New semi-automated process introduced by F1000 and the Wellcome Sanger Institute to accelerate publication and review of genome notes
The Wellcome Sanger Institute’s Tree of Life program has announced ambitious plans to accelerate publication of genome notes from approximately 30 per month to 200, expanding access to research that is supporting advances in agriculture, conservation, and medicine. This significant increase will be facilitated by a new specialized workflow developed by F1000 and the Wellcome Sanger Institute for Wellcome Open Research.
The Darwin Tree of Life program, led by the Wellcome Sanger Institute, aims to sequence the genome of every findable species in the UK and Ireland. It is part of the broader Earth BioGenome Project, a moonshot for biology which brings together groups to sequence all life on earth. Each completed genome produced by the Tree of Life program is reported in an open research genome note, enabling the international scientific community to interpret, reference, and reuse the data.
Powered by innovative open research publisher F1000, the Wellcome Open Research platform launched its Tree of Life Gateway in May 2021. Over 1,900 genome notes from researchers at universities, museums and horticultural organizations across the UK and Ireland are now included in the Gateway, including the genome sequences of the red squirrel, Eurasian river otter, and the deathwatch beetle.
To realize the Tree of Life program’s ambition to publish and index genome notes for each of the approximately 30,000 findable UK and Irish species, a new process was developed which combines an innovative publishing workflow with robust research integrity standards.
James Cleaver, Head of Publishing at F1000, explained: “The highly structured nature of the Tree of Life genome notes created a unique opportunity to reimagine the entire publication workflow. We’ve partnered with the teams at the Wellcome Sanger Institute to design a streamlined process that combines the opportunities of new publishing technology with human expertise. That human oversight remains central to ensuring the integrity and reliability of published research. We are delighted to be helping to accelerate the impact of the genome notes and the Tree of Life program’s genome sequencing efforts.”
The first stage of the new workflow uses computer-aided review of each submission. This records metrics on genome continuity, structural accuracy, base accuracy, functional completeness and chromosome status. These metrics are embedded directly into published articles, providing transparency for both reviewers and readers.
Following online publication and the computer-aided review, the genome notes undergo Wellcome Open Research’s post-publication open peer review process, with an invited expert reviewer or a peer reviewer panel. This combined approach, using automated benchmarking and independent human review, has been approved by indexers such as PubMed.
Professor Mark Blaxter, Head of the Tree of Life program at the Wellcome Sanger Institute, said: “The reference genomes produced here at the Sanger Institute are released to the global community to transform the way biological science is done, at pace. Genome Notes provide a rapidly-published and citeable resource that credits our collector and taxonomist collaborators as well as our genome sequencing teams. Now genome note publication will be able to better keep up with our sequencing machines.”
About F1000
F1000 provides innovative open access publishing platforms offering rapid publication and open peer review, whilst supporting data deposition and sharing for the research community.
F1000’s own publishing platform, F1000Research, was launched in 2013 and was the first open research publishing platform combining the ability to publish rapidly with functionality to ensure transparency, robustness and reproducibility of research.
Building upon the growth and success of its core platform, F1000 also provides fully managed, open research publishing services directly to research funders, learned societies and institutions, including Wellcome, the Gates Foundation and the European Commission.
F1000 Research Ltd is wholly owned by Taylor & Francis.
About the Wellcome Sanger Institute
The Wellcome Sanger Institute is a world leader in genomics research. We apply and explore genomic technologies at scale to advance understanding of biology and improve health. Making discoveries not easily made elsewhere, our research delivers insights across health, disease, evolution and pathogen biology. We are open and collaborative; our data, results, tools, technologies and training are freely shared across the globe to advance science.
Funded by Wellcome, we have the freedom to think long-term and push the boundaries of genomics. We take on the challenges of applying our research to the real world, where we aim to bring benefit to people and society.
Find out more at www.sanger.ac.uk or follow us on Bluesky, X, Instagram, Facebook, LinkedIn and on our Blog.
Media contacts
F1000: Mark Robinson, mark.robinson@tandf.co.uk
Wellcome Sanger Institute: Carmen Denman Hume, press.office@sanger.ac.uk
Graphic: Professor Mark Blaxter, Wellcome Sanger Institute. Used with permission.