FSS SSJ - N3C and Data COUNTS Scientific Operations and Technical Support-Redacted.pdf

“Source Selection Information – see FAR 2.101 and 3.104”

1. Identification of the agency and contracting activity.

a. Federal agency and contracting activity.

Department of Health and Human Services (HHS) National Institutes of Health (NIH) Office of Acquisitions (OA)

b. Sponsoring organization.

National Institutes of Health (NIH) National Center for Advancing Translational Sciences (NCATS)

c. Project Officer information.

Jennie Conroy, COR III 9609 Medical Center Dr/1E606 Rockville, MD 20892 Email: Jennie.conroy@nih.gov Phone: 301-594-8165

2. Nature and/or description of the action being approved, including a description of the supplies or services required to meet the agency’s needs and the estimated value.

a. Acquisition purpose and objectives.

On August 15, 2025, the NIH Director’s Priorities https://www.nih.gov/aboutnih/nih-director/statements/advancing-nihs-mission-through-unified-strategy were published with specific reference to a Real-World Data Platform. The priority states “Real-World Data Platform: NIH is establishing a robust and secure national infrastructure to integrate and link data from various real-world sources consistent with a deep respect for individual privacy rights. This new Real-World Data Platform will provide advanced computational analysis resources for investigators across numerous research areas, including neurodevelopmental disorders and chronic diseases.” Rather than creating a new system, it has been determined to be in the best interest of the government to utilize and enhance existing infrastructure that exists within N3C and Data COUNTS.

During this transition phase, the Palantir platform that hosts the N3C was abruptly taken offline while HHS determined its acquisitions strategy for Palantir software. HHS recently executed a contract with Palantir allowing N3C to come back online publicly, reopening March 2, 2026. Based on these negotiations, N3C is now hosted within a different cloud provider with a different set of features. These changes required NCATS to pivot its focus away from the original objectives of integrating N3C and Data COUNTS.

Federal Supply Schedule (FSS) Sole Source Justification (SSJ) mailto:Jennie.conroy@nih.gov https://www.nih.gov/aboutnih/nih-director/statements/advancing-nihs-mission-through-unified-strategy https://www.nih.gov/aboutnih/nih-director/statements/advancing-nihs-mission-through-unified-strategy

The purpose of this acquisition is to provide NCATS and the community of N3C contributors and researchers continuity. The abrupt shutdown of the N3C platform was highly disruptive to researchers utilizing the N3C to fulfill commitments on grants, write their dissertations, and continue working on projects built over the past six years.

The overarching objective of this work has been reduced from fifteen objectives to nine. These core objectives of integrating N3C and Data COUNTS, while transitioning N3C to a Dynamic Workspaces architecture, ensuring operational continuity, enhancing data utility for the research community, and achieving full compliance with all CADR requirements. To accomplish this, NCATS has identified objectives across nine workstreams that will need to be run by the Awardee. Therefore, objectives are written in alignment with the workstreams:

Program Strategy, Governance, and Leadership: This objective provides for expert leadership and strategic consultation to NCATS during the bridge period. The work will focus on supporting NCATS in ideation, strategy, and planning for the future-state platform and the successful transition to a new vendor. This includes developing strategic roadmaps, advising on the technical and governance requirements for the platform recompete, and leading community and stakeholder engagement to manage expectations and ensure alignment with the new program direction.

Modular Application Development: This objective involves the design, development, testing, and documentation of a set of modular, platform-agnostic web applications. This work is focused on creating standalone user-facing tools for core N3C services, including applications for registration and data access management, a concept set explorer, and a phenotype builder. These components will be built as portable, flexible applications, designed to be deployed on any future platform and to address CADR security and access control requirements.

Platform-Agnostic Data Infrastructure: This objective focuses on the operations and maintenance of platform-agnostic data infrastructure. This work represents the comprehensive oversite of the data lifecycle, intended to be a portable, efficient, and well-documented service. This includes engineering data acquisition, data quality, linkage, and OMOP harmonization pipelines.

