Data Submission to EBI and NCBI Service

EMBL-ABR’s Data Submission to EBI and NCBI ServiceEMBL-icon-data

Background

Making data publicly available is integral to the dissemination of research output. However, data submission to international repositories can be challenging.

Identifying what metadata needs to accompany data submissions, packaging data and metadata, and submitting large numbers of entries is complex and sometimes difficult for individual researchers.

The EMBL-ABR Data Submission Service refers to the guidance and support provided by the EMBL-ABR:QCIF Node to help Australian life science researchers with the process of curating, formatting and managing research data for transfer to existing international data repositories from the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI) — where it will be findable and publicly accessible for reuse.

This service is open to all Australian life science and medical researchers.

Data Submission Service

The QCIF Node team uses a range of scripts and standard operating procedures to support the submission of Australian sequence-based data to the EBI European Nucleotide Archive (ENA) and the NCBI Sequence Read Archive (SRA). The service includes:

  • management of ENA and SRA data submission accounts accessible by researchers
  • automation of upload processes saving researcher’s time
  • optimisation of data transfer processes to ensure data integrity and reduce transfer failure
  • provision of staging infrastructure to facilitate submissions from the researcher’s perspective
  • verification and collation of required metadata prior to submission
  • submission of researcher data to ENA and SRA
  • submission of selected Bioplatforms Australia data
  • maintaining boutique data submission tools such as Tox|Note for venom-gland transcriptome data submission and toxin card creation on Arachnoserver
  • a helpdesk for support.

For an overview of our activity to date, LINK HERE to our June 2018 Summary Report

Do you need help to submit data to EBI or NCBI?

If you have sequence-based data (reads, genome assemblies and assembled sequence and/or annotations) to submit to EBI or NCBI, and you’d like some help, please contact the Data Submission Service team: dc@embl-abr.org.au.

We are also working towards supporting other data types so feel free to contact us to ask for advice on other data types as well.

 

EMBL-ABR Data Submission team

  • Main contact person
  • ENA process design and improvement
  • Quality control of metadata
  • Data submission to EBI ENA
  • Technical support

  Nick Rhodes, QCIF Node

        dc@embl-abr.org.au

  • Manipulation of BAM files using SAM tools
  • Process implementation

  Mike Thang, QCIF Node

  • Process implementation
  • Data submission to NCBI SRA
  • Technical support

  Thom Cuddihy, QCIF Node

Other EMBL-ABR: QCIF Node team members are available on-demand, according to the type of domain knowledge required.