Thirty participants gathered virtually for a workshop, Using wikidata to capture and share information about people in paleontology, on March 29-31, 2022. This workshop was a hands-on introduction to finding, editing, and using data in wikidata, using people associated with paleontology collections (e.g., collectors, researchers, collections staff) as subjects. Wikidata offers a centralized, accessible platform for working collaboratively to disambiguate people associated with collections and mobilize biographical information about them.
Since we are virtual again this year we created a way to digitize some of that organic mentoring magic that happens at every conference through the virtual Digital Data Mentorship Program.
Three ways to introduce your biodiversity collections to the world during April’s WeDigBio event (Thursday–Sunday, April 7–10, 2022) and the broader Citizen Science Month!
Let us know your plans by Wednesday, March 23, so that your activities can appear on the calendar and we have enough time to get the WeDigBio stickers and tattoos to you for your participants.
Draba verna flowering. Image taken from: https://awkwardbotany.com/2018/05/23/tiny-plants-draba-verna/
Every year around this time I think about Aldo Leopold’s ode to Draba, a tiny, inconspicuous plant that can serve as an early sign of spring in some areas for the extra observant.
Joshua Benjamin explains to participants what they are seeing when looking in the microscope at the Subalusky's Lab table during the Resource Fair.
The Society of Herbarium Curators and iDigBio are pleased to announce an 8-week "Strategic Planning for Herbaria” online course.
Take this opportunity to introduce new purpose and excitement into your organization. Prepare to relate your herbarium’s compelling vision to stakeholders and discuss long-term goals and strategies with administrators.
Synopsis of Program:
Happy 2022 to all collections’ community colleagues. iDigBio is excited about the biodiversity community’s collective successes in 2021 and is looking forward to an adventurous upcoming year with many new activities on its workplan.
Contributed by Molly Phillips
The end of 2021 is now on the horizon but, if you are like me, your schedule is as busy as ever! I have been thinking about how nice it would be to roll into a ball and block out the world for a little while, which made me think of the marvelous pillbug.
Ghost Jelly (Cyanea nozakii)
Contributed by Lauren Bradley (University of Florida Student and 2021 iDigBio Summer Intern)
Dead Leaf Butterfly! (Kallima inachus)
Contributed by: Lauren Bradley
Autumn is right around the corner, and what a beautiful season it is! Here in Florida, we see the occasional red or yellow leaf during the autumn months, but really, all we can hope for is some cooler weather, and even that isn’t guaranteed. The Kallima inachus seems to agree with us humans in admiring the beauty of autumn, as they have evolved to imitate dead leaves! (Thus giving them their common name, the dead leaf butterfly).
Digitized paleontological collections recontextualize the ecology of introduced turkeys in California
Contributed by: Ashwin Sivakumar & Alexis Mychajliw
Contributed by: Molly Phillips
iDigBio launched its new Digitization Academy this summer with an inaugural course, Introduction to Biodiversity Specimen Digitization. This free, online course focuses on introducing the creation of digital data about biodiversity specimens to those who are just beginning this activity.
iDigBio researchers and staff joined nearly 2000 other attendees from over 60 countries at the virtual Botany Conference, July 18-23, 2021. Talks throughout the conference showcased the essential role of herbaria–and digitized data associated with herbarium specimens–in the botanical sciences.
TDWG 2021, the annual conference of Biodiversity Information Standards, will be held virtually October 18-22, 2021, hosted by the University of Florida. The theme of this year’s conference, Connecting the world of biodiversity data: standards uniting people, processes, and tools, will build on lessons learned during the preceding 18 months of virtual interaction and collaboration during the COVID-19 pandemic. TDWG 2021 will be held on the virtual platform Whova, and the schedule will include keynote lectures, symposia, workshops, demos, contribut
Assessment of the pinned specimen digitization progress of the University of Alaska Museum Insect Collection
Ashley L. Smith, Derek S. Sikes, Taylor L. Kane, Adam Haberski, Jayce B. Williamson, Renee K. Nowicki, Michael J. Apperson
University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, USA
This article was originally published in the Alaska Entomological Society Newsletter AKES_newsletter_2021_n1_a01.pdf (akentsoc.org)
Written by Erica Krimmel.
Thoreau still contributes to climate change research
New study uses Henry David Thoreau’s observations of fruiting times
Digitized museum specimens, such this bluebead lily (Clintonia borealis), were used to determine the time of fruit ripening. © Consortium of Northeast Herbaria.
