Data Submission to EBI

EMBL-ABR’s Data Submission to EBI 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 need to accompany data submissions, packaging data and metadata, and submitting large number 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 researchers with the process of curating, formatting and managing research data for transfer to existing international data repositories (primarily those at the European Bioinformatics Institute (EBI)), where it will be publicly accessible for reuse.

The QCIF Node team uses a range of scripts and standard operating procedures to support the submission of Australian genomics data to the European Nucleotide Archive (ENA), which is regularly synchronised with the NCBI Short Read Archive (SRA). Since early 2016, the EMBL-ABR: QCIF Node team has been working to further develop and support the service.

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

 

Data submission services 

•  Management of ENA data submission accounts accessible by researchers
•  Helpdesk
•  Submission of researcher data to ENA
•  Submission of selected Bioplatforms Australia data to ENA
•  Improvements to existing ENA data submission processes and infrastructure
•  Broadening the range of supported datatypes for submission
•  Maintaining boutique data submission tools such as Tox|Note for venom-gland transcriptome data submission and toxin card creation on Arachnoserver

 

Do you need help to submit data to EBI?

If you have genomics data (sequencing reads, genome assemblies and assembled sequence and/or annotations) to submit to ENA, and you’d like some help, please contact us.

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
  • Technical support
Nick Rhodes, QCIF Node
dc@embl-abr.org.au
  • Manipulation of BAM files using SAM tools
  • Process implementation
Mike Thang, QCIF Node

 

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