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.

• 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.

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 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, 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. 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: 20)

            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)

            8. Spatial 'omics (minimum samples: 20)

            9. Plate-based drug screening (minimum samples: 20)

            10. Automated multiplexed imaging (minimum samples: 20)

         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. NTAP and PI should decide if the optional datasets should be added to the data sharing plan (DSP).

4. Sage SOW-reviewer submits the pre-filled DSP and a member of the Sage NF-OSI DCC will review it on GitHub.

5. After internal approval, Sage NF-OSI DCC sends 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

6. 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

7. 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.

8. Sage NF-OSI DCC generates the Data Sharing Plan for the project in Word format and 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.

9. NTAP sends the following emails to respective parties:

   1. Award letter to AWARDEE (PI) after confirming the DSP and SOW. NTAP includes an introduction referencing the role of Sage and Synapse in data upload as expected for the NTAP award.

   2. Final SOW to Sage NF-OSI DCC

      1. Sage will upload and stores this in a private Synapse project here [Add link] accessible by NTAP and Sage for future reference.

10. Sage NF-OSI DCC sends email to AWARDEE (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)

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.