(Press-News.org) Imagine the scientific discoveries that would result from a searchable online database containing millions of plant, algae, and fungi specimen records. Thanks to a new set of workflow modules to digitize specimen collections currently preserved in herbaria, something like that might be within reach. The modules are provided by the National Science Foundation's (NSF) Integrated Digitized Biocollections (iDigBio), which is facilitating a collective effort to unify digitization projects across the nation.
"North America's herbaria curate approximately 74 million specimens and only a fraction have made it online," says iDigBio's digitization specialist Dr. Gil Nelson. "Having these data available at one's fingertips will enable advanced queries and new discoveries while ensuring inclusion of the so-called 'dark data' that reside in a significant percentage of the United States' more than 600 active herbaria."
According to recent estimates, approximately half of U.S. herbaria and universities have yet to begin mobilizing data. Nelson coordinated the development of the workflows, working alongside 28 other contributing authors, to provide guidance to institutions just beginning digitization programs as well as those seeking to streamline and tweak their current digitization configuration.
The 14 modules, each organized in seven to 36 easy-to-follow and customizable tasks, cover everything from setting up an imaging station to georeferencing. They also include methods to organize outreach events for public participation in imaging and data transcription. They are downloadable as Portable Document Format (PDF) and editable word processing files on GitHub and as PDF files at iDigBio. A full description of the workflows and their development, along with editable word processing files of the workflow modules, is available in the September issue of Applications in Plant Sciences.
iDigBio first launched working groups in 2012 to address a deficit in online biodiversity data. Six initial modules sparked an increase in digitization, but evolving digitization and curatorial practices made possible more comprehensive task lists. The latest set of modules is the result of continued collaborations, virtual meetings, visits to many herbaria, iDigBio workshops involving over 50 researchers, and contributions from 15 NSF-funded digitization projects.
"The greatest challenge in producing generic, broadly applicable workflows was determining and presenting a consensus statement of agreed-upon components while preserving maximum flexibility for institutional implementation over a broad array of herbaria," says Nelson.
For Nelson, digitization is the starting point of new avenues to guide biological and ecological research. He envisions huge multi-organismal data sets that will enable researchers to study yet-to-be recognized ecological, biological, and cultural relationships. The work at iDigBio is laying the foundation for a very powerful online resource.
iDigBio provides digitization education and resources to institutions across the United States and is funded by the NSF's Advancing Digitization of Biodiversity Collections program (ADBC).
INFORMATION:
Nelson, G., P. Sweeney, L. E. Wallace, R. K. Rabeler, D. Allard, H. Brown, J. R. Carter, et al. Digitization workflows for flat sheets and packets of plants, algae, and fungi. Applications in Plant Sciences 3(9): 1500065. doi:10.3732/apps.1500065
Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal focusing on new tools, technologies, and protocols in all areas of the plant sciences. It is published by the Botanical Society of America, a nonprofit membership society with a mission to promote botany, the field of basic science dealing with the study and inquiry into the form, function, development, diversity, reproduction, evolution, and uses of plants and their interactions within the biosphere. APPS is available as part of BioOne's Open Access collection.
For further information, please contact the APPS staff at apps@botany.org.
COLUMBUS, Ohio - Would a color by any other name be thought of in the same way, regardless of the language used to describe it?
According to new research, the answer is yes.
A new study examines how a culture of nomadic hunter-gatherers names colors, and shows that they group colors into categories that align with patterns of color grouping evident in 110 other world languages.
This study population - the Hadza people of Tanzania - has relatively few commonly shared color words in its language. During the study, the most common response by Hadza participants to a ...
Seasonal flare-ups in patients with multiple sclerosis are caused by plummeting levels of melatonin in the spring and summer, according to research published September 10 in Cell. The study reveals that relapses in patients with this autoimmune disorder are much less frequent in the fall and winter, when levels of the so-called darkness hormone are at their highest, but the reverse is true in the spring and summer seasons.
