Hole-y Plant Databases! Understanding and Preventing Biases in Botanical Big Data
Data Curation Profiles—An Information Science framework for data managers
-- Contributed by Wade Bishop and Kelly White, The University of Tennessee, School of Information Sciences
Data curation profiles (DCPs). DCPs give scientists, researchers, and data managers an enhanced and detailed understanding of the “data story” from the perspective of the data. A DCP “captures requirements for specific data generated by researchers articulated by the researchers themselves” (http://datacurationprofiles.org/purpose) and provides data managers a framework to acquire an in-depth understanding of the particular data curation needs of producers and their intended users. Read more about Wade & Kelly's work with the iDigBio community here.
Using specimens to create a pollinator community assessment of restored tallgrass prairie
-- Contributed by Heather Cray, Department of Environment and Resource Studies, University of Waterloo
Animal species need space – a place to forage, grow, and nest. This is especially true of Lepidoptera (butterflies and moths), whose caterpillars generally feed exclusively on one genus or species of host plant (think monarch butterflies and milkweed). For the 4,000 or so species of native bees in North America, required forage plants and nesting sites vary from common suburban offerings (e.g., patches of bare ground, maples, willows, clover), to specialized needs which are ecosystem-specific. Enter tallgrass prairie – a grassland ecosystem with high forb diversity that supports a dizzying array of invertebrate life. As our continent’s most endangered ecosystem, the 1-3% that remains is a mix of remnant and restored habitat, and restoration efforts-- both large and small, are ongoing. Read more here.
Publishing a new species? Add the unique identifiers!
Citation of voucher specimen data can be problematic. There are currently no formulated rules for how to cite a digital specimen in a publication, but data aggregators such iDigBio, GBIF, and VertNet offer suggestions. Pensoft is leading the way by providing efficient methods for publishing digital data (see their blog post here) - but it still rarely happens, or occurs in a non-systematic way. Recently, with my colleague Dr George Argent, a new species of Rhododendron from Mount Yule, Papua New Guinea was published in the February 2017 online volume of the Edinburgh Journal of Botany. The digital data for the isotype housed at the Bishop Museum is available through iDigBio and we wanted to cite this information in the published paper. As a test case, we added the Darwin Core occurrenceID and a link to the iDigBio record page. Read more here.
The scientific view from behind the microphone
Imagine it. The sweaty palms, the nervous fidgeting. You're sitting in the waiting room of the radio station, the governors' office, or waiting to speak with the Chair of your Department. You begin question your preparation - What is the key message and main talking points? Is there an engaging and relevant story to highlight the science? Does it fit with the audience you will be engaging with? You begin cursing that you didn't have more practice!
By Deborah Paul, with contributions by Matthew Collins and Alex Thompson
Collecting trends: how wars and human history influence biological collections
-- Contributed by Vaughn Shirey, The Academy of Natural Sciences of Drexel University
A large portion of my research in The Gelhaus Lab at The Academy of Natural Sciences of Drexel University relies heavily on digitized specimen data and metadata, specifically the who, when, and where of specimen collection. “Big data” research has risen in popularity since high-performance computing has made it easier for researchers to conduct analyses of groups of organisms overnight; however, additional considerations to the use of large datasets should be taken into account. My research focuses on the historical biases present in natural history collection data, including identifying collection bias and gaps in data due to human history. Read more here.
Allocating more memory to OpenRefine - and other helpful information for handling large datasets
-- Contributed by Chris Evelyn, University of California - Santa Barbara, along with Deborah Paul and Shelley James, iDigBio
This month's Research Spotlight contribution resulted from a recent iDigBio workshop where participants learned the basics of OpenRefine. Finding a limitation to the size of the dataset that could be manipulated, Chris found the following solution to working with large datasets from iDigBio and other biodiversity data aggregators. OpenRefine (formerly Google Refine) is a powerful tool for helping with the cleaning of messy data - ideal for natural history collection managers, data managers, and researchers using biodiversity data alike. Read more here.
TDWG 2016: Highlights for biodiversity research
The Biodiversity Information Standards (TDWG) annual meeting in 2016 had the theme of "Standards Supporting Innovation in Biodiversity and Conservation". Understanding the use of biodiversity standards, and having clear and concise documentation, is essential for the creation, aggregation and downstream use of biodiversity data, and it is exciting to see the diverse TDWG community helping to clarify and expand on the already existing data standards. Read more here.