Scientific and Technical Research and Support: To showcase the power of the N3C model, a team of Real World Evidence (RWE) Subject Matter Experts (SMEs) is needed to create high-caliber studies, tools, and resources. This objective includes providing these scientific services and supporting other high-impact special projects that leverage the unique capabilities of the N3C platform.

N3C Education and Training: Rebuilding and advancing N3C Education to support the evolving needs of the research community as the program transitions to a new platform and Dynamic Workspace model. It includes providing pedagogical leadership, recovering and redesigning legacy training materials, and developing a scalable, platform-agnostic education infrastructure. Core activities involve creating new registration processes, training tools, and a synthetic dataset; integrating updated resources such as data visualization and phenotype tools; and implementing modern content and learning management systems. The effort ensures that educational materials and training programs remain aligned with NCATS priorities, are easily accessible, and effectively equip users to leverage the new N3C environment.

Enhance Capabilities of the Data COUNTS Initiative: In partnership with data contributing healthcare organizations, enhance the current capabilities of the Data COUNTS initiative to facilitate delivery of EHR data to NIH.

Enhance Coordination of the Data COUNTS Ecosystem: Provide coordination and engagement of the Data COUNTS partner health institutions with NIH.

Facilitate Prize Competitions: Facilitating prize competitions require a group of SMEs to be able to manage, evaluate, and give recommendations on targeted public health questions that require a high level of methodological rigor to answer.

b. Project background.

The National Institutes of Health (NIH) is the Nation's leading Medical Research Agency and the primary Federal Agency whose mission is to seek fundamental knowledge about the nature and behavior of living systems and apply that knowledge to enhance health, lengthen life, and reduce illness and disability by supporting and making medical discoveries. The National Center for Advancing Translational Science (NCATS) at the NIH focuses on all aspects of the translation of research with an innovative pipeline of treatment discoveries for all diseases.

NCATS' mission is to improve health through smarter science that results in more treatments for all people more quickly.

The National Clinical Cohort Collaborative (N3C) began as a collaborative vision for a national data resource that turned real-world evidence into the knowledge urgently needed to address the pandemic. It systematically collected data derived from electronic health records (EHRs) and other important repositories from different institutions and harmonized these data in a centralized resource available for collaborative research. The program has since expanded beyond its initial narrow focus to be a resource ready to leverage real world evidence based data to answer questions about any disease.

Building upon this successful foundation, N3C has transitioned to be composed of a set of robust, scalable, and secure platform-agnostic components and data infrastructure. These include portable data pipelines, reusable knowledge objects (such as phenotypes and concept sets), and modular web applications (such as for data access management). This approach ensures all components are designed for compliance with stringent government requirements for Controlled-Access Data Repositories (CADR). This work also focuses on preserving the core principles of centralized data harmonization and a secure analytical environment while supporting capabilities that grant institutions granular control over the use of their data.

The Data COUNTS initiative serves as a foundational EHR data collection engine that ensures full provenance, traceability, and minimal data loss from health systems. Data COUNTS provides federated collection of EHR and other clinical data, as well as data and transmission architecture based on open-industry data and interoperability standards. It supports a broad array of use cases across HHS with appropriate adherence to data privacy, security, and data access policies.

Together with the Data Collect Once Use Numerous TimeS (COUNTS) Initiative, N3C forms the foundational infrastructure of the NIH wide real-world evidence-based research. The infrastructure will integrate vast amounts of real-world data from EHRs, insurance claims, pharmacies, and other sources. Building on prior NIH-funded efforts, the combined N3C and Data COUNTS efforts will eliminate redundancies from data collection, linkage, and analysis infrastructures, and will dramatically reduce administrative overhead by relying on a unified set of data use and governance agreements. It will provide direct access to advanced computational resources to support cutting-edge artificial intelligence/machine learning (AI/ML) modeling, petabyte-scale storage/compute, and high-throughput analytics.

