Attachment 1 informatics_datavisualization SOW2-18.docx

Statement of Work- for informatics, epidemiologic, and data programming services to support the Division of Population Health and Data Science at the Massachusetts Veterans Epidemiology Research and Informatics Center (MAVERIC)

1.0 Description:

1.1 The Contractor shall provide informatics, epidemiologic, and data programming expertise to support the Division of Population Health and Data Science at the Massachusetts Veterans Epidemiology Research and Informatics Center (MAVERIC) at the Boston VA Healthcare system.

1.2 The mission of the Division of Population Health and Data Science is to enhance VA healthcare delivery by promoting VA-based population research by developing and applying bioinformatics approaches for phenotyping and analysis of high-dimensional datasets directly translatable to clinical research studies and clinical care.

1.3 Due to the tremendous amount and complexity of clinical data in the VA, new and innovative methodologies and analytical pipelines are needed to capture, extract, and understand meaningful and valuable data for clinical research and clinical care.

2.0 Scope: To achieve the aforementioned mission, VA Boston Health Care System requires services and support to develop novel and comprehensive backend data formatting and processing pipelines for visualization and interactive web application tools. The Contractor shall provide specialized bioinformatics expertise in machine learning and implementation that requires an understanding of the complexity of VA’s large Electronic Health Record (EHR) data and leveraged to provide expert services on the design and development of data visualization tools These tools will be integrated to VA’s knowledge platform in support of VA EHR data optimization for clinical research at large. All work will be done on VA systems and software already owned by the VA. The Contractor shall:

2.1 Provide expertise in informatics and computer programming to expand the network of data information integration (knowledge network).

2.2 Provide demonstration of the expanded knowledge network and create detailed documentation of the analytical pipeline developed to create the knowledge network.

2.3 Utilize all available data including narrative concepts and other omics data.

2.4 Provide novel data models to VA team as requested (determined by VA team’s priority and according to VA team’s planned milestones and timelines) to enhance the process of developing EHR based computable phenotype algorithms based on user-submitted summary statistics.

2.5 Generate complex data models that can be applied in the interactive visualization of the data and output.

2.6 Upon integration and/or successfully operationalizing in the pipelines on VA data, the Contractor should provide detailed documentation to VA team of the processes and operational instructions for the pipeline used. The documentation will facilitate maintenance and long-term success for VA team to continue to implement.

2.7 Develop initial data models for interactive interface for the VA team to evaluate its utility for the clinical dashboard that enables clinicians to visualize relevant medical history to make informed decisions. Iteratively improve models and interface based on VA feedback until prototype established is acceptable to VA team as determined through meetings and mutual agreement.

2.8 Perform customized quality control based on the business requirements from the VA team.

The VA team will require from the Contractor’s domain expertise in EHR complexities and the ability to tailor the process pipelines as this is a critical part of the development.

2.9 All work will be done on VA systems and software already owned by the VA.

2.10 Expected Deliverables/Milestones:

The annual deliverables and milestones will be developed by the VA team leads according to VA team’s annual goals and objectives. It will follow same timeline as VA team's annual review cycle. During the year, we will have weekly meetings to discuss updates, quarterly meeting to evaluate our progress and timeline followed by an annual performance evaluation to summarize overall productivity into a report. The Contractors' work will be assessed based on their timeliness, completeness, and quality of the work by the VA team leads as agreed upon by both parties. The Contractor should invoice the VA on a monthly basis according to the work completed.

2.10.1 Year 1:

2.10.1.1 Contractor will create data models for deployment of large knowledge network visualization, including priority data domain of narrative concepts.

2.10.1.1.1 Contractor will generate user guide and or standard operating procedure for applying data model in specified VA’s use cases.

2.10.1.1.2 Contractor will create data programming scripts into generalizable summary modules and packages and provide documentation for VA users to use the resources created upon successful implementation.

2.10.1.1.2.1 Provide assistance to VA team as scripts are deployed and utilized over time

2.10.2 Year 2

2.10.2.1 Contractor will develop initial elastic search engine allowing semantic searches for disease phenotypes.

2.10.2.1.1 Contractor will develop a scalable data model for a knowledge network including genomic features; iteratively improve the model based on VA user feedback, testing, and priorities.

2.10.2.1.2 Contractor will develop a pilot tool for online feature selection and phenotyping.

2.10.2.1.3 Contractor will create data programming scripts into generalizable summary modules and packages and provide documentation for VA researchers to use the resources created upon successful implementation.