The Guatemala Biodiversity Portal, a national digitization effort using Symbiota
Contributed by Samanta Orellana
by: Vaughn Shirey, Michael Belitz, Vijay Barve, Rob Guralnick
As the hub for digitization of U.S. natural history collections, iDigBio aims to engage our community in promoting a more diverse, equitable, inclusive, and actively anti-racist community. To that end, the iDigBio team focused on issues of Education, Outreach, Diversity, and Inclusion has compiled this reading list to begin conversations in the classroom, in museum collections, and among colleagues.
Photo courtesy of Jeffrey Weinell, University of Kansas Biodiversity Institute and Natural History Museum
Dear iDigBio Enthusiasts,
I am delighted to report that iDigBio enjoyed an exceptionally successful and productive 2020 made possible in large part by contributions of the many collaborators whose consistent support, involvement, and input have been highly valued and much appreciated. We enter the new year eager to continue integral involvement in the biodiversity collections community.
This latest development for the first time enables shared data management across iDigBio and GBIF, in addition to facilitating a unified, more efficient, and more exhaustive list of US Collections.
Contributed by: Libby Ellwood, Austin Mast, Robert Bruhn and Kevin Love
Contributed by: Molly Phillips
iDigBio is pleased to announce a 7-week "Strategic Planning for Biodiversity Collections” online course.
Take this opportunity to introduce new purpose and excitement into your organization. Prepare to relate your collection’s compelling vision to stakeholders and discuss long-term goals and strategies with administrators.
Unlocking the secret histories of bats in natural history collections
Article by: Caitlin J.Campbell, Graduate Assistant at the UF Department of Biology
Contributed by Cat Chapman
Have you ever been out on a walk through nature, or even in your neighborhood, and saw what appeared to be a clump of tiny leaves, debris, or lichen… only to see it move?
Upon closer inspection of this mysteriously motile clump of detritus, you may see that it has tiny little legs underneath it. It’s alive!
Meet the trash bug!
Written by Erica Krimmel.
Contributed by: Aaron Goodman, Graduate Student Department of Entomology, California Academy of Sciences.
Article by: Zoliswa Nhleko, PhD candidate at the UF School of Natural Resources and Enviroment
Article by: Nattapol Kraisitudomsook, PhD student from the Smith Lab at the University of Florida
Many things have changed rapidly and these are unprecedented and stressful times, but one positive for our team now all working remotely are all of the new coworkers!
Aye-aye, Daubentonia madagascariensis
Deborah L Paul, Capacity Development Manager
Welcome to all of the newly NSF-funded Advancing Digitization of Biodiversity Collections (ADBC) projects. This year we have three new Thematic Collections Networks (TCNs) and six Partners to Existing Networks (PENs) joining the community.
Article contributed by Julie Bokor (UF Center for Precollegiate Education and Training)
Contributed by: J Ryan Allen, Dina Clark and Erin Tripp (University of Colorado)
The 99th Annual Meeting and Centennial Celebration of the American Society of Mammalogists took place 28 June to 2 July 2019, at the birthplace of ASM, Washington, DC. iDigBio helped to mark this important milestone through organizing a session on broadening representation in mammalogy as well organizing the first ever Data Help Desk at ASM.
Climatic Niche Modeling for Beetleweed
(Galax urceolata, Diapensiaceae)
Contributed by: Shelly Gaynor
Bioblitz group photo (Florida Museum Photo Department)
Emerging frontiers in phenological research
Libby Ellwood, Katelin Pearson, and Gil Nelson
Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates
Image Credit: Joe Poston
Augustus Fendler Herbarium Specimens: A Locality Improvement Project
A component of the Southern Rocky Mountain Flora Database Project
Lance J. Gloss and Timothy J. S. Whitfeld
Brown U. Herbarium (BRU)
Dec 2017 - May 2018
Summit 2018 group photo
Utilising publicly available species occurrence records to generate contemporary estimates of medically important snake species distributions
Contributed by: Joshua Longbottom, Liverpool School of Tropical Medicine
European honey bee, Apis mellifera
Image Credit: USGS Bee Inventory and Monitoring Lab
Workshop Group Photo
Contributed by: Timothy J. Baroni & Andrew N. Miller
State University of New York, Cortland, NY and University of Illinois, Champaign, IL
Chlorophyllum molybdites (Image courtesy of Roy Halling)
Rattails and Grenadiers (Family Macrouridae)
Images courtesy of NOAA Okeanos Explorer
Contributed by Randy Singer
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.
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
Dear iDigBio Enthusiasts,
New Insights from Old Herbarium Specimens
“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
by Deborah Paul, Libby Ellwood, Christina Alba, Larry Page
with contributions from our speakers: Dave Tazik, Jennifer McGuire, Anna Monfils, Barry Sinervo, and Elizabeth Martin; and from some participants present at this symposium including (at least): Vince Smith, Mary Klein, Herrick Brown, and Jason Knouft
‘What do we need to leave behind today to position our future selves for success?’