In FY 2024 the scientific and technical support services for the N3C and Data COUNTS were procured together on GS35F023GA-75N95023A00001 BO 14 National Clinical Data Collaborative COUNTS (NacDacC). Procuring these services through one vendor on one task order has allowed the NCATS and ODSS to begin working together and creating efficiencies across N3C and Data COUNTS. In FY 2025 a 6-month sole source logical follow-on contract (GS-35F- 023GA/75N95025F00079) was awarded under FAR Subpart 8.405-6(a)(1)(i)(C).

By continuing under one unified task, NCATS and ODSS could economically and efficiently make changes to the N3C and Data COUNTS programs to allow them to fulfil the vision of the NIH Director’s Real- World Data Platform priority.

During this transition phase, the Palantir platform that hosts the N3C was abruptly taken offline while HHS determined its acquisitions strategy for Palantir software. HHS recently executed a contract with Palantir allowing N3C to come back online publicly, reopening March 2, 2026. Based on these negotiations, N3C is now hosted within a different cloud provider with a different set of features. These changes required NCATS to pivot its focus away from the original objectives of integrating N3C and Data COUNTS. A sole-source award to the existing vendor through the same GSA contract is needed to allow time to accomplish the initial integration objectives while also rebuilding N3C based on HHS’s new requirements for Palantir environments. Competing the requirement now would add unacceptable additional cost, delay, complexity, or uncertainty of execution.

3. Description of the supplies or services required to meet the agency’s needs (including the estimated value).

a. Project title.

N3C and Data COUNTS Scientific Operations and Technical Support

b. Project description.

The overarching objective of this work is integrating N3C and Data COUNTS, while transitioning N3C to a Dynamic Workspaces architecture, ensuring operational continuity, enhancing data utility for the research community, and achieving full compliance with all CADR requirements

Requirement type.

Research & development (R&D) R & D support services Support services (non-R&D) Supplies/equipment ☒ Information technology (IT) Construction Architect-engineer (A & E) services Design-build Other (specify):

• Type of action.

New requirement Follow-on to the same services ☒ Other (specify): Only one vendor available

• Proposed contract/order type.

☒ Firm-fixed-price Other fixed-price (specify, e.g., fixed-price award-fee, fixed-price incentive-fee):

Cost-plus-fixed-fee Other cost reimbursement (specify, e.g., cost-plus-award-fee, cost-plus-incentive-fee):

Time and materials Indefinite delivery (specify whether indefinite quantity, definite quantity, or requirements):

Other (specify):

• Acquisition identification number. The Contracting Officer will identify a new solicitation and award number.

a. Total estimated dollar value and performance/delivery period.

The Independent Government Cost Estimate (IGCE) is for a potential period of performance of 9 months, from 03/29/2026 – 12/31/2026; the total potential value is $9,820,652.70

4. Authority and supporting rationale (see GSAR 538.7104-3(b)(1)) and, if applicable, a demonstration of the proposed contractor’s unique qualifications to provide the required supply or service, Identification of the statutory authority permitting other than full and open competition.

a. Acquisition Authority

☒ This acquisition is conducted under the authority of the Multiple Award Schedule Program. Consideration of schedule contractors will be restricted to fewer than the number required by GSAR 538.7104, as follows:

☐GSAR 538.7104-3(b)(i), need is of such unusual urgency that following the procedures would result in unacceptable delays in fulfilling that need.

☒ GSAR 538.7104-3(b)(ii), only one source is capable of providing the products, services, or solution required at the level of quality required because the products, services, or solutions are unique or highly specialized.

The 9-month period of performance is being sought to provide NIH leadership the time required to reestablish N3C in full CADR compliance while deciding the path forward for consolidation of real world data resources. NIH Leadership is pursuing alignment of resources in support of the NIH Director’s announced priority of the NIH Real World Data Platform.

N3C has a very large ecosystem that needs continued support, oversight, advocacy, and operational leadership, to facilitate a smooth and orderly transition to the new requirement. To support the extensive amount of governance required for the transition to the Dynamic Workspace model and to ensure full compliance with new data repository standards, the below aims are needed:

• Lead the development and revision and integration with Data COUNTS of a comprehensive agreement framework for the transfer, use, and linkage of real-world data across the CTSA and other data partners that supports the disease-agnostic data contribution model and other Data COUNTS use cases.

