Getting Started

Quickstart FaceBase Data Philosophy

Using FaceBase

Key Concepts for FaceBase Users Browsing and Filtering Data Visualizations in FaceBase Data Sharing and Citing Data Exporting Data from FaceBase Accessing Data Programmatically Using 3D Viewers Viewing NIfTI files Converting TIFF to OME-TIFF (using Bio Formats)

Requesting Controlled-Access Human Data

Controlled-Access Human Data - Policy and Requests A. Read and complete the Data Use Certificate Agreement (DUC) B. Complete the online Data Access Request (DAR) form C. Select the Requested Datasets D. Print, Gather Signatures and Submit the DUC and DAR forms E. Receive notification and further instructions F. Create and upload your encryption keys G. Renew access

Submitting Data - Basics

Video Tutorials for Contributors Key Concepts for Data Contributors Data Submission Process Guidelines for Submitting Controlled Access Data Creating a Dataset Creating Experiments and Biosamples Uploading Data Files Quality Control Rules Releasing Your Dataset Self-guided Tutorial

Submitting Data - Advanced

Using the Annotations Editor (2D images) Defining Surface Models for the Surface Mesh Viewer (3D models) Linking Thumbnails to Files

Tools

DERIVA Tools - Bulk upload and export

Support

Getting Help FAQs

Data Submission Process

Data Submission Overview

When Should You Contact FaceBase?

We recommend filling out the Data Submission Form (see below) once your grant is funded and even as you’re generating your data (ie, sooner than later).

Advantages include:

We can help you organize your data as you are collecting it to make uploading easier in the future.
We also encourage entering your metadata even before you’re ready to upload your data to make the process run more smoothly.
Helps “future proof” your data management process. Many times, the member of your lab who generated the data may not still be available once it’s time to publish.
We will be able to provide proper data citations for your publication. You do not have to upload your data until your publication is released, but we can still generate Digital Object Identifiers (DOIs) for your datasets before you submit your publication.

Before You Begin

If you have not already submitted data for your current project or investigation, please make a request for review of your upcoming data submission. The request will be reviewed by a committee for FaceBase. Notification of approval to submit data to FaceBase should take no more than about 2 weeks.

Review the page How to Submit Data and follow its link to the “Data Submission Form” and fill it out. Note that this form is for grants that have been funded.
FaceBase will contact you within approximately 2 weeks with a decision on your data submission request.
Upon approval, FaceBase will setup a Project record on FaceBase and send you a link to create a FaceBase account (if you do not already have one) and to join your new Project. We also encourage scheduling a one-on-one tutorial with us to discuss specific details for your project.

You may then begin the data submission process described next.

Data Submission Process

The process for submitting data will generally include the following steps (in this order):

Create a Dataset entry
Create Experiment and Biosample entries
Upload data files
Finally, review and revise your dataset:
- Review your completed datasets with your collaborators, PI or Co-PIs. Your data is only viewable by your project until you agree to release it.
- Notify us at help@facebase.org to release your datasets to the public.
- FaceBase curators review and may have questions or suggestions about your entries to help make them more discoverable.
- We release the datasets once they have gone through final Quality Control review and at this point, the dataset is viewable by the public.

IMPORTANT Your datasets are not released until the we review them and updates their release status. Until FaceBase has released your datasets, they are not visible and usable by the public.

So once you have joined the right group and are logged in to the FaceBase Data Browser, you are ready to get started with Creating a Dataset.

Submitting Human Subjects Data (Controlled Access Data)

Please see the data access policy on the FaceBase site, regarding what data are classified as ‘controlled access’ (human subjects) data.

If you have already deposited your data at dbGaP, or another similar repository, you should include the dbGaP accession numbers for the relevant data in the “Related Datasets” field of your Dataset entries on FaceBase.

If your research was not sponsored by the NIH, we will request the following documentation: Federalwide Assurance (FWA) number, IRB approval letter (or letter from equivalent ethics board at your institution), description of variables, and contact information of PIs.

For more details about submitting human subjects data, see Guidelines for Submitting Controlled Access Data.