Green digitization: online botanical collections data answering real-world questions
An iDigBio-hosted Symposium at the XIX International Botanical Congress in Shenzhen, China
The Society for Preservation of Natural History Collection's (SPNHC) 2017 Conference, "The Next Generation in Best Practices" is being held in Denver, Colorado, from June 18 - 24, 2017, hosted by the Denver Museum of Nature and Science and the Denver Botanic Gardens.
Second Update: Inaugural Digital Data in Biodiversity Research Conference, 5-6 June 2017, Ann Arbor, Michigan. Conference sponsors include iDigBio, the University of Michigan Museum of Zoology, the University of Michigan Herbarium, and the University of Michigan Museum of Paleontology.
Contributed by Deborah Paul (iDigBio – FSU), Shelley James (iDigBio- UF)
Biodiversity research is a constantly evolving field of science, and scientists are continuously looking for knowledge and skills for the analysis of biocollections data to advance the understanding of the natural world. iDigBio can offer professional training opportunities through workshops, webinars and conferences. Here we outline some tutorials and workshop lessons and webinars already available that you might find useful for biodiversity data research.
iDigBio will be participating in a workshop to consider future research opportunities arising from current national initiatives to digitize and mobilize images and associated data from U.S. biodiversity collections. The meeting will be held in Washington, DC, on January 5-6, 2017, and is being sponsored by the Biodiversity Collections Network (BCoN) Research Coordination Network. Participation in this workshop is by invitation only.
Research Spotlight: December 2016
Downloaded data from iDigBio serve as a base for important biodiversity research. It is important to understand how to interpret the way data are represented in the Darwin Core Archives (DwC-A) that you retrieve from our download system either through the portal or the download API. For more information about our data processes and how to use our data, feel free to email firstname.lastname@example.org.
by Deb Paul
iDigBio had a blast at ICE XXV International Congress of Entomology, held September 25-30, in Orlando, Florida.. The event brought together thousands of scientists from around the world under the theme “Entomology without Borders.” iDigBio staff participated in two symposia, the Insect Expo, and hosted the iDigBio booth in the ICE Exhibit Hall.
Mapping Life – Quality Assessment of Novice vs. Expert Georeferencers
-- Contributed by Elizabeth R. Ellwood, Florida State University, with Henry L. Bart, Jr., Michael H. Doosey, Dean K. Jue, Justin G. Mann, Gil Nelson, Nelson Rios, Austin R. Mast
Citizen scientists participate in a host of activities that advance scientific research. These individuals are not trained scientists, but their contributions to research enable scientists to scale up their research across taxa and geographies. Read more here.
Bees, bees and more bees - or are there? Monitoring the status of US bee populations using biological collections.
-- Contributed by Jillian Goodwin, iDigBio, interviewing Sam Droege, USGS Patuxent Wildlife Research Center
Sam Droege heads the USGS Native Bee Inventory and Monitoring Lab based at the Patuxent Wildlife Research Center, Maryland, and is working with other researchers to assess the status of bees nationwide.
Using island biogeography to investigate a weird and scenic landscape in southern Idaho
-- Contributed by Katie Peterson, PhD Student, Parent Lab, Department of Biological Sciences, University of Idaho
I am currently a third year PhD student at the University of Idaho in the Parent Lab. The Parent Lab studies the biodiversity and evolution of organisms that have recently colonized novel, “blank slate”, environments on islands....read more here.
For the third straight year, iDigBio hosted a full-day workshop on research methods using digitized herbarium specimen data at the annual Botany conference (Botany 2016, Savannah, GA), sponsored by the Botanical Society of America and its affiliated societies. After successful workshops on Georeferencing (
Specimens collected in Nicaragua by American mycologist Charles Leonard Smith in the late 19th century were thought to have been lost for over 100 years.Through records created on the MyCoPortal, Gregorio Delgado and Ondřej Koukol of EMLab P&K (Phoenix, AZ) and Charles University (Prague, Czech Republic), respectively, were able to
Island Biology and iDigBio - expanding the role of biological specimens in evolution, ecology, and island conservation research
Preserving historic bee specimens to protect future bee biodiversity
-- Contributed by Joan Meiners, PhD Student, Ernest Lab, School of Natural Resources and Environment, University of Florida
For my PhD research in Dr. Morgan Ernest's lab at the University of Florida, I am using large datasets of occurrence records of native bees and their habitat associations to try to understand native bee biodiversity and foraging patterns...read more here.
An iDigBio-hosted Symposium at the International Botanical Congress in Shenzhen, China