2.10.2.1.3.1 Documentation to include source code documentation, description of algorithms, logic, and resources for using the scripts

2.10.2.1.3.2 Documentation to be accessible to VA researchers on a central location, either Git, CIPHER, or similar platform

2.10.3 Year 3

2.10.3.1 Contractor will development of interactive data framework interface for the clinical dashboard that enables clinicians to visualize relevant medical history for a test case.

2.10.3.1.1 Contractor will deploy (and make continuous improvements based on VA priorities and domains) a knowledge network including genomic features

2.10.3.1.2 Contractor will deploy online feature selection and phenotyping tools for priority phenotyping methods and to address new VA EHR challenges

2.10.3.1.2.1 Contractor will make data programming scripts into generalizable summary modules and packages and providing documentation for VA users to use the resources created upon successful implementation.

2.10.3.1.2.1.1 Documentation to include source code documentation, description of algorithms, logic, and resources for using the scripts

2.10.3.1.2.1.2 Documentation to be accessible to VA researchers on a central location, either Git, CIPHER, or similar platform

2.10.4 Year 4

2.10.4.1 Deploy interactive interface to support the clinical dashboard that enables clinicians to visualize relevant medical history for a test case.

2.10.4.2 Develop knowledge network including detailed relationships between entities.

2.10.4.3 Maintain visualization tools and provide updates as necessary. Ensure tool is being updated for user feedback and update source code when applicable due to environment updates, changes, or improvements.

2.10.4.4 Make data programming scripts into generalizable summary modules and packages and providing documentation for VA users to use the resources created.

2.10.4.4.1 Documentation to include source code documentation, description of algorithms, logic, and resources for using the scripts

2.10.4.4.2 Documentation to be accessible to VA researchers on a central location, either Git, CIPHER, or similar platform

2.10.5 Year 5

2.10.5.1 Deploy and refine of interactive interface to support the clinical dashboard that enables clinicians to visualize relevant medical history for necessary test cases and update to incorporate feedback from physicians.

2.10.5.2 Deployment and refinement of knowledge network including detailed relationships between entities.

2.10.5.3 Maintenance of visualization software and provide updates as necessary.

2.10.5.3.1 Ensure tool is being updated for user feedback and update source code when applicable due to environment updates, changes, or improvements.

2.10.5.4 Make programming language packages and provide documentation for VA users to use the resources created upon successful implementation.

2.11 Performance monitoring

The Government shall ensure productivity and progress to achieve expected deliverables/milestones. The Contractor and VA team will meet with the Contractors weekly, both via online meetings and once a month in-person to review progress. VA team will document quarterly and annual goals, and through reports will document the progress and evaluate productivity and timeline based on the planned milestones. The Contractor will be expected to produce updates monthly for invoicing/progress and evaluation and quarterly for the quarterly deliverables and timeline updates each quarter.

2.11.1 The monthly and quarterly reports shall be submitted to the CORs and contain:

2.11.1.1 Tasks/Projects assigned and a narrative summary of status of those tasks and projects. The summary shall explain which projects were completed and those still in progress. For projects in progress, the reports shall provide summary of progress and estimated completion dates. Expectation for narrative is no more than a paragraph for each task.

2.11.1.2 Hours worked by task/project for each labor category.

2.12 Presentations and Publications

2.12.1 Resulting work products and knowledge will be disseminated through presentations at relevant conferences and meetings specified by the VA team milestones. Up to two Contractors will participate in either team or individual presentations by attending relevant domain meetings, such as the American Medical Informatics Association (AMIA) annual meeting and the American Society of Human Genetics (ASHG) meetings.

2.12.2 Using novel methodologies and data use cases developed and utilized to achieve milestones, the Contractor will participate in generating manuscripts for publications as part of knowledge dissemination effort under current scope.