• Work with NCATS stakeholders to revise the agreements and documents to align with all new Controlled-Access Data Repositories (CADR) requirements, including those for user verification and institutional attestations, and prepare for re-execution with all participating institutions.

• Develop, document, and test the new Data Access Committee (DAC) review process for Data Access Requests (DARs), ensuring the process evaluates feasibility, compliance, and alignment with N3C goals.

• Design and formalize the institutional review workflow, including the secure dashboard-based notification system and the "opt-out" mechanism that preserves institutional authority over data use.

• Support the creation and expansion of governance policies and procedures to support the overall governance of N3C and the secure management of dynamic Workspaces. This includes establishing policies for:

a) The sharing and reuse of phenotypes as knowledge objects.

b) The limited embargo option for newly submitted phenotypes.

c) Defining access tiers (e.g., de-identified vs. limited data) and associated researcher eligibility requirements.

• Establish and document procedures for CADR-mandated user compliance, including requirements that DARs be submitted by permanent, senior-level employees and certified by an Institutional Signing Official.

• Implement and maintain the fully revised Governance Policies and Procedures for the overall N3C and Data COUNTS programs.

• Serve on the N3C Download Committees and perform regular review of download requests.

• Provide overall technical leadership across all N3C workstreams.

• Coordinate with NCATS Project Managers, Leadership, and Scientists to identify and manage subcontracts for key SMEs and Teams instrumental in the execution of N3C and Data COUNTS strategy, planning, and operations.

• Manage, coordinate, and communicate between these individuals/teams and NCATS to ensure the needs of NCATS are met in a timely and efficient manner.

• Work with intramural and extramural stakeholders to communicate the revised and unified vision of the N3C Dynamic Workspace model.

• Maintain and run the N3C Publication Committee, adapting its procedures as needed for research originating from dynamic Workspaces.

• Provide ongoing support, communications, content, and leadership for all Domain Teams and the Logic Liaisons Group.

• Given the complexity and diversity of the data contributed by various clinical sites to N3C, this effort focuses on ensuring that all data is accurately ingested, harmonized, and maintained to support the Dynamic Workspace model. The work involves adapting data acquisition pipelines to support a unified, disease agnostic data contribution approach and ensuring that this broadly applicable dataset can support a wide variety of research questions. It also includes facilitating secure linkage of external datasets using privacy-preserving methods, the development of reusable phenotypes, and vigilant, continuous monitoring of data quality to give researchers transparency into potential biases or limitations.

Recompeting at this time when the N3C has just been reopened in new infrastructure would present unrealistic requirements to the vendor community that may mislead vendors on the validity and value of the ‘business opportunity’ with NIH. Secondly, transitioning to a new vendor at this time will only add to the disruption that the N3C community has experienced over the last 6 months with the shutdown of the platform.

☐ GSAR 538.7104-3(b)(iii), The order should be issued on a sole source basis in the interest of economy and efficiency because it is a logical follow-on to an FSS order already issued on a competitive basis.

☐ GSAR 538.7104-3(b)(iv), necessary to place the order with a particular FSS contractor to satisfy a minimum guarantee established in the FSS BPA.

☐ GSAR 538.7104-3(b)(v), law expressly authorizes or requires that the purchase be made from a specified source.

☐ This acquisition is conducted under the authority of the Multiple Award Schedule Program. Consideration of schedule contractors will be restricted only to the item peculiar to one manufacturer as provided in GSAR 538.7104-4 Items peculiar to one manufacturer.

b. Demonstration that the proposed contractor(s) unique qualifications or the nature of the acquisition requires use of the authority cited.

• Name and address of the proposed contractor(s).

Axle Informatics, LLC

6116 EXECUTIVE BLVD

STE 400

NORTH BETHESDA, MD 20852-4931

• Nature of the acquisition and proposed unique qualifications of the contractor(s).

