Automating LIMS Bioinformatics Workflow Configuration and Enhancing Lab Quality Management with AI

Section 1: Use Case Identifiers

Use Case ID: HHS-CDC-00028
Agency: HHS
Op Div/Staff Div: CDC
Use Case Topic Area: Mission-Enabling (internal agency support)
Is the AI use case found in the below list of general commercial AI products and services?
None of the above.
What is the intended purpose and expected benefits of the AI?
The tool proposed will impact the laboratory bioinformatics workflow configuration within the Core Laboratory's Genomics Sequencing Lab (GSL). Specifically, it will improve the efficacy with Clarity LIMS for tracking and processing Next Generation Sequencing (NGS) samples. This includes the creation and customization of bioinformatics workflows in the Laboratory Information Management System, which is currently a time-consuming and expertise-intensive task for bioinformaticians and laboratory scientists.

The RAG system can potentially reduce the time required to configure Clarity LIMS workflows, enabling rapid deployment which is particularly crucial during pandemics or outbreak responses. By simplifying the workflow customization process through natural language inputs, it lowers the barrier to entry for laboratory scientists and bioinformaticians who may not be familiar with XML scripting. The system also enhances team learning and training by providing easy access to relevant documents on quality management and regulations, ensuring that all team members are well-informed about best practices.
Describe the AI system's outputs.
We propose to use a Retrieval-Augmented Generation (RAG) framework for two primary functions: It converts natural language lab protocols into precise XML workflows that are compatible with Clarity LIMS. This conversion process involves understanding technical documentations and generating corresponding script code. In addition, it serves as an interactive knowledge base for documentation of Clarity LIMS and Laboratory Quality Management and Regulations.
Stage of Development: Initiated
Is the AI use case rights-impacting, safety-impacting, both, or neither?
Neither

Section 2: Use Case Summary

Date Initiated: 01/2024
Date when Acquisition and/or Development began: N/A
Date Implemented: N/A
Date Retired: N/A
Was the AI system involved in this use case developed (or is it to be developed) under contract(s) or in-house?
N/A
Provide the Procurement Instrument Identifier(s) (PIID) of the contract(s) used.
N/A
Is this AI use case supporting a High-Impact Service Provider (HISP) public-facing service?
N/A
Does this AI use case disseminate information to the public?
N/A
How is the agency ensuring compliance with Information Quality Act guidelines, if applicable?
N/A
Does this AI use case involve personally identifiable information (PII) that is maintained by the agency?
N/A
Has the Senior Agency Official for Privacy (SAOP) assessed the privacy risks associated with this AI use case?
ongoing

Section 3: Data and Code

Do you have access to an enterprise data catalog or agency-wide data repository that enables you to identify whether or not the necessary datasets exist and are ready to develop your use case?
N/A
Describe any agency-owned data used to train, fine-tune, and/or evaluate performance of the model(s) used in this use case.
N/A
Is there available documentation for the model training and evaluation data that demonstrates the degree to which it is appropriate to be used in analysis or for making predictions?
N/A
Which, if any, demographic variables does the AI use case explicitly use as model features?
N/A
Does this project include custom-developed code?
N/A
Does the agency have access to the code associated with the AI use case?
N/A
If the code is open-source, provide the link for the publicly available source code.
N/A

Section 4: AI Enablement and Infrastructure

Does this AI use case have an associated Authority to Operate (ATO) for an AI system?
N/A
System Name: N/A
How long have you waited for the necessary developer tools to implement the AI use case?
N/A
For this AI use case, is the required IT infrastructure provisioned via a centralized intake form or process inside the agency?
N/A
Do you have a process in place to request access to computing resources for model training and development of the AI involved in this use case?
N/A
Has communication regarding the provisioning of your requested resources been timely?
N/A
How are existing data science tools, libraries, data products, and internally-developed AI infrastructure being re-used for the current AI use case?
N/A
Has information regarding the AI use case, including performance metrics and intended use of the model, been made available for review and feedback within the agency?
N/A