NF Data Portal Documentation
NF Data Portal Documentation
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SOP: Opening a New Project on the NF Data Portal

Purpose

This SOP outlines the step-by-step process for opening a new project on the NF Data Portal.

Procedure

Step 1: Approve Project for NF Data Portal and Notify NF-OSI DCC

1.1 Determine if the Project Meets “Identification of Key Data” Criteria

Funder or Sage (on behalf of CTF) evaluates if data to be generated in grant meets at least one of the following minimal requirements. 

  • High-throughput sequencing  (≥5 samples), including, but not limited to: 

    • Bulk RNA Sequencing (RNA-seq)

    • Single Cell RNA Sequencing (scRNA-seq)

    • Spatial Transcriptomics

    • Whole Genome Sequencing (WGS)

    • Whole Exome Sequencing (WES)

    • Targeted Gene Panel Sequencing

    • Methylation Sequencing 

    • ATAC-seq (Assay for Transposase-Accessible Chromatin)

    • ChIP-seq (Chromatin Immunoprecipitation Sequencing)

    • Mass Spectrometry-based Proteomics

    • Targeted Proteomics

    • Single-cell Proteomics

    • Metabolomics

    • Lipidomics

  • Whole Slide or other high throughput imaging (≥20 images or ≥5 samples)

  • Clinical Imaging (≥20 images or ≥5 samples/patients)

  • Plate-based High Throughput Drug Screening (≥5 samples)

  • Automated Multiplexed Imaging (≥5 samples)

  • Patient reported outcomes or similar data that use standardized measures

  • Validation data for newly developed methods

  • Other meritorious data deemed of special interest by the funder.

1.2a If  the Project Meets “Identification of Key Data” Criteria

The Funder finalizes the funding package, including the common data sharing agreement between Funder and Awardee, and shares documentation with Awardee. 

  • Proposal Central or Funder uploads draft Statement of Work (SOW) or grant narrative that includes information about datasets to a designated private Synapse folder for the funder. 

  • Proposal Central or Funder sends a notification to nf-osi@sagebionetworks.org about the new project and the synapse ID of the file uploaded in step 6. This notification will also include the following information:

    • ProposalCentral Grant DOI (if not available, provide all items in Step 3 1-15)

    • Embargo End Date (grant end date + 12 months)

    • PI Email

1.2b If  the Project does not meet “Identification of Key Data” Criteria

  • The Funder finalizes funding package and documentation with Awardee. 

  • Proposal Central or Funder sends the Award Letter and Notice of Award (NOA) to the Awardee. 

  • Funder will provide the following information to NF-OSI DCC:  

    • Name of study

    • PI of the study

    • DOI of the grant

  • NF-OSI DCC completes a DSP for the project and marks “data sharing waived” 

  • NF-OSI DCC provisions a “shell” project and NF Data Portal listing for the project marked as “Data Not Expected”. Portal users will be instructed to reach out to investigators if they would like to access raw data. 

  • ⚠️This is the final step for these studies. 

Step 2: Pre-fill Data Sharing Plan (DSP)

The Data Sharing Plan (DSP) is initially pre-filled by a party with expertise in the domain and data sharing practices. This may be either the NF-OSI DCC or Program Officer (or similar role) from the Funder, depending on the funder’s internal workflow. 

The Data Sharing Plan (DSP) is pre-filled by the designated party using a web form.  The pre-filled DSP includes both study metadata and a preliminary table of datasets expected for deposit.  

Study metadata includes: 

  • Reference ID of Study (Format: Initiative_InvestigatorLastName_Year)

  • Study summary

  • Funding Agency

  • Funding Initiative

  • Grant DOI

  • Grant Start Date

  • Grant End Date

  • Embargo End Date

  • Disease Focus

  • Disease Manifestation

  • Primary Investigator

  • PI Email

  • Single Data Lead

  • Synapse Principal User ID

  • Institution

Datasets to be deposited includes: 

  • Aim

  • Folder Name

  • Description

  • Type

  • Assay

  • Upload Date

  • Milestone # (if applicable) 

Refer to Identification of Key Data section above for guidance on dataset eligibility. 

⚠️Data governance information must be completed by the Awardee to ensure data sharing expectations align with prior agreements made with the Funder.  

Once the DSP is pre-filled, the  NF-OSI DCC or Program Officer sends the draft web form link to the Awardee. A completion time frame of two weeks is recommended.  Suggested time to complete the data sharing plan is 2 weeks. NF-OSI DCC sends DSP draft link via email to Awardee with Funder in CC, requesting that they complete it within two weeks. 

Step 3: Complete and Submit DSP

Awardee will complete the data sharing plan, reviewing for accuracy, making necessary changes, and completing the data governance section, and click submit.

If not submitted, NF-OSI DCC will follow up after two weeks for a second request. If not completed after the second request, NF-OSI DCC will escalate to Funder who will ensure Awardee completes the data sharing plan. If an extension from the Funder is granted to complete the DSP, the Funder should notify the NF-OSI DCC of the expected submission date.

Step 4: Review and Finalize DSP

  1. NF-OSI DCC receives notification of DSP submission via GitHub and performs initial review.

  2. DCC verifies completeness, including:

    • Single Data Lead

    • Synapse Principal User ID 

    • Completed data governance section

  3. Any final clarifications required are resolved through email discussion with the Awardee and Funder.

  4. Once reviewed, the DSP pull request is merged into GitHub, and the project assets are provisioned. 

Step 5: Provision Project Assets

  1. NF-OSI DCC provisions required project assets, which include::

    • A Synapse project workspace

      1. A pre-structured folder hierarchy reflecting expected datasets from DSP and annotations 

      2. The final DSP PDF uploaded to Synapse project workspace 

    • Study page on NF Data Portal

  2. NF-OSI DCC communicates with Awardee, Funder, and for CTF only: Proposal Central, providing: