This checklist contains the tasks required for Sage Bionetworks and a funder to start a “study” on the NF Data Portal. A “study” is a funded project, and usually corresponds to one specific grant (though sometimes can be more than one grant).
Award and Milestones:
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NTAP: Confirm that all documents required for award are present in NTAP shared drive.
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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.
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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.
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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.
NTAP
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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, no)
Sage
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Dataset contains more than 20 samples in the dataset or generated from patient samples (N > 5)
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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 contains data generated using high-throughput methods that output raw data presented in a widely used systematic format
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. 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
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Dataset considered to be of interest to the funding partner
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Sage: Perform research/literature review on new data types and file formats of proposed novel experiments (if needed) to propose expectations of formats and number of files for experiments proposed in the SOW
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Sage: File an internal pull request on NF-OSI study-configs repository to start preparing a YAML file to generate a table outlining the Milestones, expected data types, expected file formats, expected number of files. The pull request should be named according to the following convention - “YYYY-NTAP-<Awardee-name>” and request internal review.
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Sage: Add the unified table (or a preliminary data sharing plan) generated from the internal review process into the SOW and send it to NTAP for review.
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NTAP: Email finalized SOW to the awardee and respond to awardee’s questions or concerns regarding the SOW.
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NTAP: Send the finalized SOW to Sage with any changes to the table of expected data.
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Sage: Commit changes to the open pull request (“YYYY-NTAP-<Awardee-name>”) according to the finalized table of expected data in the SOW.
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Sage: Merge the finalized pull request and generate finalized and filled out Data Sharing Plan for the awardee
NTAP: Sends an award letter to awardee after confirming the SOW and introduces Sage to the awardee. The introductory email includes the following:
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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 SOW-reviewersubmits the pre-filled DSP 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, Sage NF-OSI DCCsends an email to both NTAP and the AWARDEE PI 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 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 are filled properly.
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.
NTAP sends the following emails to respective parties:
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
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Expectation of Data Sharing plan to be filled with the tables in SOW and sent to Sage to start the project intake process
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Expected embargo end date for data release for the project
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Proposal central DOI for the awarded project
Synapse Study Creation/ Project Intake:
Sage: 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
Filling out the Project Intake form as described in NF Data Portal’s documentation page
Awardee: Sign the data sharing form and upload it to the Project Intake Form
Established Synapse project space with link to access the project
Link to Study page in NF Data Portal
Sets Study Status to “Active”
Uploads the final data sharing plan to the project space in a folder named “Admin”.
Final SOW to Sage NF-OSI DCC
Sage will upload and stores this in a private Synapse project accessible by NTAP and Sage for future reference.
Sage NF-OSI DCC sends email to AWARDEE (PI) with the following details:
Link to Synapse project space (synapse.org)
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 Portal Docs (synapse.org)
Sage: Send email to awardee confirming the following
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.