Axle Informatics brings a team with proven, cohesive partnerships to the N3C program, grounded in their successful execution to date of the existing N3C Dynamic Workspaces contract. Through the successful delivery of the N3C Dynamic Workspace framework and the Data COUNTS initiative, Axle Informatics, with its subcontractors diConsentes and Fleet Health have developed highly specialized, complementary capabilities that directly mitigate the risks of large-scale translational science and decentralized clinical data integration. Further, these teams represent a leadership who deeply understands the complexities of national scale federally controlled real world data platforms in a way that no other contractor can replicate.

Axle Informatics serves as the technical subject matter experts and primary systems integrator for this effort. Axle’s team has helped to successfully ideate, build the strategy for, and engineer/implement the overarching N3C Dynamic Workspaces framework, designing secure, logically distinct dynamic workspaces alongside the individual and institutional registration system to seamlessly handle end-to-end data access requests, legal agreement management, role assignment and permissions, as well as study design and implementation. Their engineering team possesses deep, hands-on expertise in the processing pipelines and management and security processes to ensure that EHR data from 100s of sites from across the country (in a variety of Common Data Models, including PCORnet, OMOP, TriNetX, and ACT) can be processed securely and scalably. Axle goes beyond basic ingestion; they successfully executed advanced harmonization efforts to bring disparate sources into OMOP version 5.4, managing complex unit conversions and macrovisit mappings while actively standardizing, converting, and integrating critical external datasets like CMS claims, SEER, and national mortality data. Each clinical site has a bespoke set of data engineering concerns, resulting in Axle’s deep expertise being unique in its ability to understand, manage, and update these pipelines without significant data latency or platform downtime.

In complex programs like N3C, it is insufficient for a vendor to just have engineering acumen for the program to move forward. Intricate understanding of the overlaps between regulatory (Institutional Review Boards), policy/legal (System of Record Notices (SORN), Federal Advisory Committee Act (FACA) management, Health Information Portability and Accountability Act (HIPAA), Common Rule, etc.) and cyber security (Controlled Access Data Repository (CADR) rules, Privacy Impact Assessments (PIA), System Security Plans (SSPs), Authorization to Operate (ATO), etc.) are needed to remain both compliant with the law but also secure. For example, a detailed understanding of how implications for CADR intersect with FACA committee roles/permissions is necessary to implement a CADR compliant registration system that is also legally compliant. Axle’s team has a deep understanding of all these aspects, helping to advise and pre-emptively negotiate and implement solutions for each of these intersectional issues. This makes Axle uniquely qualified to complete the originally envisioned integration work and get the project to a transferrable state where it can be competed to build to the national scale.

Further, while the above skills are necessary they are not sufficient to successfully build the next phase of N3C and Data COUNTS. Deep community relationships, understanding of training and education needs, and trust with both researchers and data providers is needed. N3C relies on voluntary community submission of data and a large part of that is trust. Making a switch from Axle during the current transitional period of the platform would undermine the trust of the community further, disrupting long standing relationships, and also reset community relations. For N3C to grow in this next phase these relationships cannot be stressed more, and therefore Axle, having already established and built all of these relationships is the only vendor who can support the completion of the transition. This also extends to Axle deeply understanding the intricate systems of governance and approval processes both on the community and the government side. To switch Axle out at this point would require months of recalibration and reduced output that would be detrimental to program success in this critical stage. This 9-month period will allow for a more appropriate transition at more stable time in the program’s evolution.

Complementing Axle’s deep platform engineering, regulatory, policy/legal, cybersecurity, community, and process expertise diConsentes provides the critical ecosystem coordination and site engagement required to operationalize decentralized data networks in hospital systems that do not have the engineering expertise to send their own data in a high-quality manner. This skillset is unique as implementing systems at sites requires trust/relationships between sites and the Data COUNTS program, deep security understanding at each sites, and deep understanding of the legal and policy agreements needed to effectualize those relationships.

