Opening a new project

The checklist provided encompasses the essential tasks for Sage Bionetworks and the funder to commence a "study" on the NF Data Portal. In this context, a "study" pertains to a funded project, usually associated with a specific grant, although occasionally it may involve multiple grants.

ROLES

FUNDER
SAGE - NF-OSI Data coordination Center
SAGE-SOW-REVIEWER
PRINCIPAL INVESTIGATOR (PI) - awardee

Please note that each role has been explicitly designated in order to provide clear and concise information regarding the time and effort commitments associated with this process.

STEP-BY-STEP PROCESS

Creating a project for a new award

FUNDER and the PI draft a statement of work (SOW) with tentative milestones and expected upload of key data. This process will be ~ 95% complete until Sage is involved.
FUNDER uploads the preliminary SOW (not the final version, but one step prior to final) to a private Synapse folder accessible only to the FUNDER and Sage and sends an email to SAGE at nf-osi@sagebionetworks.org. See NTAP Folder Here
1. The following information is required:
  1. Project name, PI, Institution, DOI Link
  2. Milestone start and due dates
  3. Overview of the Aims
  4. For each experiment within the milestones the following information is needed.
    1. Name of the assay (i.e. RNA sequencing, MRI-imaging, proteomics, etc)
    2. Short description of the experiment (i.e. Performing RNA sequencing on cutaneous neurofibromas extracted from patients with x treatment, etc.)
    3. Number of samples (i.e. number of patients, animal models, specimens etc.)
    4. Species (i.e. human, mouse, etc)
    5. If protocol is required to upload (yes, no)
SAGE-SOW-reviewer reviews preliminary SOW and drafts the data sharing plan using the web link (https://dsp.nf.synapse.org/).
1. SAGE-SOW-reviewer is responsible for completing the following information in the web form:
  1. Reference ID of Study (Format: Initiative_InvestigatorLastName_Year)
  2. Study summary
  3. Funding Agency
  4. Funding Initiative
  5. Grant DOI
  6. Grant Start Date
  7. Grant End Date
  8. Embargo End Date
  9. Disease Focus
  10. Disease Manifestation
  11. Primary Investigator
  12. PI Email
  13. Single Data Lead
  14. Synapse Principal User ID
  15. Institution
  16. Data Sets to be Deposited (See Identification of Key Data)
    1. Aim
    2. Folder Name
    3. Description
    4. Type
    5. Assay
    6. Upload Date
2. Identification of Key Data
  1. Key datasets generally fulfill at least one of the following criteria.
    1. Dataset contains data generated using high-throughput methods that output raw data presented in a widely used systematic format. Examples of assays and minimum sample numbers are listed below:
      1. Whole Genome Sequencing (minimum samples: 5)
      2. Whole Exome Sequencing (minimum samples: 5)
      3. RNA Sequencing (minimum samples: 5)
      4. Single Cell RNA Sequencing (minimum samples: 5)
      5. Whole slide imaging (minimum samples: 20 images or N = 5 samples)
      6. MRI (minimum samples: 20 images or N = 5 samples)
      7. Spatial transcriptomics (minimum samples: 5)
      8. Spatial 'omics (minimum samples: 5)
      9. Plate-based drug screening (minimum samples: 5)
      10. Automated multiplexed imaging (minimum samples: 5)
    2. Dataset considered to be validation data for a new method that is being developed in the funded grant (see an example here - Admin access only)
    3. Dataset that is deemed of interest to funder (see an example here - Admin access only)
    4. Any optional datasets identified in the SOW should be called out in comments in the SOW during review. FUNDER and PI should decide if the optional datasets should be added to the data sharing plan (DSP).
SAGE-SOW-reviewer submits the pre-filled DSP and a member of the Sage NF-OSI DCC will review it on GitHub. SAGE-SOW-reviewer uploads the reviewed SOW to the private Synapse folder only accessible to the funder and Sage. See NTAP Folder Here
After internal approval, SAGE sends an email to both FUNDER with the following information:
1. A word document (Admin access only) “packet” that contains:
  1. Original SOW with markup for optional datasets
  2. Description of the draft pre-filled DSP and expectations for next steps (see example attached above)
  3. Pre-filled DSP form with link to webform and instructions
PI fills out the form to complete all remaining sections of the DSP and clicks “submit”.
1. The PI is responsible for completing:
  1. Species
  2. Number of Samples
  3. File Format
  4. Number of Files
  5. Progress or Milestone Report Number
  6. Governance section
SAGE gets notified of the newly submitted DSP updates via GitHub and reviews the changes to confirm that all required fields are filled properly.
PI and FUNDER discuss DSP and finalize. Any changes to the DSP are submitted by the PI and steps 6 and 7 are repeated
FUNDER sends the following emails to respective parties:
1. Award letter to PI after confirming the DSP and SOW. FUNDER includes an introduction referencing the role of Sage and Synapse in data upload as expected for the FUNDER award.
2. Final SOW to SAGE
  1. Sage will upload and stores this in a private Synapse project accessible by FUNDER and Sage for future reference.
SAGE generates the Data Sharing Plan for the project in Word format and emails document to FUNDER. At the same time, SAGE adds “provision” tag to the DSP GitHub pull request to trigger the Synapse Study Creation process. At this point the study is active and visible on the NF Data Portal.
SAGE sends email to PI with the following details:
1. Link to Synapse project space (synapse.org)
2. Link to Study page in NF Data Portal (nf.synapse.org)
3. Link to the final DSP uploaded to a folder in the Synapse project
4. Link to documentation NF Data Portal Docs (synapse.org)
Any changes to the data sharing during the duration of the project, the PI should update the DSP using the link and a new DSP pdf file will be sent to Synapse by Sage team.

Additional scenarios:

Handling Synapse Projects When a PI Changes Institutions

If a Principal Investigator (PI) moves to a new institution during an active award, should a new Synapse project be created, or should the existing project be maintained?

In most cases, the PI will continue using the same Synapse project. Sage will update the PI's contact information and add the new institution. Additionally, members from the new institution may need to be added to the project. If a new ProposalCentral grant link has been created, it will be associated with the existing project. This approach assumes that the project's research focus remains unchanged.

However, if the research focus has shifted significantly, creating a new Synapse project may be necessary. Another key consideration is whether the previous research topic will still be pursued.

If the original research will continue at the previous institution, it is advisable to create a second Synapse project to separately track contributions from both institutions.
If no further data collection is expected for the original project, it may be more practical to retain the existing Synapse project and update its topic/title accordingly.

Creating Shell projects for previously completed projects

FUNDER sends the following information about the project to SAGE:
1. Name of study
2. Summary
3. Initiative
4. PI of the study
5. Institutions
6. Manifestation (e.g. cutaneous NF, plexiform NF, other)
7. diseaseFocus
8. DOI of the grant
SAGE adds information to portal via back-end of NF data portal. No data sharing plan is needed.