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This checklist

The checklist provided encompasses the essential tasks for Sage Bionetworks and the funder to commence a "study" on the NF Data Portal. A “study” is In this context, a "study" pertains to a funded project, and usually corresponds to one specific grant (though sometimes can be more than one grant)usually 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)

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.

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Award and Milestones:

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Creating a project for a new award

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: Send uploads the preliminary SOW (not the final version, but one step prior to Sage with the following required informationfinal) to this private Synapse folder accessible only to NTAP and Sage and sends an email to NF-OSI DCC at nf-osi@sagebionetworks.org.

   1. The following information is required:

      1. Project name

      and

      1. , PI, Institution, DOI Link

      2. Milestone start and due dates

      3. Overview of the Aims

      4. For each

      milestone:

      1. Description of the experiment included in an Aim

      2. Name of the assay being performed

      3. Number of samples in that assay

      4. Species used for the assay

      5. Whether protocol for the assay is needed: Yes/No

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

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

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

      1. 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)

3. 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

      (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: 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 

      1. 1. grant (see an example here - Admin access only)

         2. Dataset

      considered to be

      1. 1. that is deemed of interest to

      the funding partner

      1. 1. funder (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. - Admin access only)

         2. 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).

4. Sage :NF-OSI DCC: Once form is submitted by the SOW-reviewer, start the internal review of the submits the pre-filled DSP .Sage: SOW-reviewer: and a member of the Sage NF-OSI DCC will review it on GitHub. Sage SOW-revieweruploads the reviewed SOW to this private Synapse folder accessible only to NTAP and Sage.

5. After internal approval, collate reviewed SOW and the pre-filled DSP (word document) into a packet and send to NTAP.

   1. Required:

      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)

6. Sage: SOW-reviewer: Archive the reviewed SOW+pre-filled DSP packet on the internal Sage-NTAP drive

7. NTAP: Email finalized SOW + pre-filled DSP to the awardee and respond to awardee’s questions or concerns regarding the SOW.

8. NTAP: Iterates over the SOW and pre-filled DSP with AWARDEE (PI) to finalize the data sharing plan.

9. NTAP: Once data sharing plan is final between NTAP and AWARDEE (PI), NTAP asks AWARDEE (PI) to update final changes to the DSP using the web-link provided on the pre-filled DSP.

10. NTAP: Send final SOW to Sage as confirmation

11. Sage:NF-OSI DCC: Review the final DSP form filled by the AWARDEE (PI) on the webform and confirm that all required fields (e.g. governance etc) are filled properly.Sage:NF-OSI DCC: Once everything is filled out, generate the executed Sage NF-OSI DCCsends an email to both NTAP and the AWARDEE PI 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 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

12. AWARDEE PI fills out the form to complete all remaining sections of the DSP and clicks “submit”.

    1. The AWARDEE 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

13. Sage NF-OSI DCC gets notified of the newly submitted DSP updates via GitHub and reviews the changes to confirm that all required fields are filled properly.

14. Sage NF-OSI DCC generates the Data Sharing Plan for the project in PDF Word format and send it to NTAP and AWARDEE (PI) for the records.NTAP: Sends an award emails document to NTAP. At the same time, Sage NF-OSI DCC 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.

15. NTAP sends the following emails to respective parties:

    1. Award letter to AWARDEE (PI) after confirming the

    SOW and introduces Sage to the awardee. The introductory email includes the following:Sage:

    1. Role DSP and SOW. NTAP includes an introduction referencing the role of Sage and Synapse in data upload as expected for the NTAP award

    2. Expectation of Data Sharing plan to be filled with the tables in SOW and sent to Sage to start the project intake process

    3. Expected embargo end date for data release for the project

    4. Proposal central DOI for the awarded project

Synapse Study Creation/ Project Intake:

1. 1. .

   2. Final SOW to Sage NF-OSI DCC

   : Follows up on the introductory email with information :

   • Pre-filled data sharing plan for the awardee to sign and upload to the Project Intake Form (Step 14 above)

   • Filling out the Project Intake form as described in NF Data Portal’s documentation page

   Sage: NF-OSI DCC: Send

   1. 1. Sage will upload and stores this in a private Synapse project accessible by NTAP and Sage for future reference.

2. Sage NF-OSI DCC sends email to AWARDEE (PI) confirming with the following details:

   Established

   1. Link to Synapse project space

   with link to access the project

   1. (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

   Study page in NF Data Portal 

3. Sets Study Status to “Active”

Uploads the final data sharing plan to the project space in a folder named “Admin”

1. documentation NF Data Portal Docs (synapse.org)

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

2. Sage NF-OSI DCC adds information to portal via back-end of NF data portal. No data sharing plan is needed.