Overview of NCBI's SARS-CoV-2 submission process and the metadata required v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Emma Griffiths ◽  
Lee Katz ◽  
Michael Weigand
Keyword(s):  
Raw Data ◽  
Data Submission ◽  
Sequence Read Archive ◽  
Submission Process ◽  
Laboratory Submission

PURPOSE: This protocol explains the metadata requirements for the following two protocols: 1. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject Step-by-step instructions for establishing a new NCBI laboratory submission account and for creating and linking a new BioProject to an existing umbrella effort. SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample. Users can modify this protocol to just create a BioSample with no linked raw data. 2. SARS-CoV-2 NCBI consensus submission protocol: GenBank Required: established BioProject and BioSamples Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data. Version history: V4: Updated metadata templates to reflect updated PHA4GE templates (V3) plus minor text edits.

SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Emma Griffiths ◽  
Duncan MacCannell ◽  
Lee Katz ◽  
Michael Weigand
Keyword(s):  
Large Volume ◽  
Web Interface ◽  
Raw Data ◽  
Data Submission ◽  
Sequence Read Archive ◽  
Specific Protocol ◽  
The Creation ◽  
Set Up ◽  
Laboratory Submission

PURPOSE: This is a SARS-CoV-2 specific protocol that covers the steps needed to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in the SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. These protocols cover submission using NCBI's Submission Portal web-interface. Complete in order:: 1. Populate your templates first. 2. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject (included protocol) Step-by-step instructions for establishing a new NCBI laboratory submission account and for creating and linking a new BioProject to an existing umbrella effort. SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample. Users can modify this protocol to just create a BioSample with no linked raw data. 3. SARS-CoV-2 NCBI consensus submission protocol: GenBank Required: established BioProject and BioSamples Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data. Version history: V4: Direct links provided to download metadata templates (instead of hosting duplicate files). Other minor edits throughout the protocol.

SARS-CoV-2 NCBI consensus submission protocol: GenBank v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Emma Griffiths ◽  
Lee Katz ◽  
Duncan MacCannell ◽  
Michael Weigand
Keyword(s):  
Large Volume ◽  
Consensus Sequence ◽  
Raw Data ◽  
Data Submission ◽  
Sequence Read Archive ◽  
Specific Protocol ◽  
Set Up ◽  
Laboratory Submission

This is a SARS-CoV-2 specific protocol that covers the steps needed to submit SARS-CoV-2 consensus sequence to GenBank. If you need a pipeline for frequent or large volume submissions, follow Step 1 in the SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. This protocol assumes (and requires) that the user has a BioProject and BioSamples(s) already registered. Complete in order:: 1. Populate your templates first. 2. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject Step-by-step instructions for establishing a new NCBI laboratory submission account and for creating and linking a new BioProject to an existing umbrella effort. SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample. Users can modify this protocol to just create a BioSample with no linked raw data. 3. SARS-CoV-2 NCBI consensus submission protocol: GenBank (included protocol) Required: established BioProject and BioSamples Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data. Version history: V3: Direct links provided to download metadata templates (instead of hosting duplicate files). minor edits throughout the protocol.

scholarly journals Radiation Therapy Digital Data Submission Process for National Clinical Trials Network

2014 ◽  
Vol 90 (2) ◽  
pp. 466-467 ◽  
Author(s):  
Jialu Yu ◽  
William Straube ◽  
Charles Mayo ◽  
Tawfik Giaddui ◽  
Walter Bosch ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Radiation Therapy ◽  
Digital Data ◽  
Data Submission ◽  
Submission Process

scholarly journals What Factors Influence Where Researchers Deposit their Data? A Survey of Researchers Submitting to Data Repositories

2015 ◽  
Vol 10 (1) ◽  
pp. 68-81 ◽  
Author(s):  
Shea Swauger ◽  
Todd J. Vision
Keyword(s):  
Survey Data ◽  
Funding Agency ◽  
Relative Importance ◽  
Data Repositories ◽  
Data Submission ◽  
Phylogenetic Data ◽  
Submission Process

In order to better understand the factors that most influence where researchers deposit their data when they have a choice, we collected survey data from researchers who deposited phylogenetic data in either the TreeBASE or Dryad data repositories. Respondents were asked to rank the relative importance of eight possible factors. We found that factors differed in importance for both TreeBASE and Dryad, and that the rankings differed subtly but significantly between TreeBASE and Dryad users. On average, TreeBASE users ranked the domain specialization of the repository highest, while Dryad users ranked as equal highest their trust in the persistence of the repository and the ease of its data submission process. Interestingly, respondents (particularly Dryad users) were strongly divided as to whether being directed to choose a particular repository by a journal policy or funding agency was among the most or least important factors. Some users reported depositing their data in multiple repositories and archiving their data voluntarily.

2008 Update on the Medicare Exceptions Process

2008 ◽  
Vol 18 (1) ◽  
pp. 10-16
Author(s):  
Robert C. Fifer
Keyword(s):  
Close Attention ◽  
Submission Process ◽  
Final Rule ◽  
Fee Schedule

Abstract Since 1999 when Medicare caps first became effective, providers have had to pay close attention to the claims process. This article summarizes the Medicare Exceptions Process that, for 2007, underwent a number of changes. The Centers for Medicare and Medicaid Services (CMS) Physician Fee Schedule Final Rule of November 27, 2007 made three important changes. These changes addressed certification for patient plan of care, personnel qualifications for therapists, and a review of Part B policies and their application to Part A settings that are projected to go into effect in July of 2008. Particular attention was given to explanations of the manual submission process and the change in definitions of “complexities” and of a “therapist.”

Responsibility for Raw Data.

1962 ◽  
Vol 17 (9) ◽  
pp. 657-658 ◽  
Author(s):  
Leroy Wolins
Keyword(s):  
Raw Data
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