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
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.
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.
Participants in the iDigBio supported Digitizing Mollusks workshop.
The iDigBio supported “Digitizing Mollusks” workshop was held immediately prior to the American Malacological Society meeting in Newark, Delaware on July 15-17, 2017. Thirty-eight collections professionals from 24 established and developing mollusk collections gathered to discuss the status of Mollusk collection digitization in North America and abroad.
Contributed by: Rod Eastwood Curator, Entomological Collection, Eidgenössische Technische Hochschule (ETH) Zürich, Institut für Agrarwissenschaften, Biocommunication & Entomology, Zürich, Switzerland
by Libby Ellwood, Katelin Pearson, Katja Seltmann, Deb Paul and Shelley James
Collections Data Reveals Complex Plant/Pollinator Network, Inspires Research
Contributed by Dylan Ricke and Annika Rose-Person, Archbold Biological Station
What is NMITA?
UPDATE!: Read all about our ESA 2017 bioblitz and booth experience: https://www.idigbio.org/content/connecting-collections-and-ecology
iDigBio heads to the Ecological Society of America, 102nd Meeting, in Portland, Oregon from August 5 - 11, 2017.
The theme of this year's ESA meeting aligns directly with iDigBio's focus on enabling use of collections data by researchers, and serves as a special opportunity to engage with the ecological research community. Theme:
From the Darwin Core Hour Team.
Hole-y Plant Databases! Understanding and Preventing Biases in Botanical Big Data
American Horseshoe crab (Limulus polyphemus)
Photo courtesy of: Florida Fish and Wildlife, Photo by: Karen Parker
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.
Contributed by: Teresa Iturriaga, Rhianna Baldree, Alex Kuhn, Andrew Miller
Mycologists long to collect
areas remote to most men
where fungi today may thrive
keeping plants, trees, and cycles alive.
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.
iDigBio staff members Bruce MacFadden, Libby Ellwood, and Molly Phillips attended the 2017 National Science Teachers Association National Meeting held on March 30-April 2 in the L.A. Convention Center in downtown Los Angeles. The conference was massive – attended by thousands of K-college science teachers from around the country and world.
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 Society of Herbarium Curators and iDigBio are pleased to announce a 6-week "Strategic Planning for Herbaria” short course.
Take this opportunity to introduce new purpose and excitement into your organization. Learn how to relate your collection’s compelling vision to stakeholders and communicate long-term objectives and strategies to administrators.
Contributed by: Donald H. Pfister, Asa Gray Professor of Systematic Botany and Curator, Farlow Library and Herbarium, Harvard University, 22 Divinity Ave., Cambridge, MA 02138
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!
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.
Dear iDigBio Enthusiasts,
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.
Contributed by Libby Ellwood and Austin Mast (iDigBio-Florida State University).
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.
Contributed by: Teresa Iturriaga, Rhianna Baldree, Alex Kuhn, Andrew N. Miller
University of Illinois, Illinois Natural History Survey, 1816 South Oak Street, Champaign, IL 61820-6970
We forget because remembering everything is impossible.
We also forget because remembering can be painful and raise too many questions that have no clear answers.
Such is the case regarding many ghost towns. They remind us of the transience of everything.
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.
Who could resist a conference where the mascot is a giant bright red Rafflesia flower, where bagpipes serenade the participants, and kilt-wearing and traditional folk dancing are encouraged, along with stimulating science? The 10th International Flora Malesiana Symposium was hosted by the Royal Botanic Garden Edinburgh, Scotland between 11-15 July 2016.
Jointweeds and Their Many Mating Systems!
-- Contributed by Lauren Gonzalez
I’m currently a graduate student in the Soltis Lab in the Florida Museum of Natural History, working on Polygonella(Polygonaceae), sometimes called the jointweeds....read more here.
For optimum results, digitization of collections needs to go faster, right? Of course, this includes addressing data quality and completeness.
Playing with biological specimen data in iDigBio – limitations and solutions for research
-- Contributed by Shelley A James
Puerto Rico – warm Caribbean seas, high biodiversity, and coqui frogs. iDigBio was invited to NatureServe’s Biodiversity without Boundaries 2016 meeting in April 2016 to share ideas and resources with members of the conservation community....read more here.
Conservation. Endangered and rare species. Species distribution maps. Habitat and landscape integrity analysis. Observational data.
