Digital Data in Biodiversity Research Conference
The Annual Conference
Research
Research Spotlight: July 2018
Digital Coyote; an online archive of skulls
Contributed by: Osrica Mclean and Declan McCabe
How can you provide an authentic opportunity for undergraduate students to study geographical variation without hauling them to major metropolitan museums and arranging access to valuable specimens? This question started a slightly obsessive odyssey that began with a single coyote skull and now stands at 125 skulls….and counting.
Workshop Report: Developing an ontology for insect natural history data
Research Spotlight: February 2018
From the Tropics to the Drawer and Back: Digitized New World Swallowtail Butterfly Specimens Inform Biodiversity Patterns
Contributed by: Hannah Owens from the Florida Museum of Natural History, University of Florida
ICEDIG: Innovation and consolidation for large scale digitization of natural heritage
Imagine an ADBC-type program for the EU and related countries with their very own version of Thematic Collection Networks and an iDigBio-like hub. This very idea is coming soon with the monicker: DiSSCo -- Distributed System of Scientific Collections. How will it be structured? What human resources will be needed? What about the cyberinfrastructure? What experiences and lessons learned can iDigBio share to benefit DiSSCo?
Research Spotlight: January 2018
New Insights from Old Herbarium Specimens
Contributed by Richard B. Primack (Boston University; primack@bu.edu) and Charles G. Willis (Harvard University; charleswillis@fas.harvard.edu)
“Live in each season as it passes - breathe the air, drink the drink, taste the fruit & resign yourself to the influence of each.” Thoreau, in his Journal. 1835
Big Data and Bugs: How Massively Collected Biodiversity Data Are Changing the Way We Do Insect Science - Symposium at EntSoc 2017
by Deborah Paul, Ana Dal Molin, and Pam Soltis, with contributions from all symposium presenters. Symposium from iDigBio and Universidade Federal do Espírito Santo, Brazil
Natural History Collections as Primary Data in Ecological Research
Prologue: Many of us in the ADBC world look for ways to expand the community of users of museum collections data and to increase the ways in which collections data are used. Recently, in Trends in Ecology and Evolution (TrEE), an opinion piece was published by Scott A. Morrison, et al. titled "Equipping the 22nd-Century Historical Ecologist." In this paper, Morrison, et al.
Research Experiences for Undergraduates in Digitized Collections Data
Contributed by Pam Soltis and Adania Flemming
iDigBio supported five students in its inaugural mini-REU site program during summer, 2017. This program, modeled on NSF’s Research Experiences for Undergraduates Program, was developed to provide undergraduates with research opportunities using digitized natural history collection data.
Research Spotlight: September 2017
Using convolutional neural networks to automate tropical pollen counts and identification
Contributed by: Derek Haselhorst, Program in Ecology, Evolution and Conservation Biology, University of Illinois
Research Spotlight: August 2017
Collections Data Reveals Complex Plant/Pollinator Network, Inspires Research
Contributed by Dylan Ricke and Annika Rose-Person, Archbold Biological Station
Shenzhen goes green for IBC 2017
Developing a Synthesis of Systematic Resources (SYNTHESYS)
contributors: Deborah Paul, Vince Smith, Laurence Livermore
Research Spotlight: June 2017
Hole-y Plant Databases! Understanding and Preventing Biases in Botanical Big Data
Research Spotlight: July 2017
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.
Research Spotlight: May 2017
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.
Research Spotlight: April 2017
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.
AIBS Communications Boot Camp
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!
Software Carpentry goes to TDWG and Costa Rica - Two Firsts
By Deborah Paul, with contributions by Matthew Collins and Alex Thompson
Research Spotlight: March 2017
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.
Research Spotlight: February 2017
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.
Research Spotlight: January 2017
TDWG 2016: Highlights for biodiversity research
-- Contributed by Shelley James & Libby Ellwood, iDigBio
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.
IBC2017: Call for abstracts
Green digitization: online botanical collections data answering real-world questions
An iDigBio-hosted Symposium at the XIX International Botanical Congress in Shenzhen, China
SPNHC 2017: Call for Abstracts
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
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.
Polygon Madness! Creating them, using them in research
Hi Everyone,
Georeferencing and visualizing biodiversity data for research
Contributed by Deborah Paul (iDigBio – FSU), Shelley James (iDigBio- UF)
Learning Center
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.
BCoN Workshop: Future 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.
Understanding iDigBio's data downloads
Research Spotlight: December 2016
Contributed by-- Matthew Collins, Dan Stoner, and Alex Thompson
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 idigbio@acis.ufl.edu.
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