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.
2019 TCNs:
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)
Contributed by: Molly Phillips, iDigBio's Education, Outreach & Diversity Coordinator
Images courtesy of Adam Fagen
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)
Libby Ellwood, Katelin Pearson, and Gil Nelson
Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates
Wood-warblers, Parulidae
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
Introduction
Luke C. Strotz, Erin E. Saupe, Julien Kimmig and Bruce S. Lieberman
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
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)
Images courtesy of NOAA Okeanos Explorer
Contributed by Randy Singer
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.
by C. Skema, Anne Barber, and Tim Block
The oldest specimen in the MyCoPortal is housed at Purdue and was collected in 1769 in Tierra Del Fuego at the southern tip of South America. It was collected by the Englishman Sir Joseph Banks and Dr.
Photo courtesy of Michael Carters
David F. Schmidt, USNM Dinomys branickii, Smithsonian Institution, NMNH, Mammals
Contributed by: Hannah Owens from the Florida Museum of Natural History, University of Florida
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
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
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:
Manta Rays
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!
-- 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.
-- 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,
-- 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.
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.
-- 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.
-- 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.
-- 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
-- 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.
The 23rd Pacific Science Congress, successfully hosted by Academia Sinica, Taipei, Taiwan brought together scientists from a broad range of fields to discuss progress being made towards a sustainable future in Asia and the Pacific.
-- 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.
UPDATE: Wiki in development https://www.idigbio.org/wiki/index.php/Georeferencing_for_Research_Use
For optimum results, digitization of collections needs to go faster, right? Of course, this includes addressing data quality and completeness.
-- 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.
-- 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.
-- Contributed by Andre Naranjo
I am a graduate student at the University of Florida, and a member of the Soltis Lab, working on a genus of scrub mints found only in the southeastern United States....read more here.
iDigBio's Jillian Goodwin and Molly Phillips traveled to St. Marks, Florida, to participate in the League of Environmental Educators (LEEF) Conference at COAST Charter School from March 18-20, 2016.
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.
-- 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.
iDigBio and the Small Collections Network (SCNet) are pleased to announce the upcoming Small Collections Symposium at SPNHC 2016, to be held in Berlin, June 20-25.
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.
Dear iDigBio Enthusiasts,
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.
On July 26, 2015, iDigBio hosted an all-day ecological niche modeling (ENM) workshop at Botany 2015, the joint annual conference hosted by the Botanical Society of America, Plant Canada, and their affiliated societies, in Edmonton, Alberta.
iDigBio API Hackathon Report Blog
We (D
eb 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!).
By François Michonneau, @fmic_ (with editorial suggestions from Judit Ungvari-Martin)
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”.
Georeferencing Procedure Outline - a guest blog by Michael Yost, Macrofungi Collection Consortium (MaCC) Project Assistant at the Denver Botanic Gardens
Greetings, fellow georeferencers!
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.
-Guest blog enthusiastically provided by course participant Rick Levy, Database Associate, Denver Botanic Gardens
By: Deb Paul, Shari Ellis, Andréa Matsunaga, Blaine Marchant
From Deb
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.
From Deb Paul, on twitter @idbdeb
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,
by Deb Paul, with Libby Ellwood and Greg Riccardi as Eds.
Nearly 200 collections professionals attended this year’s Entomological Collections Network (ECN) conference, 15-16 November 2014 in Portland, Oregon.
The Advancing Digitization of Biological Collections Annual Summit, hosted by iDigBio, took place in Chattanooga, Tennessee, at 