Got research data? Need to submit your important data and media associated with biological voucher specimens to a data repository as part of your data life cycle best practices workflow? Are you thinking iDigBio would be the ideal repository for your data?
Although iDigBio is a repository for recordsets of primary biodiversity data of vouchered natural history collections, it is not a "data repository" as defined by most journals. Accepting individual researcher datasets, even those consisting of vouchered, natural history specimen digitized data and media, currently falls outside of the Scope of iDigBio.
Ever wondered where to start with analyzing a large biodiversity data set you've downloaded from iDigBio's portal or the iDigBio API? Wondering what software tools are available for cleaning your collections dataset or running some interesting queries? Finding a local Software Carpentry course is an excellent first step.
Polyploidy in ferns: biodiversity data documenting speciation!
-- Contributed by Blaine Marchant
My research for iDigBio addresses ecological and evolutionary questions by utilizing the enormous dataset provided by digitized natural history specimens from across North America. My current project is aimed at investigating the ecological differentiation of polyploid plant species from their diploid progenitor species....read more here.
Using herbarium specimen data to understand native mint distribution, evolution, and ecology
-- Contributed by Andre Naranjo
Permanent, globally unique identifiers are increasingly critical for the efficient analysis, publishing, tracking and reuse of dig data, including biological, geological and ecological information. Practical Hacking On Identifiers at BiOSphere2 (PHOIBOS2) took place at The University of Arizona’s Biosphere 2, Oracle, Arizona, from Feb 17-19, 2016. The Biosphere2 was an ideal location for a workshop - remote, spiny vegetation,
iDigBio is pleased to announce the upcoming Symposium "Data and digital images: progress, tools and scientific need for digitizing Pacific biological specimen collections" at the 23rd Pacific Science Congress: Science, Technology and Innovation, June 13-17, 2016 in Taipei, Taiwan.
We invite presentations from students and professionals about the digitization of natural history collections data in the Asia-Pacific region and the use of mobilized collections data for research.
During its inaugural year, the Worldwide Engagement for Digitizing Biocollections Event, WeDigBio 2015, engaged thousands of citizen scientists from >50 countries in transcribing specimen labels over four days.
Using museum specimens to refine models of species distribution
-- Contributed by Charlotte Germain-Aubrey
Using distribution models are crucial for estimating levels of biodiversity at the landscape level. Museum specimens are a significant source of information for these models as they witness current but also past habitats...read more here.
Gehen Sie zu der SPNHC 2016 Konferenz? Are you going to the Society for Preservation of Natural History Collection's (SPNHC) 2016 Conference? It's in Berlin this year, from June 20 - 25, 2016.
Hundreds of volunteers around the world transcribed >30,000 specimen labels at 25 events over four days (Oct 22–25, 2015) in the first Worldwide Engagement for Digitizing Biocollections (WeDigBio) event. Events spanned a range of formal and informal education venues, from middle-school and undergraduate science classrooms to county libraries to museums, universities, and botanical gardens, such as the Smithsonian's National Museum of Natural H
Location: BIS (TDWG) 2015 Biodiversity Information Standards:
An amazing 2 weeks in Nairobi, Kenya.
by Deb Paul, input from Libby Ellwood and Matt Collins.
iDigBio was delighted with Axiell's generous invitation to present a half-day digitization workshop at the annual meeting of the EMu user group Natural History Special Interest Group (NHSIG), held October 7 at the Penn Museum in Philadelphia. After determining via survey what EMu users would be interested in hearing about, we fashioned the following well-received agenda:
by Heather Appleby, former undergrad intern, Tri-Trophic Thematic Collection Network (TTD-TCN). Katja Seltmann (TTD-TCN), Deb Paul, Alex Thompson, and Matt Collins Eds.
from Deb Paul @iDigBio
Data exploration for large datasets is always challenging. Often you are left with deciding between subsetting the dataset (randomly or on some facet), making slow progress waiting for results just to find that something needs to be fixed, or optimizing code for performance when you don't even know if the result is going to be interesting. Having a high-performance system capable of ad-hoc investigation has always been difficult and/or expensive.
iDigBio API Hackathon Report Blog
We (Deb Paul, Cathy Bester, and Molly Phillips) had a fun and productive time staffing the iDigBio exhibit at the 95th Annual meeting of the American Society of Mammalogists Conference in Jacksonville, Florida, June 12-15, 2015. We set up the 10’ exhibit with the TV displaying the iDigBio Explore Research video series (thank you to Kevin Love and Chris Baker for helping us set up!).
