RFC: LIMS

[max3903]

LIMS

Description: Base of the LIMS modules based on LOINC.

LOINC Codes can be updated from here.

Depends on: mail

Configuration

The base LIMS module can be used with minimal initial configuration. It also allows for many advanced features, which require a more in-depth configuration.

Stages

The stage of an order is used to monitor its progress. Stages can be configured based on your company's specific business needs. A basic set of stages comes pre-configured for use.

1. Go to LIMS > Configuration > Stages
2. Create or edit a stage
3. Set the name for the stage.
4. Set the sequence order for the stage.
5. Select Order type to apply this stage to your order.
6. Additionally, you can set a color for the stage.

Laboratories

You can manage different laboratories.

Advanced Configurations

Additional features can be enabled in the General Settings panel for LIMS.

1. Go to LIMS > Configuration > Settings
2. Enable additional options
3. Configure new options

Manage Teams

Teams can be used to organize the processing of analysis
into groups. Different teams may have different workflows that an analysis
needs to follow.

1. Go to LIMS > Configuration > Teams
2. Create or select a team
3. Set the team name, description, and sequence

You can now define custom stages for each team processing orders.

1. Go to LIMS > Configuration > Stages
2. Create or edit a stage
3. Select the teams for which this stage should be used

Manage Tags

Tags can be used to filter and report on orders.

1. Go to LIMS > Configuration > Orders > Tags
2. Create or select a tag
3. Set the tag name
4. Set a color index for the tag

Manage Templates

Templates allow you to create standard templates for your orders.

1. Go to LIMS > Master Data > Templates
2. Create or select a template
3. Set the name
4. Set the standard information that will be used to overwrite the order

Usage

To use this module, you need to:

Add Operators

Operators are the people responsible for performing an order. These operators may be subcontractors or the company's own employees.

1. Go to LIMS > Master Data > Operators
2. Create an operator

Process Orders

Once you have established your data, you can begin processing your orders.

1. Go to LIMS > Dashboard > Orders
2. Create or select an order
3. Follow the instructions of the tests and methods using the instruments
4. Enter the results
5. Process the analysis through each stage as defined by your business requirements

Models

Stage

• name

Laboratory

res.partner

• is_laboratory: Boolean

Team

• name

LOINC Code

• loinc_code (PK, e.g., "1975-2")
• long_common_name (e.g., "Glucose [Mass/volume] in Serum or Plasma")
• short_name (e.g., "Glucose SerPl-mCnc")
• component (e.g., "Glucose")
• property (e.g., "Mass/volume")
• time_aspect (e.g., "Pt" for Point in time)
• system (e.g., "Ser/Plas" for Serum or Plasma)
• scale_type (e.g., "Qn" for Quantitative)
• method_type (e.g., "Colorimetric")
• unit_code (e.g., "mg/dL")
• class (e.g., "CHEM")
• status (e.g., "ACTIVE")
• version_added
• last_updated

Operator

res.partner

• is_lims_operator: Boolean

Template

• operator_id: m2o to res.partner filtered with is_lims_operator = True. "Assigned To"
• ordering_physician_id: many2one to res.partners filtered by contact
• test_ids

Test

• name (e.g., "Fasting Glucose")
• loinc_code (FK to LOINC_Codes.loinc_code)
• description
• normal_range_min
• normal_range_max
• uom_id
• method_id (FK to Methods table)
• instrument_id (FK to Instruments table)
• cost
• template_ids

Specimen

• sample_barcode
• partner_id: Many2one to res.partner
• collection_date
• collection_time
• specimen_type (e.g., "Blood", "Urine")
• storage_location
• stage_id (e.g., "Collected", "Received", "Processed", "Discarded")
• order_id (FK to Orders table)

Order

• partner_id: Many2one to res.partner
• ordering_physician_id: Many2one to res.partner
• date
• required_by
• stage_id (e.g., "Pending", "Completed", "Cancelled")

Order Test

• order_id (FK to Orders.order_id)
• test_id (FK to Tests.test_id)
• operator_id: m2o to res.partner filtered with is_lims_operator = True. "Assigned To"
• stage_id (e.g., "Ordered", "In Progress", "Resulted")

