Parkinson’s Disease Knowledge Platform Overview for Users

Sharing PD data with the scientific community is a key objective of the AMP PD program.  The AMP PD program shares data with all interested, qualified, and approved investigators, to encourage academic productivity. In preparation for this level of data sharing, all cohort studies included in the AMP PD program incorporate broad data sharing language within subject consent documents and receive Institutional Review Board approval for their studies.

AMP PD data is hosted in open or controlled access environments.

• Open access data is defined as aggregate data available on the public site, or through limited queries of aggregate data on the public site. This access does not require creating an account.
• Controlled access data is defined as de-identified individual level data files within the AMP PD and Global Parkinson’s Genetics Program (GP2) Knowledge Platforms. Controlled access requires creating an account for access, acceptance of the Accelerating Medicines Partnership® Parkinson’s Disease (AMP® PD) Data Use Agreement, henceforth the ‘Data Use Agreement’, by appropriate signing authorities, 2-factor authentication of the account requestor, and approval of account requests by the Access and Compliance Team.

Registering for AMP PD Knowledge Platform Access

AMP PD Knowledge Platform users will have the opportunity to register for the following levels of data access:

• Tier 1 - Limited dataset access to the individual-level clinical data, omics summary results, and related meta data will be granted through the completion of an online registration form, electronic acceptance of the Data Use Agreement, and verification of the email address.
• Tier 2 - Full dataset access to the individual-level clinical and omics data as well as meta data will be granted through the completion of an online registration form, signature on the  Data Use Agreement with the individual requestor’s Authorized Institutional Business Official signature, and verification of the email address.

Once registered, AMP PD Knowledge Platform users will have access to:

• AMP PD Unified Cohort data and Federated GP2 Cohort Data, learn more here.
• AMP PD Data Explorer to visualize data and create cohorts.
• AMP PD Terra AMP PD Researcher Workbench via the Terra platform. Please note, to use the AMP PD Researcher Workbench users are required to register with a researcher's Google account with Terra. By registering in Terra, users are added to a special Google Group created for that user called a Proxy Group. A Proxy Group is specific to an individual user and contains both the user's Google address as well as one or more Google service accounts.

Registration Process and Application Tracking

A web-based, semi-automated Data Sharing Application and Tracking system will be instituted to manage the data requests. Users will complete a web-based application form and a Data Use Agreement. When the application is received, the prospective user will be required to verify contact information through 2-factor authentication prior to data access approval. Once approved, the applicant will be given permission to access the data through the AMP PD Knowledge Platform.

Applicants will be required to provide the following information:

• Name
• Address and Contact information
• Academic Affiliation (if any) or Institution/Company Name
• Proposed analyses with a named lead investigator on each analysis
• Certification to each point of the Data Use Agreement.

To comply with local laws and regulations around data access from locations where data was generated, the Access and Compliance Team will on occasion be required to share the user information in bold with the principal investigators of those studies that generated the data.  

Applicants will receive annual requests to update their registration information. These requests will also solicit responses to the following queries about manuscripts:

• Title of each manuscript in development
• Lead (or senior) author of each manuscript in development and contact information for that author
• Status of each manuscript in development (In development, In submission, In press/published)
• Citation of each published manuscript
• Upload a file of each published manuscript

Non-compliance with the required updates will jeopardize further access to the AMP PD Knowledge Platform and AMP PD data.

Data Science in the Cloud

Cloud processing increases security by reducing the number of copies of the data and increases collaboration by encouraging all data users to create a knowledge base within a single tool.

While the AMP PD program encourages cloud analysis it also seeks to understand use cases for data downloads. The AMP PD program does enable download of some AMP PD hosted data components. In order to create the best platform possible for sharing and collaborating in research, including best practices for data security, users who want to download AMP PD data to local servers must provide an institutional signature verifying that their host institution adopts responsibility for the security of the downloaded data. Users will also be required to document in the Portal why they are downloading the data. Users who download data will be responsible for the costs associated with download.