Each year, iDigBio surveys its internal team and the collections community, broader scientific community, partners, stakeholders, and others interested in the national digitization effort to find out how we are doing. We use the feedback to inform our decision-making and to help us set priorities and determine next steps. We are grateful to the nearly 250 individuals who participated in this year’s survey!
June 3-5, 2015 (iDigBio API Hackathon) – Team Integration blog, by Jorrit Poelen (Global Biotic Interactions), Dmitry Mozzherin (Global Names), Jon Lauters (U.
On Friday, May 29, Florida State University held a transcription blitz for attendees of the Florida Native Plant Society Annual Conference. This was the third digitization blitz hosted by iDigBio, the Southeastern Regional Network of Expertise and Collections Thematic Collections Network, and FSU's Robert K. Godfrey Herbarium.
The Florida Museum of Natural History and partners hosted the 30th Annual Meeting of the Society for the Preservation of Natural History Collections (SPNHC) from May 17-23, 2015, at the Hilton University of Florida Conference Center in Gainesville, Florida. The theme of the conference was “Making Natural History Collections Accessible Through New and Innovative Approaches and Partnerships”.
UF CAIRES (Center for Adaptive Innovation, Resilience, Ethics, and Science) sponsored a two-day Sustainability and Social Media Conference on Friday, April 17-18 2015, at the Levin School of Law. iDigBio graduate student Randy Singer was fortunate enough to be invited as a panelist for a session on Digitizing Nature.
From Deb Paul, @idbdeb
This 4-day hands-on short course in March investigated current trends in collecting, and focused on best practices and skills development for supporting the collection and sharing of robust, fit-for-research-use data.
By: Deb Paul, Shari Ellis, Andréa Matsunaga, Blaine Marchant
Managing Natural History Collections Data for Global Discoverability is fourth in a series of biodiversity informatics workshops at iDigBio and we are currently accepting applications! Don't wait, space is limited.
Deadline to Apply is May 1st, 2015.
SPNHC 2015 30th Annual Meeting and Gala Celebration
Making Natural History Collections Accessible through
New and Innovative Approaches and Partnerships
May 17, 2015 to May 23, 2015
Goal: Design, develop, implement, test and/or document uses of iDigBio data via its APIs
Location: University of Florida, Gainesville, FL
Dates and times: June 3-5, 2015; 8 am - 5 pm each day
To apply: https://ufl.qualtrics.com/SE/?SID=SV_6Wr1womZuY7O5o1 deadline February 28, 2015. Invited applicants will be notified by March 9th.
Dear iDigBio Friends and Family,
iDigBio staff participated in the Florida Museum of Natural History’s annual event ButterflyFest “A Celebration of Wings, Wildlife and Biodiversity”. The event was held Saturday, October 4, at the Florida Museum of Natural History in Gainesville Florida.
The use of sequencing and other molecular data now plays a critical role in the majority of research across the fields of systematics, ecology, and evolutionary biology. In addition, DNA barcoding offers an efficient way to identify specimens for large efforts like biodiversity inventory projects or biological resource management.
By the numbers:
A workshop on data modeling took place at the East-West Center in Honolulu, March 24-25, 2014. The workshop immediately preceded the Biological Collections Digitization in the Pacific workshop and focused on data modeling and requirements for biodiversity information repositories.
Written by Libby Ellwood, iDigBio Postdoctorial Associate, Florida State University.
Deb Paul and I attended the Ecological Society of America conference in Sacramento, CA to represent iDigBio with an exhibitor booth. We set up our table with computers, brochures, posters, videos, newsletter sign-up sheets and, of course, enticing candy.
Amanda Neill, Director of the Herbarium, Botanical Research Institute of Texas
August 15th, 2014
Larkin infrared thermal imaging demo-SPNHC 2014 DemoCamp
Often at iDigBio sponsored workshops, symposia, and outreach events, we are asked the question: “How can I write a successful ADBC proposal?”
“Those millions of bugs on pins, pressed plants, preserved animals and fossils hold a wealth of information about the adaptive abilities of our natural world, not to mention the DNA and curative uses yet to be discovered.”
The BIOSPEX Management System—Provision, Advertise, and Lead Crowdsourcing Projects
There may be no place better than the University of Texas to conduct a broad-based paleo imaging workshop. This certainly seemed the consensus the week of 29 April at the co-sponsored iDigBio and Jackson School of Geosciences imaging event.
Fifteen undergraduate students from seven Florida colleges and universities converged on the Florida Museum of Natural History April 17-19 for an all-expense-paid opportunity to shadow museum professionals and explore careers in the biological sciences.