Fleet Health completes the team by delivering the proprietary, privacy-preserving edge technologies essential for secure upstream data extraction. Their delivery on the previous contract demonstrated an exceptional ability to deploy their Edge Node software modules directly within partner hospital IT environments without disrupting local operations and remaining compliant with each sites’ bespoke security requirements. Fleet Health’s unique technical qualification lies in their highly configurable data handling. They enabled partner sites to extract and share datasets in both de-identified and identifiable formats based strictly on mutual agreements, all while maintaining rigorous, individual-level tracking of consent, provenance, and permissions. By establishing secure connections between participating networks and the honest broker enclave, Fleet Health established the technical strategy and harmonization standards that make secure, distributed health data querying possible at a national scale.

5. Determination by the Contracting Officer that the order represents a fair and reasonable price consistent with GSAR 538.7102-2(d)(2) and 538.7104- 2(a)(3).

GSA Multiple Award Schedule (MAS) has already determined the prices of supplies, fixed-price services, and rates for services offered at hourly rates, to be fair and reasonable under its MAS contracts. The Contracting Officer will determine both the best value to the Government and whether the price is fair and reasonable based on a comparison of proposed prices to the independent government cost estimate (IGCE) and historical prices paid, as provided in the current contract. The basis of estimate for this follow-on contract was established using the current contract which was awarded competitively.

6. Description of the market research conducted among schedule holders and the results, or a statement of the reasons market research was not conducted.

Reviewed other available GWAC/IDIQ contracts that provide similar services such as the NHLBI ITAC Agile Development, Data Science, and Strategy BPA; NCI IT BPA, SOAR, GSA MAS, and NITAAC. GSA MAS was determined to be the best fit contract.

7. Any other facts supporting the use of other than full and open competition.

In projecting NCATS acquisition needs, we examined the relationship to the prior order and considered the minimum acceptable period necessary to meet mission requirements. 9 months was determined because it provides time needed to encourage and solicit competition for a future requirement without critically disrupting services or relationships with data contributing institutions.

8. Statement of the actions, if any, the agency may take to remove or overcome any barriers that led to the restricted consideration before any subsequent acquisition for the supplies or services is made.

a. Removal of barriers to competition.

N3C was brought back online March 2, 2026, this milestone allowing NCATS to pivot back to its original goals of integrating N3C and Data COUNTS. The programs can now move towards a logical point for competition of the services. We anticipate future needs for similar services. We plan to continue to examine ways to increase competition, while balancing small business goals, and category management.

b. Listing of sources, if any, that expressed an interest, in writing, in the acquisition.

No sources expressed an interest for this continued service.

9. Ordering Activity Certification

Program office certification.

This is to certify that the portions of this justification that have been developed by the undersigned program office personnel, including supporting information and/or data verifying the Government’s minimum needs, schedule requirements and other rationale for other than full and open competition, are accurate and complete.

Official Name & Title Signature

Project Officer Jennie Conroy, Program Director

Project Officer’s

Immediate Supervisor

Michael Kurilla, Director, Division of Clinical Innovation

Head of the Sponsoring

Program Office

Joni Rutter, Director, NCATS

Contracting Officer certification.

I hereby determine that the anticipated price/cost for this contract action will be fair and reasonable and certify that this justification is accurate and complete to the best of my knowledge. I approve this sole source justification subject to availability of funds, and provided that the services and supplies herein described have otherwise been authorized for acquisition.

Contracting Officer

For Shirley Ruiz-Lundgren

OPDIV Competition Advocate Approval (required for proposed contract over $900,000 but not exceeding $20 million value calculated including all options):

I have reviewed this justification and find that it adequately supports an exception to fair opportunity.

OPDIV Competition Advocate

Dr. Kathryn Partin, Ph.D.

Director of Research Integrity, National Institutes of Health

OPDIV HCA Approval (required for proposed contract over $900,000 but not exceeding $20 million value calculated including all options):

Head of Contracting For Olga M. Acosta Activity (HCA) Contracting Activity Head of the Contracting Activity, Director of Office of Acquisition and Logistics Management, OM, NIH