Opening a new project

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 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 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:

         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, etc.)

         4. Species (i.e. human, mouse, etc)

         5. If protocol is required to upload: [Yes or No]

3. 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)

   3. 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.)

   4. Omics data derived from unbiased techniques

   5. Dataset considered to be validation data for a new method that is being developed in the funded grant  (see an example here)

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

4. 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. 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 pre-filled DSP.

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

7. PI updates the DSP form on the weblink.

   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)

8. When the PI fills out the form, Sage will be updated via GitHub and will confirms that all required fields (e.g. governance etc) are filled properly. generate the executed Data Sharing Plan for the project in PDF format

9. 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 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

10. NTAP sends the final SOW to Sage.

Synapse Study Creation/ Project Intake:

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

   • Established 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”

For projects

• studyName

• studyId

• summary

• initiative

• studyLeads

• institutions

• manifestation

• diseaseFocus

• studyStatus

• dataStatus

• fundingAgency

• accessRequirements

• acknowledgementStatements

• dataType

• relatedStudies

• studyFileviewId

• id

• grantDOI

• Resource_id