Studies show that as girls transfer from middle to high school, they can perceive science as ‘uncool’ and subsequently loose interest in scientific careers. iDigBio postdoctoral associate Dr. Charlotte Germain-Aubrey, external vice-president of the Women in Science and Engineering (WiSE) at the University of Florida, created the WiSE Girlz Spring Science Camp to contradict this notion.
This article was generated from a webinar presented as an addendum to the iDigBio Education & Outreach Workshop held in Gainesville, FL, January 15-17, 2014. Participants were interested in finding out more about applying for grants available through the National Science Foundation (NSF) for Education and Outreach.
If you are targeting the National Science Foundation (NSF) for Education and Outreach funding, you may be looking for money in all the wrong places. With creativity and knowledge you can find the right places.
The Education and Outreach Workshop, held in Gainesville, FL from January 15-17, 2014, brought together representatives from each TCN to broaden our knowledge of E&O opportunities, resources, and strategies. Education and outreach are critical components of iDigBio TCNs. These activities are as wide-ranging and diverse as the TCNs themselves, and have likewise engaged a variety of students.
The CITSCribe Hackathon, co-organized by Zooniverse's Notes from Nature Project and iDigBio brought together over 30 programmers and researchers from the areas of biodiversity research and digital humanities for a week to further enable public participation in the transcription of biodiversity specimen labels.
Any doubt about the importance of small herbaria or the enthusiasm of their curators was certainly dispelled at the recent Mobilizing Small Herbaria workshop held at Florida State University the week of December 9th. Co-sponsored by iDigBio, the Robert K. Godfrey Herbarium at Florida State, the North American Network of Small Herbaria, and the Small Collections Network (SCNet), the event brought together about 30 collections professionals from 25 institutions representing 16 states.
by Deborah Paul, on Twitter @idbdeb
The iDigBio Summit III was held in Tallahassee, Florida, at the Aloft Hotel, November 18-21, 2013. Sixty attendees from more than 31 institutions met and focused on shared goals, challenges and opportunities, and collaboration among stakeholders.
The University of Florida, the Florida Museum and iDigBio hosted a visit from the attendees at the Science Writers Conference. Some 400 of the nation's top science writers were in town from November 1-5 for the annual meeting of the National Association of Science Writers and the Council for the Advancement of Science Writing.
iDigBio, University of Central Florida, and the Florida Museum of Natural History are pleased to announce a workshop for undergraduate students focused on increasing participation of underrepresented populations in the biological sciences. The workshop will be held at the University of Central Florida, February 1, 2014 and is open to college freshmen, sophomores, juniors, and seniors as well as recent college graduates. The goal of the workshop is to share important highlights about career and graduate study opportunities in the biological sciences.
Florida Museum of Natural History (FLMNH) curators Larry Page, Pam Soltis, and Bruce MacFadden presented a seminar about iDigBio to the Biology Department last Tuesday, November 5, 2013. This seminar provided an opportunity for the department to learn what the iDigBio project is all about and what research and educational opportunities are available.
On October 19-20, iDigBio was represented by iDigBio project staff Cathy Bester, Kevin Love, Joanna McCaffrey and David Jennings along with post doc Charlotte Germain-Aubrey and graduate student Claudia Segovia at the Florida Museum of Natural History’s “ButterflyFest” in Gainesville Florida.
More than 60 paleontologists representing 41 institutions assembled in New Haven, CT the week of September 23rd, 2013 to share ideas, protocols, preferences, and strategies. This was iDigBio’s most populous workshop to date, with an assortment of excellent presentations and ample opportunities for rich discussion.
Austin Mast interviews Libby Ellwood, our newest postdoctoral scholar.
Mast: It's my pleasure to welcome you as iDigBio's newest postdoctoral scholar, Libby. Your research focus will be on broadening public participation in the digitization of biodiversity research specimens. This is a goal to which your previous research background is well suited. What do you see as the most relevant aspects of your previous graduate and postdoctoral research for this new position?
Ellwood: Thanks, I’m thrilled to be a part of iDigBio’s dynamic team. I learned quickly in my graduate career that there is a wealth of information contained in museum specimens and that they are extremely useful in contemporary scientific research.
I earned my PhD in Biology from Boston University where my research focused on the effects of climate change on plants and animals. The metric I used to assess how much plants and animals were affected was phenology, the timing of biological events. Phenology includes the timing of when plants flower, when insects emerge and when migratory birds arrive, and many of these annual activities are impacted by temperature. In order to evaluate whether an organism’s phenology has changed, I first needed to understand the historical phenology—the date that a certain plant was flowering a hundred years ago, for example. Old journals, including those of Henry David Thoreau, were invaluable for this research. Some of these resources I found digitized online, while many others were tucked away deep in the special collections of museums and libraries. These records, combined with modern-day observations of the same plants and animals, allowed me to track phenology over 160 years. Several interesting discoveries came from this research, including the finding that many plant species are now flowering up to three weeks earlier now than they were in the 1850’s when Thoreau was observing them!
