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| Table of Contents | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
The checklist provided includes encompasses the necessary essential tasks for Sage Bionetworks and a the funder to initiate commence a "study" on the NF Data Portal. A In this context, a "study" refers pertains to a funded project typically , usually associated with a specific grant, although occasionally it may involve multiple grants.
| Info |
|---|
ROLES : |
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.
| Info |
|---|
STEP-BY-STEP PROCESS |
...
Creating a project for a new award
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.
NTAPsends an email with uploads the preliminary SOW (not the final version, but one step prior to final) to this private Synapse folder accessible only to NTAP and Sage and sends an email to NF-OSI DCC at nf-osi@sagebionetworks.org.
The following information is required:
Project name, PI, Institution, DOI Link
Milestone start and due dates
Overview of the Aims
For each experiment within the milestones :the following information is needed.
Name of the assay (i.e. RNA sequencing, MRI-imaging, proteomics, etc)
Short description of the experiment (i.e. Performing RNA sequencing on cutaneous neurofibromas extracted from patients with x treatment, etc.)
Number of samples (i.e. number of patients, animal models, specimens etc.)
Species (i.e. human, mouse, etc)
If protocol is required to upload : [Yes or No] (yes, no)
Sage : SOW-reviewer reviews preliminary SOW and drafts the data sharing plan using the web link (https://dsp.nf.synapse.org/).
Sage SOW
-reviewer is responsible for completing the following information in the web form:
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
Data Sets to be Deposited (See Identification of Key Data)
Aim
Folder Name
Description
Type
Assay
Upload Date
Identification of Key Data
Key datasets generally fulfill at least one
of the following criteria
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)
.
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:
Whole Genome Sequencing (minimum samples: 5)
Whole Exome Sequencing (minimum samples: 5)
RNA Sequencing (minimum samples: 5)
Single Cell RNA Sequencing (minimum samples: 5)
Whole slide imaging (minimum samples: 20 images or N = 5 samples)
MRI (minimum samples: 20 images or N = 5 samples)
Spatial transcriptomics (minimum samples: 5)
Spatial 'omics (minimum samples: 5)
Plate-based drug screening (minimum samples: 5)
Automated multiplexed imaging (minimum samples: 5)
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)
Dataset
that is deemed of interest to
funder (see an example here
- Admin access only)
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).
Sage :NF-OSI DCC: Once form is submitted by the SOW-reviewer, start the internal review of 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.
After internal approval, collate reviewed SOW and the pre-filled DSP (word document) into a “packet” and send Sage NF-OSI DCCsends an email to both NTAP and the AWARDEE PI.
Required to include in the packet:
Add the section that explains what the pre-filled DSP is
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:
A word document (Admin access only) “packet” that contains:
Original SOW with markup for optional datasets
Description of the the draft pre-filled DSP and expectations for next steps (see example attached above)
Pre-filled DSP form with link to webform and instructions
AWARDEE PI fills out the form to complete all remaining sections of the DSP and hits clicks “submit”.
The AWARDEE PI is responsible for completing:
Species
Number of Samples
File Format
Number of Files
Progress or Milestone Report Number
Governance section
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.
Sage : NF-OSI DCC: generates the executed Data Sharing Plan for the project in PDF Word format and emails confirmation document 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. At this point the study is active and visible on the NF Data Portal.
NTAP sends an award the following emails to respective parties:
Award letter to AWARDEE (PI) after confirming the
Role DSP and SOW. NTAP includes an introduction referencing the role of Sage and Synapse in data upload as expected for the NTAP award
Expectation of Data Sharing plan to be filled with the tables in SOW and sent to Sage to start the project intake process
.
Final SOW to Sage NF-OSI DCC
Synapse Study Creation/ Project Intake:
- Sage:
Sage will upload and stores this in a private Synapse project accessible by NTAP and Sage for future reference.
Sage NF-OSI DCC: Send sends email to AWARDEE (PI) confirming with the following details:
EstablishedLink to Synapse project space
Link to Study page in NF Data Portal (nf.synapse.org)
Link to the final DSP uploaded to a folder in the Synapse project
Link to
documentation NF Data
Sets Study Status to “Active”
Creating Shell projects for previously completed projects
...
NTAP sends the following information about the project to Sage : NF-OSI DCC:
Name of study
Summary
Initiative
PI of the study
Institutions
Manifestation (e.g. cutaneous NF, plexiform NF, other)
diseaseFocus
DOI of the grant
Sage NF-OSI DCC adds information to portal via back-end of NF data portal. No data sharing plan is needed.