1 Training Video
2 Who can access the Query?
- 2.1 Fields description
- 2.2 Operators description
3 Example
4 Default Queries

Generally, users want to know the data collected for different/ particular collection protocols based on different criterias. E.g., Saliva Samples from Male participants, Participants that are turning 18, Samples from the participants that have consented, etc.

OpenSpecimen reporting modules help the users to search within or across collection protocols and various criteria to get the required results.

Training Video

Who can access the Query?

By default Super and Institute Admins have access to query
Users with the role of Create, Update, Delete, Import, Export Query privileges can access the Query.

PHI data of the participant is hidden/shown based on the role privilege.

Refer to the wiki page for more information on Roles and Privileges.

Fields description

Field	Description
Select a Collection Protocol	Helps to search through a Collection Protocol/Collection Protocol Group. If none is selected, search is done across all collection protocols. For flexibility and reusability of queries, When a saved query is used in other areas like ‘Catalog' or 'Sub-query’, the CP/CPG selected in this option is not carried over.
Add Filter	Used to create queries based on calculations(Temporal Queries). Refer to the wiki page for more details.
Collection Protocol	Helps to search based on fields of Collection Protocol. E.g., Coordinator, sites, etc,.
Participant	Helps to search based on fields/forms of participants, e.g., gender, name, date of birth, race, etc.,
Visits	Helps to search based on fields/form of visits, e.g., name, status, event code/label, etc,.
Specimens	Helps to search based on fields/forms of specimens, lineage, type, etc,.
Specimen Kits	Helps to search based on fields of kits, e.g., receiving/sending site, specimen label, etc,.

Operators description

Operator	Description

Operator	Description
Equals	Search based on particular name/value.
Not Equals	Search excluding the single value.
Exists	Searches the data where the field value is entered.
Not Exists	Searches the data where the field value isn’t entered.
All
Starts with	Searches for the data where the value starts with the mentioned character/number/alphabet.
Ends with	Searches for the data where the value ends with the mentioned character/number/alphabet.
Contains	Searches for the data where the value exists with the mentioned character/number/alphabet.
Is One Of	Searches based on multiple values, where any value specified is true.
Is Not One Of	Searches excluding the multiple values specified.
Between	Searches the data between specified date/numeric range.
Less than	Searches the data that is less than specified date/numeric range.
Greater than	Searches the data that is greater than specified date/numeric range.
Greater than or equals	Searches the data that is greater than or equal to specified date/numeric range.
Less than or equals	Searches the data that is less than or equal to specified date/numeric range.

Example

User wants to search for female participants in the Skin Cancer Study who have DNA specimens collected and are available.

Navigate to Queries -> +Create
Select the Collection Protocol Skin Cancer Study from the dropdown.

Click on the Participant → Select Gender. Add a filter with Operator 'Equals' and select 'Female' under the Condition Value.

Click on Specimens → Select Type. Add a filter with Operator 'Equals' and select DNA under the Condition Value.

Click on Specimens → Select Availability. Add a filter with Operator 'Equals' and select Available under the Condition Value.

Click on ‘Get Count’ to get the number of counts of participants, visits, and specimens for the query created.

Click on View Records to view the data pulled for the query.

Features

Features	Description

Features	Description
Create new queries	Create queries based on fields across standard, custom forms, and fields with complex expressions (AND, OR, NOT, intersection, hierarchical, and parenthesis). See: Sample queries
Get counts (pivot tables)	Run the queries to get the count of participants and specimens that match the filters.
Get raw data	Run queries to get raw data from the system. See: Query Results view
Save query	Save query so that it can be reused for later use.
Folders and sharing	Saved queries can be organized in folders and shared with other users. E.g., 2-3 users are working on shortlisting specimens for a project can share the same set of queries. See: Share queries
Privileges	Data is filtered as per the user's privileges. E.g., if the user does not have PHI access, the patient identifier fields will be hidden. Access to the Query module can be controlled using the Query privilege. See: Query Privilege (v6.3)
Data export (CSV)	Data from the query results view can be exported as a CSV file.
Custom fields and forms	The custom forms and field added via form builder is available for querying the reports.
Calculated fields	Difference between two dates (e.g., age at the collection, warm ischemia time, etc.) See: Calculated fields (Temporal Queries)
Hierarchical queries	To support queries like, show any DNA aliquot whose parent specimen's "warm ischemia time" is less than x minutes.
Import and Export queries	One can import and export queries from one instance to another—E.g., test server to production server.
Aggregate functions	Supports functions like sum, max, min, etc.
Dashboards	Create visually appealing dashboards with graphs and numeric counters based on query results. See: Dashboard changes using query

Default Queries

Query	Description

Query	Description
Cart specimens report query	Saved query to use for generating cart specimens report
Container specimens report query	Saved query to use for generating container specimens report
Distribution order data query	Saved query to use for creating distribution report when DP specific report is not configured
Shipment report query	Saved query to use for exporting shipment details
Specimen kit report query	Saved query to use for exporting specimen kit details