A guiding principle of the AMP PD Publication Policy is that all AMP PD stakeholders work together in a pre-competitive manner (i.e., research conducted cooperatively without potential marketing activities or patenting) in the interests of accelerating and advancing research outcomes. The intent of this publication policy is to promote best publication practices amongst all those that are using AMP PD developed resources, including the following practices:

• AMP PD research findings are published fully, accurately, and expeditiously;
• AMP PD cohort contributors and their members are recognized for their contribution to study design, acquisition, and analysis of all data and collection of biospecimens;
• AMP PD publications will be tracked in order to maintain a complete record of the findings resulting from AMP PD efforts; and,
• AMP PD publications are open and available to the public free of charge. This will be achieved by preferentially publishing papers in open-access journals and/or uploading to preprint servers (e.g., biorxiv) when submitted to a journal for review.  All original research resulting from AMP PD data will be made available from PubMed Central when feasible. In addition, authors will apply a Creative Commons (CC-BY) public copyright license to any author accepted manuscripts (AAMs) when feasible. If the authors allow others to own copyright in AAMs, the authors must ensure these copyright holders grant such a license.

Any publications funded by the Aligning Science Against Parkinson’s (ASAP) Initiative and implemented by The Michael J. Fox Foundation for Parkinson’s Research (MJFF) grants will need to follow ASAP’s and MJFF’s additional open-access publication requirements, https://www.gp2.org/resources/publicationpolicy/.

AMP PD Data Based Publications by Non-AMP PD Funded Investigators

Non-AMP PD funded investigators are encouraged to analyze and publish papers based on AMP PD data where AMP PD data access has been granted to these investigators through the AMP PD Access and Compliance Team. As set forth in the Data Use Agreement, such publications must reference the AMP PD program and the Cohorts that contributed data to the AMP PD program in the Acknowledgments section of the relevant publications. Upon application to the AMP PD Knowledge Platform for AMP PD data, non-AMP PD investigators will also be encouraged to pre-register their intended analyses on the AMP PD Knowledge Platform.

Researchers using AMP PD data must submit manuscripts to the AMP PD Publications Committee (PC) at manuscript@amp-pd.org two weeks prior to planned journal submission for review of AMP PD authorship citations.  Response from the AMP PD PC will be within 2 business days after receipt of the manuscript by the AMP PD PC members.  Non-response within the 2-business day window will indicate AMP PD PC’s concurrence with the authorship information provided in the manuscript. Authors are required to notify the AMP PD PC of acceptance or rejection of the manuscript and to provide the AMP PD PC with the manuscript citation and, if possible, URL to the article, upon acceptance.

AMP PD Program Manuscripts Authorship Guidelines

The overall premise of the AMP PD program is to work together in a pre-competitive manner to speed and advance research observations. This approach requires a culture of trust and respect between all AMP PD investigators. These guidelines are designed to ensure that culture is represented within our scientific output. They are designed explicitly for cross-program manuscripts that are initiated by the AMP PD Steering Committee or AMP PD Working Groups or Teams. Individual teams are not expected to adhere to these guidelines when publishing their own work and should instead follow the terms of the Data Use Agreement.

• Program authorship: “AMP® PD program” will be listed in the author line of all manuscripts that result from AMP PD program-wide results.  This group authorship name will index all members of AMP PD working groups. A list of program members will be approved, updated, and maintained annually at minimum on amp-pd.org. Both the list and link are to be included in the manuscript appendix or supplementary materials whenever possible, in accordance with journal requirements, to improve searchability of contributing members.
• Cohort authorship:  Biosamples and clinical data utilized in the AMP PD program were derived from a number of independently funded cohort studies and as such publications utilizing either the clinical data (including imaging) and/or the biosample data derived from the use of the cohort biosample collections must acknowledge the cohort(s) based on the terms outlined in the Data Use Agreement. Cohort contributors can elect to maintain a list of key personnel and links as described in the Data Use Agreement. Both the list and links are to be included in the manuscript appendix or supplementary materials whenever possible, in accordance with journal requirements, to improve searchability of contributing members.
• Named authorship: Individuals that directly contributed to the work described in the manuscript will be directly named as authors, as follows:
  • Authors will represent all academic and industry teams that contributed data or analysis to the manuscript. Team authorship will include both researchers actively involved in the work described in the manuscript and their PI(s) or lead manager(s).
  • When data were collected as part of team deposits to the AMP PD Knowledge Platform, representation will be by the bioinformatics lead(s) and PI(s) responsible for data generation and deposit, and overall PIs of the project/grant that supported data generation.
  • When data were generated directly for analysis represented in the manuscript (e.g., sample swap data), the data generation team(s) will provide a list of individuals that contributed to data generation.
  • All individuals that contributed active analyses to the manuscript and their PIs will be authors. Authorship will require individuals contributing analyses to also contribute to manuscript write-up by describing and interpreting their work.
  • Authorship order will be determined by contribution with opportunities for multiple individuals to be represented as either first author or corresponding author.
  • Where applicable, every effort will be made to promote junior or early-stage investigators in lead authorship positions.

