EukRef – PR2 integration

We are pleased to send an update on the status of EukRef, the 18S annotation initiative. The concept of EukRef was presented in 2014 and officially launched in the summer of 2015. In late 2015 EukRef partnered with a bigger community effort, UniEuk, in what has been a fruitful collaboration. Since its inception, we have organized three curation workshops, in Vancouver, Barcelona, and Roscoff. 60 students have attended these workshops under the supervision of 20 advisors curating more than a hundred eukaryotic groups that represent a significative fraction of the eukaryotic diversity. The initiative has been cited in 20 papers and has generated two publication so far: 1) the curation of the ciliates published in Environmental Microbiology and 2) the EukRef whitepaper published in PLoS Biology. Many of the curation end products have yet to be released, but we will be actively working with curators to facilitate release in the coming months. Through the EukRef initiative, we have put together and released a set of tools to facilitate and speed up annotation of eukaryotic 18S rRNA sequences that have been used in workshops and in the community more broadly. We have also actively promoted curation efforts at workshops and beyond. But, most importantly, we have built a community, facilitating the interaction between taxonomic experts and ecologists, students and senior scientists, students with their peers. We hope these interactions will seed future collaborations in protistology.

A primary aim of EukRef has always been to improve the reference databases that host 18S ribosomal RNA data and to become self-sustaining by partnering with existing efforts. We have worked with GenBank, SILVA and PR2. SILVA and GenBank are valuable resources that cover all cellular life. In contrast, PR2 aims to put together curated releases of protist rRNA sequences.  The focus on protists and flexibility of PR2 that arises because of its narrower mandate mean that PR2 and EukRef share common interests and collaborate closely. We’ve realized working more closely together to build an integrated workflow from curation to database integration is a promising path forward. We are very happy to announce that in the following weeks EukRef will integrate with PR2. EukRef pipelines, curation outputs, and our team will become part of PR2.  We hope this joint effort will enable us to push forward ongoing curation and to organize future workshops that will allow us to cover the remaining groups of eukaryotes.

What does this mean? EukRef’s policies on data release will not change; we will continue to make curation products available to other databases and other stakeholders. The curated data will be transferred to UniEuk as a starting point for their taxonomy. Principally, integrating with PR2 means that curation outputs will be directly integrated into the PR2 database, and we will provide tools to make this happen. We will continue to support unconstrained numbers of ranks in curated taxonomies, and these will be released on the EukRef GitHub site along with alignments and trees. 

Thanks for your support through the years, and we look forward to working together in this renewed direction.

All the best,

Javier del Campo
Laura Wegener Parfrey
EukRef Coordinators

Daniel Vaulot
PR2 Coordinator

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2 Responses to “EukRef – PR2 integration

  • Hi,
    Do you have news about the date of the release of EukRef-PR2 integrated database?
    Thank you
    Best regards
    Rob

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