NCBI Databases Overview¶

Table of Contents¶

• General
  • What is NCBI
  • NCBI Center Account
  • Key NCBI Repositories TOSTADAS Supports
• More Information For Each Database

General¶

TOSTADAS lets users submit samples to various NCBI databases with ease. For many of the databases, the pipeline leverages FTP communication to submit samples in an automated manner. TOSTADAS creates many custom log files locally for the submission process and returns valuable information / documents created at the NCBI endpoint as well. Through frequent conversations with personnel from NCBI, TOSTADAS will be continuously updated with any improvments to existing submission mechanisms and/or the implementation of completely new ones from NCBI, in order to provide the best experience for our users.

What is NCBI?¶

The National Center for Biotechnology Information (NCBI) is a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). NCBI plays a crucial role in advancing bioinformatics, genomics, and computational biology. Its primary mission is to provide access to and facilitate the use of a vast array of biomedical and genomic information.

NCBI continues to evolve, offering a wide range of tools and resources to support researchers, healthcare professionals, and the broader scientific community in accessing and utilizing biological information.

NCBI Center Account¶

To submit to NCBI using TOSTADAS, you first need to establish an account with NCBI. If you're submitting on behalf of a group (e.g., a CDC branch, or a state Public Health Lab), you will want to create one account for your center to use. NCBI has information on how to create an account here. You may already have a personal NCBI account, but you should create a Center-level account. You will need to configure the TOSTADAS submission config file with your NCBI account username and password to facilitate submissions via ftp.

TO create a Center Account:

*   Contact the following e-mail for account creation: sra@ncbi.nlm.nih.gov and provide the following information:
    *   Suggested center abbreviation (16 char max)
    *   Center name (full), center URL & mailing address (including country and postcode)
    *   Phone number (main phone for center or lab)
    *   Contact person (someone likely to remain at the location for an extended time)
    *   Contact email (ideally a service account monitored by several people)
    *   Whether you intend to submit via FTP or command line Aspera (ascp)
*   Gain access to an upload directory: Following center account creation, a test area and a production area will be created. Deposit the XML file and related data files into a directory and follow the instructions SRA provides via email to indicate when files are ready to trigger the pipeline.
*   GISAID: GISAID support is not yet implemented but it may be added in the future.

Key NCBI Repositories TOSTADAS Supports:¶

1. BioProject / BioSample:¶

• Description: BioProject and BioSample are databases that organize and store information about biological projects and samples, respectively, providing context for genomic data submissions.
• URL: BioProject / BioSample

2. SRA:¶

• Description: SRA is a repository that archives and provides access to raw sequence data, including next-generation sequencing data, facilitating the exploration of genomic datasets.
• URL: SRA

3. GenBank:¶

• Description: GenBank is a DNA sequence database that collects and archives genomic data from researchers worldwide. It plays a pivotal role in the sharing and dissemination of genetic information.
• URL: General GenBank Docs
• URL2: Formatting for GenBank

More Information For Each Database¶

Each database under NCBI has different functions/use-cases, and therefore each requires a unique set of files, as well as formatting/content properties for each.

It's important to note that the specific requirements for data submission to these databases can evolve, and it's recommended to refer to the latest guidelines provided by the National Center for Biotechnology Information (NCBI) or the respective databases for the most up-to-date information.