Result

• order_test_id (FK to Order_Tests.order_test_id)
• specimen_id (FK to Specimens.specimen_id)
• result_value
• result_unit (Could pull from Tests or LOINC_Codes)
• interpretation (e.g., "Normal", "High", "Low")
• result_date
• validated_by_user_id (FK to Users table)
• stage_id (e.g., "Preliminary", "Final", "Approved")
• reference_range_used (actual range used at time of result)

Method

• name
• description
• manufacturer: Many2one to res.partner

Instrument

• name
• stage_id

Menu items

• Dashboard
  • Laboratories (Kanban)
  • Teams (Kanban)
  • Orders (Kanban, Timeline, Activity)
  • Tests (Kanban, Timeline, Activity)
• Operations
  • Batches (List, Form)
  • Orders (List, Form)
  • Tests (List, Form)
  • Results (List, Form)
• Master Data
  • Customers
  • Templates
  • Specimens
  • Operators
  • Instruments
• Reporting
  • Orders (Graph, Pivot)
  • Tests (Graph, Pivot)
• Configuration
  • Settings
  • Stages
  • Laboratories
  • Teams
  • LOINC Codes
  • Orders
    • Tests
    • Methods

Groups

• LIMS / Administrator: Access to all menu items
• LIMS / User: Access to Dashboard, Operations and Master Data
• LIMS / User: Own documents
• LIMS / Multiple Laboratories
• LIMS / Use Teams
• LIMS / Use instruments

Security

• Access groups
• Record rules:
  • Multi-company
  • Multi-laboratory
  • Own Documents

Settings

• Laboratories
  • Manage Laboratories
• Operators
  • Manage Teams (a team shares the same process/stages)
• Instruments
  • Manage Instruments
  • Activate Maintenance
• Orders
  • Activate Account
  • Activate Sales
  • Activate Purchase
  • Activate Stock
• Integrations
  • HL7

References

From @etobella:

• [ADD] lims tegin/lims#1
• https://hl7.org/fhir/diagnosticreport.html

[max3903]

Interested:
@NICO-SOLUTIONS
@cvinh
@demeort
@jasiel-osi

[NICO-SOLUTIONS]

Ref: NIST LIMS Roadmap – provides a comprehensive overview of fundamental concepts and principles of LIMS. Recommended as background reading

[etobella]

BTW, if you are interested:

• https://github.com/tegin/medical-fhir/tree/16.0/medical_certify This modules allows to create a signature field in each report. That is quite interesting because in some scenarios they require a certificate where you ensure that nothing was changed.
• https://github.com/tegin/medical-fhir/tree/16.0/medical_diagnostic_report Is the implementation of diagnostic report. It is complicated as it has a lot of dependancies, but includes some information relevant, of, for example, how to handle the values and so on (even some widgets)
• https://github.com/tegin/medical-fhir/tree/16.0/medical_diagnostic_report_graph For the same module, allows to insert graphs. That is something usual in Healthcare.

[max3903]

https://en.m.wikipedia.org/wiki/Laboratory_information_management_system

[max3903]

https://loinc.org/get-started/what-loinc-is/
https://www.hl7.org/index.cfm

[etobella]

@max3903 LOINC is a nomenclature system. similar to SNOMED-CT
HL7 shown in LOINC website is HL7v2. That is only used for sending basic information.

However, a lot of Analysis machines uses HL7v2 for communicating results to the LIS.

[cvinh]

@max3903 LOINC is a nomenclature system. similar to SNOMED-CT HL7 shown in LOINC website is HL7v2. That is only used for sending basic information.

However, a lot of Analysis machines uses HL7v2 for communicating results to the LIS.

Loinc is meant to be a standard for internationalization, that's the purpose why @max3903 referenced it here. Labs has the very bad habit to build their own nomenclature according to their small perimeter (system + machines) that does a mess when they want to communicate with external systems. Including Loinc side by side with HL7v2 at the really beginning of the project is an added value IMHO. WDYT ?