  
• Copy Number Variation
  
• Microarray Expression
  
• RNA-seq Expression
  
• Metadata Filters
  

Sequence Variants

1. In the Cohort Query screen, click the Genomic Data category, then click Sequence Variants.
2. You can search on Specimen Type or Anatomical Site.

   To search for a Specimen Type:

   1. Either enter part or all of the value for Specimen Type or click the search icon ().
   2. In the Select Specimen Type window, select the condition for Specimen Type Name, Specimen Type Code or Code System and enter part of the code.
   3. Select the specimen code, name and code system that you want to use in your query from the left side and move them into the right side using the arrow ().
   4. Click Submit.

   To search for an Anatomical Site:

   1. Either enter part or all of a value for Anatomical Site or click the search icon ().
   2. In the Select Anatomical Site window, select one of the Search Modes:

      - Classic Search. More search conditions are available.

      - Hierarchy Drill-in Search. You can drill down to see the patient count for any sub-level.

   3. Search for an anatomical site either by Anatomical Site Name, Anatomical Site Code, Code System ID, or Code System Name and click Search.
   4. Select any Anatomical Site codes, names and code systems that you want to use from the left side and move them into the right side using the arrow ().
   5. Click Submit.

3. You can also search for patients by different genomic criteria. In the Select Patients based on section, select one:
   • having Variants in selected Genes: this enables you to search variants in specific genes.
   • having selected Genomic Variants enables you to search for variants by their Cosmic or dbSNP identifiers.
   • having Variants within specified Genomic Region enables you to search variants in specified genomic location.
   • having Zygosity enables you to search variants with specific zygosity: Any, Homozygous, Heterozygous or Hemizygous.
   • having Amino Acid enables to search for specific amino acid changes in selected genes or caused by specific genomic variant.
     • Enter a Hugo Symbol with an optional parameter of amino acid change (such as K483Q,33_34insGA, R603*, 601Kdel, T1738Ifs, K2137delinsRE, K224_D225delinsN) and you can see list of amino acid changes existing in the database.
     • Enter a variant identifier like Cosmic dbSNP or HGVS identifier and you can see all associated amino acid changes.

     Select the amino acids of interest and submit to search for patients or subjects having these amino acid changes. having Genotypes enables you to search for specific genotypes like AT, or AA, or wildtype (same as reference), and so on.

4. After selecting the genomic criteria, expand the Variant Location section and specify a value for the selected option.
   1. Select either at Genomic Variant or at Genomic Position. Add a value.
   2. Select an Assembly Version.
   3. Click View Available Genotypes.
5. Under Insert as select either:

   - Inclusion to include the criteria in the query.

   - Exclusion to exclude the criteria from the query.

   Tip:

   This applies to all of the criteria specified above.
6. Click Submit.

(Optional) Step 2 Additional criteria

To add additional parameters to your query in the Step 2 tab:

1. In the Sequence Variants window, click Step 2 (Optional).
2. Select any or all of the following parameters:

   Variant Attribute:

   1. Specify Variant Types from the options below: Substitution, Insertion, Deletion, Indel, or Complex.
   2. Select a Variant Impact: Synonymous, Missense, Nonsense, Unknown.
   3. Select a Variant Status: Select Any, Known, or Novel.
   4. Strand: Select Any, + for forward, or - for reverse.

   Nonsynonymous Substitution Scores:

   1. Select either with Polyphen option or the with SIFT option.
   2. Select a condition for the Version.
   3. Either enter a Transcript ID or search for one by clicking the search icon .

   Variant Parameters Depending on the Sequencing File Type:

   1. Select either VCF, MAF or CGI master var.
   2. Select the condition for all active fields according to your choice in Step a.

3. Under Insert as select:

   - Inclusion to include the criteria in the query.

   - Exclusion to exclude the criteria from the query.

4. Click Submit.

See "Metadata Filters".

Back to "Build a cohort query".

Have you checked "Before you begin building your query" yet?

Copy Number Variation

1. In the Cohort Query screen, click the Genomic Data category, then click Copy Number Variation.

   To search for a Specimen Type:

   1. Either add the Specimen Type or click the search icon ().
   2. In the Select Specimen Type window, select the condition for Specimen Type Name, Specimen Type Code or Code System and enter part of the code.
   3. Select the specimen code, name and code system that you want to use from the left side and move them into the right side using the arrow ().
   4. Click Submit.

   To search for an Anatomical Site:

   1. Either enter part or all of a value for Anatomical Site or click the search icon ().
   2. In the Select Anatomical Site window, select one of the Search Modes:

      - Classic Search. More search conditions are available.

      - Hierarchy Drill-in Search. You can drill down to see the patient count for any sub-level.

   3. Search for an anatomical site either by Anatomical Site Name, Anatomical Site Code or Code System and click Search.
   4. Select any Anatomical Site codes, names and code systems that you want to use from the left side and move them into the right side using the arrow ().
   5. Click Submit.

2. In the CNV Attributes, specify the CNV Result Type using the two options: numeric or categorized.
   1. If you select numeric, specify a numeric value for the:
      • Log2 Ratio
      • Copy Number
   2. If you select categorized, specify a condition for the CNV Type, a value for the CNV Type Score, a condition for Called Ploidy and a value for the Ploidy score.
3. Specify the CNV Location using any or all options from the in Genes from list: Ad-hoc List, Pathway or Gene Set.
4. Enter or search for a value for any or all of the options you selected above.
5. Select a value for in Gene Region.
6. Specify the Assembly Version.
7. Specify the DNA Reference Version.