Some AMP PD publications may utilize existing or external datasets derived from independently funded studies. Such publications will acknowledge the non-AMP PD datasets and funding as is appropriate.

The AMP PD program will work together to ensure transparency in all authorship designations. Researchers interested in submitting a manuscript on behalf of the AMP PD program will develop the author list according to the above guidelines and will provide this author list to the AMP PD PC by submission to manuscript@amp-pd.org. Program papers will be presented in advance to the AMP PD Steering Committee. The PC will distribute the list to all AMP PD partners for review. AMP PD partners will typically be provided 2 business days to submit any concerns or amendments to the proposed author lists, though turnaround for time-sensitive items such as conference abstracts may be shorter. Disputes to authorship lists will be settled prior to manuscript submission. If the AMP PD PC cannot resolve a dispute or has a conflict of interest, resolution will be provided by the AMP PD Steering Committee co-chairs.

Tracking of Data Use and Publications for Registered AMP PD Knowledge Platform users
The AMP PD program will on occasion host links to publications and pre-prints on the AMP PD Knowledge Platform’s news and updates. To ensure your work has the opportunity to be highlighted, authors will be required to:

1. Add AMP PD acknowledgement (see Data Use Agreement)
2. Add AMP PD cohort(s) acknowledgement(s) if data used is derived from the cohorts represented in the AMP PD program (see Data Use Agreement)
3. Include recommended language describing AMP PD methods and data gathering
4. Cite AMP PD funding partners (see Data Use Agreement)
5. Provide manuscript to AMP PD PC for review 2 weeks prior to planned submission (see Data Use Agreement)
6. Apprise AMP PD PC of acceptance or rejection at manuscript@amp-pd.org
7. Provide manuscript citation to AMP PD PC upon acceptance at manuscript@amp-pd.org
8. Provide URL to published work, if possible.

The Privacy Policy is a separate privacy policy document that explains how the AMP PD program uses and protects personal information received in connection with the AMP PD Knowledge Platform from casual visitors to the public website and users that register with the site. By using this AMP PD Knowledge Platform, you accept the terms and conditions of the Privacy Policy.

Oversight, Audits and Adjudication

The Access and Compliance Team monitors public activities on the AMP PD Knowledge Platform through periodic audits to assess compliance with the AMP PD governance policies. For example, through these audits, the Access and Compliance Team verifies that public content shared on AMP PD Knowledge Platform is being appropriately shared and acknowledged. The Access and Compliance Team does not actively monitor activities or content placed inside Terra private workspaces; however, the Access and Compliance Team may audit private workspaces if it believes data is being improperly shared therein. The Access and Compliance Team supports ethical use of the AMP PD Knowledge Platform, including adjudicating suspected unauthorized and/or unethical use of data. The Access and Compliance Team relies on the community of researchers and research participants for vigilance against unauthorized and/or unethical use of the AMP PD Knowledge Platform. Additionally, the AMP PD program relies on the community to hold itself to the highest standard of collegial behavior. Users unable or unwilling to meet these standards will have their access to the restricted portions of the AMP PD Knowledge Platform revoked.

The Access and Compliance Team membership is made up of representatives from the National Institutes of Health (NIH) and includes representatives from the National Institute of Neurological Disorders and Stroke (NINDS) and the National Institute on Aging (NIA). NINDS representatives are responsible for all access and compliance activities related to the AMP PD Unified Cohorts and NIA representatives are responsible for all access and compliance activities related to the Global Parkinson’s Genetics Program (GP2) Cohorts.

Please contact the Access and Compliance Team (AMP PD ACT, act@amp-pd.org, and GP2 ACT, act@gp2.org) if you have questions or suggestions about AMP PD Knowledge Platform governance, including the policies, ethics, or rules.