Data Submission to International Repositories

We are a Node in the EMBL Australia<br />
Bioinformatics Resource community network. Link here to learn more about this network

EMBL-ABR Data Submission Service

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 Data Submission Service of EMBL-ABR (Australian Bioinformatics Resource) helps 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.

EMBL-ABR’s Data Submission Service is open to all Australian life science and medical researchers.

EMBL-ABR’s Data Submission Service

The QFAB team from the EMBL-ABR:QCIF Node 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 include:

  • 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.

 

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:QCIF Node 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 involved on-demand and according to the type of domain knowledge required.