Amateur naturalists, such as the fossil club participants pictured here (Friends of the Calvert Marine Museum) are potential downstream users of iDigBio.
From June 17-21, seven members of iDigBio (Gil Nelson, Pam Soltis, Joanna McCaffrey, Larry Page, Bruce MacFadden, Kevin Love and Deborah Paul) participated in SPNHC 2013, which is the annual meeting of the Society for the Preservation of Natural History Collections (http://www.spnhc.org/), fondly referred to as “spinach.”
iDigBio has developed a pamphlet featuring brief descriptions about the aims of ADBC and iDigBio, with colorful, eye-catching digitization-related images. This material provides a simple and visual representation of iDigBio‘s mission, suitable for all audiences. We would love for you to distribute these within and beyond your institution in order to promote interest in iDigBio and digitization. If you would like one or more shipped to you domestically (no international), please send a request via this webform. You may also download a print-ready copy (22 MB PDF)
Members of the iDigBio UF staff recently visited the new University of Florida Data Center at the Eastside Campus facility. The tour, led by Associate Director of Data Center Operations David Burdette, led visitors through the newly constructed $14M facility. The tour allowed visitors to see the complete operation, from the large server rooms, the monster backup power supplies, and the room chilling equipment.
Registration for the 2013 meeting of the Society for the Preservation of Natural History Collections is now open. This meeting is being held June 17-22 on the campus of the South Dakota School of Mines and Technology in Rapid City, South Dakota, home of the Museum of Geology.
iDigBio Augmenting OCR Working Group provides a detailed update on the recent Hackathon and presentations at iConference 2013, held in Forth Worth, TX, February 12-15.
On Monday, February 25th, iDigBio PI's and project staff met with Walter Jetz,Ph.D. from the Map of Life project. Dr. Jetz shared with us how the The Map of Life assembles and integrates different sources of data describing species distributions worldwide. These data include expert species range maps, species occurrence points, ecoregions, and protected areas from providers like IUCN, WWF, GBIF, and more.
Over the past 16 weeks, the aOCR wg has successfully orchestrated multiple initiatives intended to address some key issues on the working group's Wish List. Here, we briefly report on our recent Hackathon, held February 13-14, 2013 in Fort Worth, Texas, and on our "BioBlitz" at the iSchools iConference 2013, which was held February 12-15 in Forth Worth. We also discuss planned papers and new interactions resulting from these events.
Please join iDigBio in congratulating Dr. Anna Monfils on her selection as our 2012 Visiting Scholar. Anna is an Associate Professor at Central Michigan University and Director of the Central Michigan University Herbarium.
Dr. Monfils' winning proposal includes building generalized, web-deliverable specimen databasing protocols, designing web-based teaching activities focused on databasing, and organizing a workshop aimed at professional botanists, students and citizen scientists from throughout Michigan.
iDigBio Augmenting OCR Hackathon
February 13-14, 2013, in Fort Worth, Texas
Be a part of helping to get "dark data" out of millions of museum cabinets and into online databases!
UPDATE! See Hackathon Wiki: http://tinyurl.com/aocrhackathonwiki and Participate Remotely!
The second annual iDigBio Summit was held on October 23-24, 2012, in Gainesville, Florida, and was completed with great success! The Summit promoted clarification of objectives, communication of progress towards achieving objectives, identification and discussion of challenges and opportunities, and collaboration among stakeholders.
Corey Toler-Franklin is a University of California President's Postdoctoral Fellow in the Computer Science Department at UC Davis. She is investigating new methods for capturing and processing digital media formats and imaging modalities to create more comprehensive representations of biological specimens. Dr. Toler Franklin's project will take her to the collections of AMNH and Duke University's Lemur Center, where she plans to use non-invasive optical capture techniques to digitize recent and fossil primates.
iDigBio has developed a poster that provides a simple and visual representation of iDigBio‘s mission. We would love for you to put one up in your institution in order to promote interest in iDigBio and digitization. If you would like one or more shipped to you domestically (no international), please send a request via this webform. You may also download a copy to print locally (65 MB PDF).
iDigBio Augmenting OCR Hackathon
February 13-14, 2013, in Fort Worth, Texas
Be a part of helping to get "dark data" out of millions of museum cabinets and into online databases!
