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….”

Green digitization: Botanical collections data answer real-world questions | EurekAlert! Science News

“Special issue of Applications in Plant Sciences explores new developments and applications of digital plant data

Even as botany has moved firmly into the era of “big data,” some of the most valuable botanical information remains inaccessible for computational analysis, locked in physical form in the orderly stacks of herbaria and museums. Herbarium specimens are plant samples collected from the field that are dried and stored with labels describing species, date and location of collection, along with various other information including habitat descriptions. The detailed historical record these specimens keep of species occurrence, morphology, and even DNA provides an unparalleled data source to address a variety of morphological, ecological, phenological, and taxonomic questions. Now efforts are underway to digitize these data, and make them easily accessible for analysis. Two symposia were convened to discuss the possibilities and promise of digitizing these data–at the Botanical Society of America’s 2017 annual meeting in Fort Worth, Texas, and again at the XIX International Botanical Congress in Shenzhen, China. The proceedings of those symposia have been published as a special issue of Applications in Plant Sciences; the articles discuss a range of methods and remaining challenges for extracting data from botanical collections, as well as applications for collections data once digitized. Many of the authors contributing to the issue are involved in iDigBio (Integrated Digitized Biocollections), a new “national coordinating center for the facilitation and mobilization of biodiversity specimen data,” as described by Dr. Gil Nelson, a botanist at Florida State University and coeditor of this issue….”

FFAR awards $1 million grant to create open source technology for gene discovery in plants | Crops | hpj.com

“The starting point will be approximately 1,000 human kinase inhibitors carefully selected from a library of chemical compounds donated to the partnership from eight pharmaceutical companies. The set will be distributed without restriction to scientists studying other plants and traits, thus serving as a broadly useful platform. The team has agreed to operate under open access principles —specifically prohibiting filing for IP on any of the results and will communicate the results widely….”

DO NOT PUBLISH, or Sometimes, open data/open access not ideal – UC Berkeley Library News

“Some fields such as paleontology and archaeology have long maintained restrictions on the publication of site locations and promoted government policies and regulations to limit collection and trade in fossils, artefacts, and culturally sensitive and/or scientifically important material. Organizations such as the U.S. Forest Service do not disclose geospatial data in order to protect research sites. Other solutions include modification of research permits so that endangered species locations are not automatically uploaded into wildlife databases and masking such records on private land, as presently occurs in some states in the United States.

Is this relevant to any public health research? Other than personally identifiable information, what types of health data should not be made widely available?”

Thoreau’s 200th birthday brings gift for botanists | Harvard Gazette

“In honor of Thoreau’s 200th birthday, on July 12, hundreds of new images of his specimens, along with the data associated with them, will be posted online, part of a larger effort to digitize and open to the public the 5.5 million dried plant specimens in the Herbaria’s collection.

“I think it’s fair to say that the data that live inside these cabinets has been dark for far too long,” Davis said. “My vision for the collections is that we make everything online and accessible to the world.”

That larger effort has meant adopting a new “open-access digitization policy,” available on the Office for Scholarly Communication website, that puts most of the images — excepting those whose copyright is held by other institutions or individuals — in the public domain….

“The Herbaria is the first Harvard museum to adopt an open-access policy for its digitization projects,” said Peter Suber, director of the Office for Scholarly Communication. “Lifting restrictions from the bulk of its digital reproductions will bring this unique botanical collection to a global audience, and advance the Herbaria’s mission of research and education.” …”

Biodiversity Heritage Library – Expanding Access to Biodiversity Literature

“Expanding Access to Biodiversity Literature, which is funded generously by the Institute of Museum and Library Services (IMLS), will significantly increase online access to biodiversity material by positioning BHL as an on-ramp for biodiversity content providers that would like to contribute to the national digital library infrastructure through the Digital Public Library of America (DPLA). The grant proposes to address challenges facing content providers—including insufficient amounts of content, indexing of scientific names, and metadata creation—and make necessary digital infrastructure enhancements by creating an innovative model for open access to data and to support collaboration among these institutions. The project would meet the goals of the IMLS National Leadership Grants for Libraries Program by increasing access to digital services, expanding the range and types of digital content available, improving discoverability, and supporting open access….The project runs from October 1, 2015 to September 30, 2017 and will be conducted by the New York Botanical Garden in partnership with Harvard University, the Missouri Botanical Garden, and the Smithsonian Institution Libraries….”

OpenPlant

“OpenPlant is a joint initiative between the University of Cambridge, John Innes Centre and the Earlham Institute, funded by the BBSRC and EPSRC as part of the UK Synthetic Biology for Growth programme. 

Synthetic Biology offers the prospect of reprogrammed biological systems for improved and sustainable bioproduction. While early efforts in the field have been directed at microbes, the engineering of plant systems offers even greater potential benefits. Plants are already cultivated globally at low cost, harvested on the giga-tonne scale, and routinely used to produce the widest range of biostuffs, from fibres, wood, oils, sugar, fine chemicals, drugs to food.

There is urgent need to improve our ability to reprogram crop metabolism and plant architecture in the face of global threats from new pathogens, climate change, soil degradation, restricted land use, salinity and drought. The next generation of DNA  tools for “smart” breeding of crop systems should be shared – to promote global innovation and equitable access to sustainable bioeconomies….”

PBJ is now a leading open access plant journal – Daniell – 2017 – Plant Biotechnology Journal – Wiley Online Library

“Welcome to the first issue of the fifteenth volume of Plant Biotechnology Journal. I would like to start this editorial by announcing the successful transition of PBJ from a subscription-based journal to an open access journal supported exclusively by authors. This resulted in enhanced free global access to all readers. I applaud the PBJ management team for offering free open access to all articles published in this journal in the past 14 years. As the first among the top ten open access plant science journals, based on 2016 citations, PBJ is very likely to be ranked among the top three journals publishing original research. PBJ is now compatible with mobile platforms, tablets, iPads, and iPhones and offers several new options to evaluate short- and long-term impact of published articles, including Altmetric scores, article readership, and citations….”