LCVP, The Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants | Scientific Data

Abstract:  The lack of comprehensive and standardized taxonomic reference information is an impediment for robust plant research, e.g. in systematics, biogeography or macroecology. Here we provide an updated and much improved reference list of 1,315,562 scientific names for all described vascular plant species globally. The Leipzig Catalogue of Vascular Plants (LCVP; version 1.0.3) contains 351,180 accepted species names (plus 6,160 natural hybrids), within 13,460 genera, 564 families and 84 orders. The LCVP a) contains more information on the taxonomic status of global plant names than any other similar resource, and b) significantly improves the reliability of our knowledge by e.g. resolving the taxonomic status of ~181,000 names compared to The Plant List, the up to date most commonly used plant name resource. We used ~4,500 publications, existing relevant databases and available studies on molecular phylogenetics to construct a robust reference backbone. For easy access and integration into automated data processing pipelines, we provide an ‘R’-package (lcvplants) with the LCVP.

 

Editorial: About the possibility of Applied Vegetation Science going Gold Open Access – vegsciblog.org

“Some time ago, IAVS was put in front of quite an important decision. Two of our journals, the Journal of Vegetation Science and Applied Vegetation Science, are currently distributed under the hybrid open-access model, when readers pay, and authors publish for free (while allowing publishing also open access articles for an extra cost). However, Wiley, our publisher, asked us to transfer AVS into the Gold Open Access model (Gold OA) when readers read for free, but authors pay. Wiley argues that the transition into OA is a current trend in publishing and meets the demands of readers and funders. However, the unsaid truth also is that the publishing landscape is changing. Researchers started to use alternative (and often illegal) ways of getting paywalled papers, and the high cost of journal subscriptions lead many libraries and institutions to cancel it. This motivates publishers to transit more and more journals into the Gold OA model, which should secure their profit and in turn also the income of associations, dependent on money from journal publishing. The downside of the Gold OA model, which may not be so apparent to readers, but becomes painfully apparent to the authors, is the costly Article Processing Charge or Article Publication Charge (APC) needed to be paid upon acceptance of the paper for the publication (for AVS currently proposed at £1900 per article)….”

Editorial: About the possibility of Applied Vegetation Science going Gold Open Access – vegsciblog.org

“Some time ago, IAVS was put in front of quite an important decision. Two of our journals, the Journal of Vegetation Science and Applied Vegetation Science, are currently distributed under the hybrid open-access model, when readers pay, and authors publish for free (while allowing publishing also open access articles for an extra cost). However, Wiley, our publisher, asked us to transfer AVS into the Gold Open Access model (Gold OA) when readers read for free, but authors pay. Wiley argues that the transition into OA is a current trend in publishing and meets the demands of readers and funders. However, the unsaid truth also is that the publishing landscape is changing. Researchers started to use alternative (and often illegal) ways of getting paywalled papers, and the high cost of journal subscriptions lead many libraries and institutions to cancel it. This motivates publishers to transit more and more journals into the Gold OA model, which should secure their profit and in turn also the income of associations, dependent on money from journal publishing. The downside of the Gold OA model, which may not be so apparent to readers, but becomes painfully apparent to the authors, is the costly Article Processing Charge or Article Publication Charge (APC) needed to be paid upon acceptance of the paper for the publication (for AVS currently proposed at £1900 per article)….”

JVS/AVS Chief Editors’ opinion on Open Access – vegsciblog.org

“This Commentary is a part of the series asking the question: should Applied Vegetation Science, the journal owned by IAVS [International Association of Vegetation Science] and published by Wiley, become Gold Open Access? For the context and link to other Commentaries, please visit Editorial….

The mission of IAVS and its journals is to serve all the vegetation scientists globally. From this perspective, changing the journals to Open Access publication model presents a risk of exclusion of many colleagues who cannot afford to pay APCs. Therefore, we prefer to wait until the systems that would guarantee equal access to publication funds are implemented in most of the countries from which we regularly receive submissions. For the moment, we propose that both journals continue to be published under the current hybrid model, in which single articles can be published Open Access if the authors can and wish to pay….”

