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CEDAR_to_NCBI_Human Pipeline

Marcos Martinez edited this page Jul 9, 2019 · 21 revisions

Welcome to the CEDAR-to-NCBI_Human Data Submission Pipeline

Introduction

The CEDAR-to-NCBI_Human data submission pipeline helps investigators and curators to edit and validate ontology-controlled metadata, and it provides a seamless interface to transmit SRA datasets to the NCBI SRA and BioSample repositories from the CEDAR Workbench following the BioSample Human package v1.0.

The template and template elements used by this pipeline are publicly available in the following CEDAR folder: All/Shared/Shared by CEDAR/CEDAR-to-NCBI Pipeline.

Do you have a CEDAR login?

To use this pipeline, you will need an account on the CEDAR Workbench. If you do not have one, you can create one.

Submission Steps

  1. Click on this link: CEDAR-to-NCBI_Human Pipeline. If you aren't already logged in, this will take you to the CEDAR login panel.
CEDAR Login Panel
  1. Log in to the CEDAR system if necessary. If you are a new user, you will have to create an account. (See above for instructions to get a new account.)

  2. After logging in into the system, you will see the 'CEDAR-NCBI Human Tissue' template. Fill out the template fields with your metadata. Fields with an asterisk (*) are mandatory. Your submission will fail if any mandatory fields are not completed. If information is unavailable for any mandatory field, please enter ‘not collected’, ‘not applicable’ or ‘missing’ as appropriate.

  1. Once your metadata is complete, click on the 'Save' button to save your metadata into your workspace.
  1. You will see a message in a green box confirming that your metadata have been successfully saved, as well as a message in a yellow box letting you know that your metadata have been saved to your personal workspace.
  1. Go to your personal workspace by clicking on the left arrow (top left corner) and then on the 'Workspace' link, or by just clicking on: https://cedar.metadatacenter.org.

  2. Once in your workspace, you will see a metadata file called 'CEDAR-NCBI Human Tissue metadata'. That file contains the metadata that you have just created and that you want to submit to the NCBI. Click on the three vertical dots on the top-right corner of the file icon to see the available file options.

  1. Click on the 'Submit' option to open the submission dialog.
  1. The 'NCBI (Human Tissue)' option will be automatically selected. Click on 'Next' to go to the next step.
  1. Click on the 'Select Files' button to upload the data files. Note that the names of the selected files must match the names in the metadata file. Otherwise, you will receive an error message when trying to start the submission.
  1. Click on the 'Submit' button to start the submission. If there are not validation errors, the selected data files and the corresponding metadata will be uploaded to the NCBI servers.
  1. Note that the submission may take several hours or even days to be processed by the NCBI. Meanwhile, you will receive status messages about your submission in your workspace (messages icon).

Citing the CEDAR-to-NCBI SRA Pipeline

To be Updated

Support or Contact

Having trouble with NCBI submission process through our pipeline? Please email to Marcos Martínez-Romero or to Syed Ahmad Chan Bukhari and we’ll help you sort it out.

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