Moreover, treatment with melatonin improved clinical symptoms in a mouse model of multiple sclerosis by restoring a healthy balance of immune cells ...
The blame for some of chemotherapy's awful side effects may lie with our gut microbes, early evidence suggests. As chemotherapy drugs are eliminated from the body, bacteria in the gastrointestinal tract can latch onto them and transform them into toxic species that cause severe diarrhea. In a Chemistry & Biology article published online on September 10, researchers present ways to shut down the ability of GI microbes to convert chemotherapy drugs to a toxic species in mice as a first step to helping cancer patients.
"The GI microbiota are the great crowd-sourcers of chemistry, ...
Have you ever touched someone else and wondered why his or her skin felt so incredibly soft? Well, now researchers reporting in the Cell Press journal Current Biology on September 10 present evidence that this experience may often be an illusion.
In a series of studies led by Aikaterini Fotopoulou of the University College London, participants consistently rated the skin of another person as being softer than their own, whether or not it really was softer. The researchers suggest that this phenomenon may exist to ensure that humans are motivated to build social bonds ...
Those of you who spend hours at the gym with the aim of burning as many calories as possible may be disappointed to learn that all the while your nervous system is subconsciously working against you. Researchers reporting in the Cell Press journal Current Biology on September 10 have found that our nervous systems are remarkably adept in changing the way we move so as to expend the least amount of energy possible. In other words, humans are wired for laziness.
The findings, which were made by studying the energetic costs of walking, likely apply to most of our movements, ...
For patients and clinicians alike, it's long been a mystery: why do symptoms of multiple sclerosis (MS) seem to get better in the winter and worse in the summer? A group led by Francisco Quintana, PhD, at the Ann Romney Center for Neurologic Diseases at Brigham and Women's Hospital (BWH) and collaborators have found an explanation that could lead to a deeper understanding of the disease and more targeted treatment options for patients. By first looking broadly at possible environmental factors and then deeply at preclinical models of MS, the research team found that melatonin ...
The face of a chimpanzee is decidedly different from that of a human, despite the fact that the apes are our nearest relative in the primate tree. Now researchers at the Stanford University School of Medicine have begun to pinpoint how those structural differences could arise in two species with nearly identical genetic backgrounds.
The key lies in how genes involved in facial development and human facial diversity are regulated -- how much, when and where the genes are expressed-- rather than dissimilarities among the genes themselves. In particular, the researchers ...
NEW YORK, NY - A timed vision test that involves rapidly reading numbers off of cards can be a valuable sideline tool for detecting whether a concussion occurred while playing sports, according to a meta-analysis and systematic review led by NYU Langone Medical Center concussion specialists.
Researchers at the NYU Langone Concussion Center reviewed studies that involved athletes who sustained a concussion during sporting activities and found the vision test, known as the King-Devick test, was 86 percent sensitive in detecting whether a concussion had occurred, as confirmed ...
HOUSTON -- (Sept. 10, 2015) - "Help us find others like Tess." Bo Bigelow's plea jumps off the page of his blog, echoing across the continent from his leafy green home city of Portland, Maine.
When he posted his call to action, all he knew was that his young daughter has a mutation in her USP7 gene and that she has global developmental delay, hip dysplasia and visual impairment caused by her brain (not a problem in her eyes themselves) among other health issues. An article in the New Yorker magazine by Seth Mnookin gave him hope that finding other children with the same ...
Cancer cells commonly rely on glycolysis, the type of metabolism that does not use oxygen to generate their energy however, researchers from Queen Mary University of London's Barts Cancer Institute and the Spanish National Cancer Research Centre (CNIO) in Madrid have now found that not all cancer cells are alike when it comes to metabolism.
PancSCs can make use of a more efficient form of metabolism, called oxidative phosphorylation or OXPHOS, which does use oxygen. OXPHOS uses a part of the cell called mitochondria and it is this which can be targeted with anti-diabetic ...