 

 

JVS/AVS Chief Editors’ opinion on Open Access – vegsciblog.org

“This Commentary is a part of the series asking the question: should Applied Vegetation Science, the journal owned by IAVS [International Association of Vegetation Science] and published by Wiley, become Gold Open Access? For the context and link to other Commentaries, please visit Editorial….

The mission of IAVS and its journals is to serve all the vegetation scientists globally. From this perspective, changing the journals to Open Access publication model presents a risk of exclusion of many colleagues who cannot afford to pay APCs. Therefore, we prefer to wait until the systems that would guarantee equal access to publication funds are implemented in most of the countries from which we regularly receive submissions. For the moment, we propose that both journals continue to be published under the current hybrid model, in which single articles can be published Open Access if the authors can and wish to pay….”

 

 

AoBP ECOS Awards – Buckley Lab at UC Davis

“Beginning in 2020, AoBP will award USD $3,000 annually to each of up to three early-career researchers who have dedicated considerable effort to advancing the goals and ideals of open science.

The AoBP ECOS Awards (Early Career Open Science) aim to promote and celebrate people who are changing science for the better. People who are willing to go against the grain of hype-driven science. Willing to resist cynical citation-chasing. Willing to share their data, code and ideas. Willing to stand up for those who have been historically excluded or mistreated in science. Willing to publish negative results. Willing to promote others who respect these things.

To be eligible for an AoBP ECOS Award, you must have been active in research involving plants and the environment within the last two years, and you must be no more than eight years post-PhD. Scientists of any rank or position are eligible (students, postdocs, technicians, faculty). Individuals can self-nominate or be nominated by others (with the nominee’s agreement)….”

Incredible 19th-Century Botanical Catalog Put Online and Made Interactive

“Designer Nicholas Rougeux has spent the last year combining his love for data visualization with his tech skills to lovingly restore and place 19th-century texts online. After the success of Werner’s Nomenclature of Colours and the geometry tome Byrne’s Euclid, Rougeux is tackling a new topic—botanical illustration.

 

After scouring the internet for different 19th-century botanical catalogs, Rougeux set his sights on Illustrations of the Natural Orders of Plants by Elizabeth Twining. This 1868 two-volume catalog is the second edition of a work first published in 1849 (volume 1) and 1855 (volume 2). The rare first edition can go for upward of £40,000 (about $49,000), but luckily for Rougeux, the second edition is available for consultation online at the Internet Archive (volume 1, volume 2) and the Biodiversity Heritage Library….”

Making a Difference- The New ‘Weeds’ Journal | Published in Weeds – Journal of the Asian-Pacific Weed Science Society

“APWSS [Asian-Pacific Weed Science Society] is aware that for some organizations, journals are an essential source of revenue, which fund other activities, such as travel grants for researchers from developing countries. However, making revenue from the journal is not a priority for our Society. Instead, Weedswill be launched as a high-quality ‘Open Access’ (OA) publishing platform, charging only a nominal administrative fee from the authors to cover the costs of using a journal-management web platform….”

Rice Galaxy: an open resource for plant science | GigaScience | Oxford Academic

Abstract

Background

Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. Comparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non?computer savvy rice researchers.

Findings

The Rice Galaxy resource has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes. The Rice Galaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice?bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented.

Conclusions

Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.

Ten years of AoB PLANTS the open access journal for plant scientists: inception and progress since 2009 | AoB PLANTS | Oxford Academic

Abstract:  AoB PLANTS is a not-for-profit, open access, plant science journal and one of three peer-reviewed journals owned and managed by the Annals of Botany Company. This article explains events and thinking that led to the starting of AoB PLANTS and how the unique features of the Journal came to be formalized prior to its launch in September 2009. The article also describes how the Journal’s management developed over the first 10 years and summarizes the Journal’s achievements in a decade where open access journals have proliferated despite subscription journals continuing to dominate the publishing of peer-reviewed botanical science.