Dr. Bruce MacFadden is Curator of Paleontology at the Florida Museum of Natural History and Director of Education and Outreach for iDigBio. His responsibilities with iDigBio include oversight of educational and outreach activities and their assessment at iDigBio, the TCNs and at other digitization projects involving biological collections. Here, he discusses his early fascination with dinosaurs and paleontology, pivotal experiences in undergraduate and graduate school that helped shape his career, and then some of his professional accomplishments.
The intensive, week-long First iDigBio Train-the-Trainers Georeferencing Workshop ended on October 12th, 2012. After a week, we are family and were sad to have to go home - but everyone seems very excited to get back to their own institutions to share what they learned and put it to good use in their own georeferencing and digitization projects.
The First iDigBio Train-the-Trainers Georeferencing Workshop is well into Day 4 now! Day one, participants and instructors met iDigBio PI Pam Soltis, Project Manager David Jennings, Biodiversity Informatics Manager Joanna McCaffrey, Cathy Bester, iDigBio Program Assistant and Kevin Love, the iDigBio IT magician who keeps us all in touch with one another and connected to the internet. Shari Ellis, iDigBio Project Evaluator, shared results of the iDigBio Pre-Workshop Survey for this workshop with all the participants.
iDigBio’s Public Participation in Digitization of Biodiversity Specimens Workshop was held on September 28-29 in Gainesville, FL.
Topics included the role of citizen science, ways to engage the public in digitization, methods to build public participant virtual communities, and an overview of biodiversity informatics software to facilitate public participation. Visit the workshop wiki page for links to the final agenda, the GoogleDoc, and the presentations.
iDigBio is very pleased to welcome Joanna McCaffrey, our new Biodiversity Informatics Manager!
Joanna comes to the iDigBio team from the Field Museum of Natural History, where she has spent the past ten years working in a variety of databasing, imaging, and collections positions.
Seeking participants for “iDigBio Augmenting OCR” workshop, October 1-2
Compiled from notes in the field from Deb Paul, iDigBio Digitization Expert:
The Southwest Collections of Arthropods Network (SCAN): A Model for Collections Digitization to Promote Taxonomic and Ecological Research kickoff meeting at Arizona State University.
August 15-16th 2012
iDigBio is very pleased to welcome David Jennings as our new Project Manager! David is an industrial/mechanical engineer with over 18 years of experience in project management and leadership and will be responsible for overseeing day-to-day operations, developing requirements, coordinating activities within iDigBio, and coordinating activities between iDigBio and other networks/collections.
On 30 June 2012, iDigBio completed its first year of operation. As the national resource for the NSF-funded Advancing Digitization of Biodiversity Collections(ADBC), our first year required that we identify and overcome major organizational hurdles as we develop a national infrastructure for the ADBC institutions. We are pleased to report that our first year was highly successful. In this article, we enumerate some of our major activities and accomplishments.
All of us at iDigBio are excited to announce the publication of Five Task Clusters that Enable Efficient and Effective Digitization of Biodiversity Collections in a ZooKeys 209:19-45 (2012) Special Issue No specimen left behind: mass digitization of natural history collections. We look forward to your comments...
Dr. Corinna Gries is PI and head of the North American Lichens and Bryophytes Thematic Collections Network. An accomplished researcher and programmer, here she is interviewed by Jill Holliday and discusses some of the history of specimen databasing, the goal of the North American Lichens and Bryophytes TCN, and the importance of public participation and crowd-sourcing to the TCN databasing projects.
Holliday: Corinna, you are the head of the North American Lichens and Bryophytes TCN.
Public Participation in Digitization of Biodiversity Specimens Workshop
University of Florida, Gainesville, FL
September 28 - 29, 2012
iDigBio, the National Science Foundation’s national HUB for Advancing Digitization of Biodiversity Collections (ADBC), is offering a workshop focused on engaging the public in the digitization of the approximately one billion biodiversity specimens housed in collections across the U.S. The workshop will explore how to involve the public in ways that are interesting and educational but also efficient and reliable for the facilities managing the digitization.
Members of the collections community gather in Gainesville, FL to produce optimized specimen digitization workflows at the Developing Robust Object-to-Image-to-Data (DROID) Workshop. Tremendous participant insight holds the promise for informative documentation that will benefit all collections conducting or initiating digitization activities.
Protocols for Slide-Scanning/Digitization of Standard Microscope Slides
Bruce MacFadden reports on the recent Paleocollections Digitization Workshop hosted by iDigBio and FLMNH. The workshop was held to assess the status and future of digitized collections within the paleontological community. Presentations, discussions and breakout sessions focused on three themes: 1) tools, datapases and portals, 2) digitization and workflows, and 3) research applications and Grand Challenges.