3.0 Contractor qualifications:

3.1 Data Visualization Specialists or similar category shall have:

3.1.1 At least a Master's Degree in statistics, data science, computer science, informatics, or other health data-related field

3.1.2 Three plus years of proficient knowledge of statistical analysis and visualization of clinical data

3.1.3 Three plus years of experience with navigating, interpreting, and visualizing large-scale biomedical data for research

3.1.4 Experience and expertise required include:

3.1.4.1 Visualization packages and software

3.1.4.2 Proficient in R Shiny, Python

3.1.4.3 Knowledge of JAVA script

3.2 Statistical Software Programmers shall have:

3.2.1 At least a Master's Degree in statistics, data science, computer science, or informatics

3.2.2 Two years of statistical programming skills using R and R shinny and experience in creating R packages

3.2.3 Knowledge of Python and C++

3.2.4 Two plus years experiences with statistical analysis of large-scale research data and machine learning algorithms

3.3 Contractor shall also have experience with the following:

3.3.1 Experience with medical ontologies and organizing/mapping Electronic Health Records

3.3.2 Experience with formation of knowledge networks and complex analysis and visualization of EHR based data.

3.3.3 Experience with development of novel data models and phenotyping methods

3.3.4 Experience with grant funded scientific research projects to support visualization of clinical research findings

3.3.5 Medical Research Tool development

4.0 Other requirements as determined by the VA team as the contract progresses.

4.1 Onboarding and IT access

4.1.1 All Contractors will be required to undergo fingerprinting, background checks, and onboarding and adhere to the same rules and regulations as new employees to VA Boston.

4.1.2 All Contractors will require PIV cards to access the VA systems. This will require that they participate in all required training with regard to security, privacy, rules of behavior, and HIPAA rules and regulations

4.1.3 All Contractors are allowed to work remotely and will be provided remote access through Citrix or Azure as required by Information Security. They will receive remote access approval but still must use their PIV card to gain access to VA systems.

4.2 RECORDS MANAGEMENT OBLIGATIONS

A. Applicability This clause applies to all Contractors whose employees create, work with, or otherwise handle Federal records, as defined in Section B, regardless of the medium in which the record exists.

B. Definitions “Federal record” as defined in 44 U.S.C. § 3301, includes all recorded information, regardless of form or characteristics, made or received by a Federal agency under Federal law or in connection with the transaction of public business and preserved or appropriate for preservation by that agency or its legitimate successor as evidence of the organization, functions, policies, decisions, procedures, operations, or other activities of the United States Government or because of the informational value of data in them.

The term Federal record:

1. includes VHA records.

2. does not include personal materials.

3. applies to records created, received, or maintained by Contractors pursuant to their VHA contract.

4. may include deliverables and documentation associated with deliverables.

C. Requirements

1. Contractor shall comply with all applicable records management laws and regulations, as well as National Archives and Records Administration (NARA) records policies, including but not limited to the Federal Records Act (44 U.S.C. chs. 21, 29, 31, 33), NARA regulations at 36 CFR Chapter XII Subchapter B, and those policies associated with the safeguarding of records covered by the Privacy Act of 1974 (5 U.S.C. 552a). These policies include the preservation of all records, regardless of form or characteristics, mode of transmission, or state of completion.

2. In accordance with 36 CFR 1222.32, all data created for Government use and delivered to, or falling under the legal control of, the Government are Federal records subject to the provisions of 44 U.S.C. chapters 21, 29, 31, and 33, the Freedom of Information Act (FOIA) (5 U.S.C. 552), as amended, and the Privacy Act of 1974 (5 U.S.C. 552a), as amended and must be managed and scheduled for disposition only as permitted by statute or regulation.

3. In accordance with 36 CFR 1222.32, the Contractor shall maintain all records created for Government use or created in the course of performing the contract and/or delivered to, or under the legal control of the Government and must be managed in accordance with Federal law. Electronic records and associated metadata must be accompanied by sufficient technical documentation to permit understanding and use of the records and data.

4. VHA and its Contractors are responsible for preventing the alienation or unauthorized destruction of records, including all forms of mutilation. Records may not be removed from the legal custody of VHA or destroyed except in accordance with the provisions of the agency records schedules and with the written concurrence of the Head of the Contracting Activity. Willful and unlawful destruction, damage, or alienation of Federal records is subject to the fines and penalties imposed by 18 U.S.C. 2701. In the event of any unlawful or accidental removal, defacing, alteration, or destruction of records, the Contractor must report to VHA. The agency must report promptly to NARA in accordance with 36 CFR 1230.

