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The checklist provided includes the necessary tasks for Sage Bionetworks and a funder to initiate a "study" on the NF Data Portal. A "study" refers to a funded project typically associated with a specific grant, although occasionally it may involve multiple grants.

• FUNDING AGENCY

• NF-OSI DCC (Sage Bionetworks)

• SOW-REVIEWER (Sage Bionetworks)

• AWARDEE (PI)

Award and Milestones:

1. NTAP and the AWARDEE (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.

2. NTAP sends an email to nf-osi@sagebase.org with the preliminary SOW (not the final version, but one step prior to final) to NF-OSI DCC.

   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 or No] (yes, no)

3. Sage : SOW-reviewer reviews preliminary SOW to identify key datasets that can be uploaded to Synapse. Key datasets generally fulfill one or more of the following criteria:

4. Dataset follows the “required” criteria for sharing as noted by the NF research community

Dataset contains more than 20 samples in the dataset or generated from patient samples (N > 5)

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

   (for example: WGS, WES, RNA-seq, scRNAseq, whole slide imaging, MRI, spatial transcriptomics, spatial biology, spatial 'omics, plate-based drug screening, automated multiplexed imaging, etc.)

3. Omics data derived from unbiased techniques

4. 1. 1. . Examples of assays and minimum sample numbers are listed below:

         1. Whole Genome Sequencing (minimum samples: 1)

         2. Whole Exome Sequencing (minimum samples: 1)

         3. RNA Sequencing (minimum samples: 1)

         4. Single Cell RNA Sequencing (minimum samples: 1)

         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: 20 images or N = 5 samples)

         8. Spatial 'omics (minimum samples: 20 images or N = 5 samples)

         9. Plate-based drug screening (minimum samples: 1)

         10. Automated multiplexed imaging (minimum samples: 20 images or N = 5 samples)

      2. Dataset considered to be validation data for a new method that is being developed in the funded

   grant 

   1. 1. grant (see an example here)

5. Dataset considered to be of interest to the funding partner (see an example here)

Sage: SOW-reviewer: Identifies required key datasets and fills out a form on https://dsp.nf.synapse.org/ to pre-fill the table outlining the Milestones, folder name, data description, and upload date. The unique reference ID of the study should be according to the following convention - “Initiative-<Awardee-name>-YYYY” and submit.

1. 1. 1. Any optional datasets identified in the SOW should be called out in comments in the SOW during review. NTAP and PI should decide if the optional datasets should be added to the data sharing plan (DSP).

5. Sage :NF-OSI DCC: Once form is submitted by the SOW-reviewer, start the internal review of the submits the pre-filled DSP and a member of the Sage NF-OSI DCC will review it on GitHub.

6. Sage: SOW-reviewer: After internal approval, collate reviewed Sage SOW and the pre-filled DSP (word document) into a “packet” and send -reviewer sends an email to both NTAP and the AWARDEE PI.

   1. Required to include in the packet:

      1. Add the section that explains what the pre-filled DSP is

      2. Add the DSP with highlights noting what needs to be updated by the recipient (AWARDEE PI)

   Sage: SOW-reviewer: Send the “packet” from step 6 to NTAP and AWARDEE PI with instructions for the AWARDEE PI to make any updates to the DSP using the webform link provided in the “packet”. with the following information:

   1. Pre-filled DSP and SOW (word document) into a “packet”

   2. Link to Webform and instructions

7. AWARDEE PI fills out the form to complete all sections of the DSP and hits “submit”.

   1. The AWARDEE PI is responsible for completing:

      1. Species

      2. # Samples

      3. File Format

   Sage:

   1. 1. # Files

      2. Report #

      3. Governance section

8. Sage NF-OSI DCC :gets notified of the newly submitted DSP updates via GitHub and reviews the changes to confirm that all required fields (e.g. governance etc) are filled properly.

9. Sage : NF-OSI DCC: generates the executed Data Sharing Plan for the project in PDF format and emails confirmation to NTAP. At the same time, Sage:NF-OSI DCC adds “provision” tag to the DSP Github PR GitHub pull request to trigger the Synapse Study Creation process.

10. NTAP sends an award letter to AWARDEE (PI) after confirming the SOW and introduces Sage to the awardee. The introductory email includes the following:

    1. Role of Sage and Synapse in data upload as expected for the NTAP awardExpectation of Data Sharing plan to be filled with the tables in SOW and sent to Sage to start the project intake process

11. NTAP sends the final SOW to Sage : NF-OSI DCC [TODO: Add link to the appropriate Synapse folder] and stores this in a private Synapse project here [Add link] accessible by NTAP and Sage.

Synapse Study Creation:

1. Sage: NF-OSI DCC: Send email to AWARDEE (PI) confirming the following

   • Established Link to Synapse project space with link to access the project

   • Link to the final DSP uploaded to a folder in the Synapse project

   • Link to Study page in NF Data Portal Sets Study Status to “Active”

Creating Shell projects for previously completed projects:

1. NTAP sends the following information about the project to Sage: NF-OSI DCC:

   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

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