   About the DNA Reference Version: it represents the Ensembl reference version for getting gene annotations. This is related to Assembly Version and by default displays the preferred DNA Reference Version, which is set in OHO. The sample value for this is Ensembl Version 70.

8. Select the radio button for at Genomic Position and enter a value for it.
9. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.

   Tip:

   This applies to all of the criteria specified above.
10. Click Submit.

See Metadata Filters.

Back to "Build a cohort query".

Have you checked "Before you begin building your query" yet?

Microarray Expression

1. In the Cohort Query screen, click the Genomic Data category, then click Microarray Expression.
2. To select patients with Microarray Expression Results:
   1. Either add the Specimen Type or Anatomical Site (both are optional) or click the search icon ().

      To search for a Specimen Type:

      1. In the Select Specimen Type window, select the condition for Specimen Type Name, Specimen Type Code or Code System and enter part of the code.
      2. Select the specimen code, name and code system that you want to use in your query from the left side and move them into the right side using the arrow ().
      3. Click Submit.

      To search for an Anatomical Site:

      1. Either enter part or all of a value for Anatomical Site or click the search icon ().
      2. In the Select Anatomical Site window, select one of the Search Modes:

         - Classic Search. More search conditions are available.

         - Hierarchy Drill-in Search. You can drill down to see the patient count for any sub-level.

      3. Search for an anatomical site either by Anatomical Site Name, Anatomical Site Code or Code System and click Search.
      4. Select any Anatomical Site codes, names and code systems that you want to use from the left side and move them into the right side using the arrow ().
      5. Click Submit.

3. Select the Microarray Attributes: the Array Type, the conditions and values for Intensity, P-value and/ or Call.
   1. The Array Type: one-channel or two-channel.

      If you select one-channel, specify the needed conditions and values for Intensity, P-value< and Call.

      If you select two-channel, specify a condition for the Log2Ratio.

4. n the Expression for Genes from select either: Ad-hoc list, Pathway or Gene Set. Then select the Assembly Version and the DNA Reference Version.
5. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
6. Click Submit.

See Metadata Filters.

Back to "Build a cohort query".

Have you checked "Before you begin building your query" yet?

RNA-seq Expression

1. In the Cohort Query screen, click the Genomic Data category, then click RNA-seq Expression.

   To select patients with RNA-seq Expression Results:

   1. Either add the Specimen Type or Anatomical Site (both are optional) or click the search icon ().

      To search for a Specimen Type:

      1. In the Select Specimen Type window, select the condition for Specimen Type Name, Specimen Type Code or Code System and enter part of the code.
      2. Select the specimen code, name and code system that you want to use in your query from the left side and move them into the right side using the arrow ().
      3. Click Submit.

      To search for an Anatomical Site:

      1. Either enter part or all of a value for Anatomical Site or click the search icon ().
      2. In the Select Anatomical Site window, select one of the Search Modes:

         - Classic Search. More search conditions are available.

         - Hierarchy Drill-in Search. You can drill down to see the patient count for any sub-level.

      3. Search for an anatomical site either by Anatomical Site Name, Anatomical Site Code or Code System and click Search.
      4. Select any Anatomical Site codes, names and code systems that you want to use from the left side and move them into the right side using the arrow ().
      5. Click Submit.

2. Select a type from Normalization Level: Gene, Exon, or Transcript.
3. Select a value for the Normalization Metrics: RPKM, TPM, FPKM, or FPKM UQ.
4. Select Raw Counts, Median Length (Normalized), or Strand based on the chosen Normalization Level (Median Length is only available for Exon).
5. Select an option for the RNA-seq Location: Ad-hoc list, Pathway, and Gene.
6. The Transcript IDs option is only available for Exon and Transcript Normalization Levels.
7. For each, either enter a value or click the search icon ().
8. 
   
   1. Select if the location is available for a certain Transcript ID and select the Assembly Version and the DNA Reference Version.
   2. Select at which Genomic Position the patient is (optional, is only available for Exon Normalization Level).
9. Under Insert as select either:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria in the query.
10. Click Submit.

See Metadata Filters.

Back to "Build a cohort query".

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Metadata Filters

This option is available at the bottom of each of the genomic criteria screens.

To add metadata filters:

1. Expand the Metada Filters option.
2. Click Add Metadata Filter to open the Select Metadata Attribute window.
3. Search for a metadata filter based on Attribute Name, Scope or Category to get a list of attributes associated with metadata.
4. Select the attributes from the list that you want to use and click Add to Filter. When you have added all the filters you need, click Done.
5. For each attribute name from the table, select a condition in the Operator column, then enter a value for it in the Value column.

   Example 2-1 Metadata Filters

   Attribute Name	Operator	Value
   ANALYSIS_ID	Starts with	TGTAID120

6. Under Insert as select:
   • Inclusion to include the criteria in the query.
   • Exclusion to exclude the criteria from the query.
7. Click Submit.

Back to "Build a cohort query".

Have you checked "Before you begin building your query" yet?