5. The Contractor shall immediately notify the appropriate Contracting Officer upon discovery of any inadvertent or unauthorized disclosures of information, data, documentary materials, records, or equipment. Disclosure of non-public information is limited to authorized personnel with a need-to-know as described in the [contract vehicle]. The Contractor shall ensure that the appropriate personnel, administrative, technical, and physical safeguards are established to ensure the security and confidentiality of this information, data, documentary material, records, and/or equipment is properly protected. The Contractor shall not remove material from Government facilities or systems, or facilities or systems operated or maintained on the Government’s behalf, without the express written permission of the Head of the Contracting Activity. When information, data, documentary material, records, and/or equipment is no longer required, it shall be returned to VHA control or the Contractor must hold it until otherwise directed. Items returned to the Government shall be hand-carried, mailed, emailed, or securely electronically transmitted to the Contracting Officer or address prescribed in the [contract vehicle]. Destruction of records is EXPRESSLY PROHIBITED unless in accordance with Paragraph (4).

6. The Contractor is required to obtain the Contracting Officer's approval prior to engaging in any contractual relationship (sub-Contractor) in support of this contract requiring the disclosure of information, documentary material, and/or records generated under, or relating to, contracts. The Contractor (and any sub-Contractor) is required to abide by Government and VHA guidance for protecting sensitive, proprietary information, classified, and controlled unclassified information.

7. The Contractor shall only use Government IT equipment for purposes specifically tied to or authorized by the contract and in accordance with VHA policy.

8. The Contractor shall not create or maintain any records containing any non-public VHA information that is not specifically tied to or authorized by the contract.

9. The Contractor shall not retain, use, sell, or disseminate copies of any deliverable that contains information covered by the Privacy Act of 1974 or that which is generally protected from public disclosure by an exemption to the Freedom of Information Act.

10. The VHA owns the rights to all data and records produced as part of this contract. All deliverables under the contract are the property of the U.S. Government for which VHA shall have unlimited rights to use, dispose of, or disclose such data contained therein as it determines to be in the public interest. Any Contractor rights in the data or deliverables must be identified as required by FAR 52.227-11 through FAR 52.227-20.

11. Training. All Contractor employees assigned to this contract who create, work with or otherwise handle records are required to take VHA-provided records management training. The Contractor is responsible for confirming training has been completed according to agency policies, including initial training and any annual or refresher training.

** VHA training for Contractors is available in Talent Management System (TMS):

Records Management for Records Officers and Liaisons, Item #3873736

D. Flow down of requirements to subcontractors

1. The Contractor shall incorporate the substance of this clause, its terms, and requirements including this paragraph, in all subcontracts under this [contract vehicle], and require written subcontractor acknowledgment of same.

2. Violation by a subcontractor of any provision set forth in this clause will be attributed to the Contractor.

4.3 Security:

4.3.1 *"The A&A requirements do not apply, and that a Security Accreditation Package is not required, except for the understanding of their participation in IT security requirements for A&A of the VA system to which they connect. The Contractor shall understands their participation in IT security requirements for A&A of the VA system to which they connect.

4.3.2 The Contractor shall understand and implement the IT security requirements for system interconnection documents required per the Memorandum of Understanding or Interconnection Agreement (MOU-ISA). The standard operating procedure (SOP) and a template for a MOU-ISA are located on the Enterprise CyberSecurity Support Division and can be provided to the Contractor.

4.4 Travel

4.4.1 Before any travel is started:

4.4.1.1 The Contractor shall provide an estimated travel itinerary and costs to COR for approval of the presentation of VA research done during the course of the contract at conferences prior to travel. At no time shall a Contractor travel without prior COR approval. The COR shall provide approval/disapproval of all travel within one week of receipt. Any travel that does not have preauthorization will not be paid.

4.4.1.2 All travel costs shall follow internal VA policy and Joint Travel Regulations. Any travel that does not follow these policies and regulations will not be paid.

4.4.1.2 Both the Contractor and COR are required to ensure there is sufficient funding for travel prior to travel start. Travel without proper funding may not be paid.

4.5 Publication Cost: the cost of publishing study/project results in major scientific journals. The Contractor must submit a request for approval through the COR for each publication. The publications must only be for collaborative VA-funded research, and the VA must be named first, giving the VA credit for the research. All publication costs cannot exceed a maximum of $7,000 per year and shall be funded prior to approval. All parties will follow VA policy and MAVERIC procedures with regard to the publication of VA research.

4.6 Task orders

4.6.1 Task Orders must contain the following:

4.6.1.1 Contract number

4.6.1.2 Period of Performance

4.6.1.3 Funded 2237 Purchase Order

4.7 Estimates: