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.

Extending U.S. Biodiversity Collections to Promote Research and Education

“Our national heritage of approximately one billion biodiversity specimens, once digitized, can be linked to emerging digital data sources to form an information-rich network for exploring earth’s biota across taxonomic, temporal and spatial scales. A workshop held 30 October – 1 November 2018 at Oak Spring Garden in Upperville, VA under the leadership of the Biodiversity Collections Network (BCoN) developed a strategy for the next decade to maximize the value of our collections resource for research and education. In their deliberations, participants drew heavily on recent literature as well as surveys, and meetings and workshops held over the past year with the primary stakeholder community of collections professionals, researchers, and educators.

Arising from these deliberations is a vision to focus future biodiversity infrastructure and digital resources on building a network of extended specimen data that encompasses the depth and breadth of biodiversity specimens and data held in U.S. collections institutions. The extended specimen network (ESN) includes the physical voucher specimen curated and housed in a collection and its associated genetic, phenotypic and environmental data (both physical and digital). These core data types, selected because they are key to answering driving research questions, include physical preparations such as tissue samples and their derivative products such as gene sequences or metagenomes, digitized media and annotations, and taxon- or locality-specific data such as occurrence observations, phylogenies and species distributions. Existing voucher specimens will be extended both manually and through new automated methods, and data will be linked through unique identifiers, taxon name and location across collections, across disciplines and to outside sources of data. As we continue our documentation of earth’s biota, new collections will be enhanced from the outset, i.e., accessioned with a full suite of data. We envision the ESN proposed here will be the gold standard for the structured cloud of integrated data associated with all vouchered specimens. These permanent specimen vouchers, in which genotypes and phenotypes link to a particular environment in time and space, comprise an irreplaceable resource for the millennia….”

BCoN Report: Extending U.S. Biodiversity Collections to Promote Research and Education

The Biodiversity Collections Network has released its new report, Extending U.S. Biodiversity Collections to Promote Research and Education.  You are invited to download and share the summary brochure and to review the longer report that provides additional detail about this vision for the future. …”

Report urges massive digitization of museum collections | Science | AAAS

“The United States should launch an effort to create an all-encompassing database of the millions of stuffed, dried, and otherwise preserved plants, animals, and fossils in museums and other collections, a U.S. National Science Foundation (NSF)–sponsored white paper released today urges. The report, titled Extending U.S. Biodiversity Collections to Promote Research and Education, also calls for new approaches to cataloging digitized specimens and linking them to a range of other data about each organism and where it was collected. If the plan is carried out, “There will be [a] huge potential impact for the research community to do new types of research,” says NSF biology Program Director Reed Beaman in Alexandria, Virginia.

The effort could take decades and cost as much as half a billion dollars, however, and some researchers are worried the white paper will not win over policymakers. “I just wish that the report focused more on the potential benefits for noncollections communities,” says James Hanken, director of the Harvard Museum of Comparative Zoology in Cambridge, Massachusetts.

For the past 8 years, NSF has sponsored the $100 million, 10-year Advancing Digitization of Biodiversity Collections program, which has paid for nearly 62 million plant and animal specimens to be digitally photographed from multiple angles for specific research studies. New technology has greatly sped up the process. Already, researchers studying natural history and how species are related are reaping the benefits of easy access to a wealth of information previous locked in museums….”

The International Tree?Ring Data Bank (ITRDB) revisited: Data availability and global ecological representativity – Zhao – – Journal of Biogeography – Wiley Online Library

Abstract:  Aim. The International Tree?Ring Data Bank (ITRDB) is the most comprehensive database of tree growth. To evaluate its usefulness and improve its accessibility to the broad scientific community, we aimed to: (a) quantify its biases, (b) assess how well it represents global forests, (c) develop tools to identify priority areas to improve its representativity, and (d) make available the corrected database….

Methods. We identified and corrected formatting issues in all individual datasets of the ITRDB. We then calculated the representativity of the ITRDB with respect to species, spatial coverage, climatic regions, elevations, need for data update, climatic limitations on growth, vascular plant diversity, and associated animal diversity. We combined these metrics into a global Priority Sampling Index (PSI) to highlight ways to improve ITRDB representativity.

Results. Our refined dataset provides access to a network of >52 million growth data points worldwide. We found, however, that the database is dominated by trees from forests with low diversity, in semi?arid climates, coniferous species, and in western North America. Conifers represented 81% of the ITRDB and even in well?sampled areas, broadleaves were poorly represented. Our PSI stressed the need to increase the database diversity in terms of broadleaf species and identified poorly represented regions that require scientific attention. Great gains will be made by increasing research and data sharing in African, Asian, and South American forests.

Main conclusions. The extensive data and coverage of the ITRDB show great promise to address macroecological questions. To achieve this, however, we have to overcome the significant gaps in the representativity of the ITRDB. A strategic and organized group effort is required, and we hope the tools and data provided here can guide the efforts to improve this invaluable database….”

New study makes 52 million tree stories more accessible to science

“The world’s primary archive of tree ring data, which holds more than 52 million cost-free records spanning 8,000 years of history, has gotten a makeover by scientists from four countries committed to making science more accessible.

 

The co-authors report in the Journal of Biogeography that the International Tree Ring Data Bank, developed in 1974 and populated by hundreds of contributing scientists and agencies, had only been used for a handful of studies at a global scale due to inconsistent data accessibility and formatting.

The team corrected thousands of formatting issues that prevented files from being read, requiring scientists to either manually correct errors or omit large portions of available data. “The data correction took weeks of intensive work,” says Manzanedo. “In the sample records, any misplaced character or erroneous empty space would make a whole file unreadable. Finding those was sometimes like finding a needle in a haystack. We kept a log with our decisions to ensure the future traceability of the process.” …”
 

Centuries-Old Plant Collection Now Online — A Treasure Trove For Researchers : NPR

“Funded by the National Science Foundation, the Mid-Atlantic Megalopolis Project will put about 800,000 records from about a dozen herbaria online via high-resolution photos of plant specimens that span the urbanized corridor from New York City to Washington, D.C….”