Blog Archives

American Society of Mammalogists (ASM) 2019

Tue, 2019-07-09 14:16 -- maphillips

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.

Research Spotlight: February 2019 (Mollusks)

Fri, 2019-02-15 13:37 -- sellis

Research Spotlight: July 2018

Fri, 2018-06-29 12:18 -- maphillips

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.

Research Spotlight: January 2018

Tue, 2017-12-12 12:24 -- maphillips

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

The Momentum for Integrating Collections and Ecological Research: Expanding Collections Stakeholders and Imagining Future Data Needs

Thu, 2017-11-30 16:52 -- dpaul

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?’

Natural History Collections as Primary Data in Ecological Research

Wed, 2017-10-18 08:45 -- maphillips

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

Tue, 2017-10-17 14:58 -- maphillips

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.

Digitizing Mollusks Workshop Report

Tue, 2017-10-17 09:30 -- maphillips


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.

iDigBio at the Ecological Society of America Meeting 2017

Fri, 2017-07-21 22:49 -- dpaul

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:

Research Spotlight: July 2017

Thu, 2017-06-01 10:19 -- grungle

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

Mon, 2017-05-01 15:05 -- grungle

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.

National Science Teachers Association Conference 2017

Thu, 2017-04-06 10:16 -- maphillips

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.

Research Spotlight: April 2017

Sat, 2017-04-01 14:00 -- grungle

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.

Strategic Planning for Herbaria Short Course

Fri, 2017-03-24 07:48 -- maphillips

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.  

Portal Curiosities: Asa Gray and the quest for Shortia galacifolia – a case study for the importance of collections

Fri, 2017-03-10 13:10 -- jvgoodwin

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

AIBS Communications Boot Camp

Thu, 2017-03-02 12:22 -- grungle

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!

Research Spotlight: March 2017

Wed, 2017-02-08 09:33 -- grungle

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

Mon, 2017-01-30 13:33 -- grungle

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

Mon, 2016-12-19 13:31 -- grungle

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.

International Congress of Entomology

Wed, 2016-10-12 09:56 -- maphillips

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.

Ghost Towns in MyCoPortal I:Nuttallburg and Lawrence William Nuttall

Mon, 2016-10-10 09:32 -- maphillips

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.

Research Spotlight: November 2016

Fri, 2016-09-30 11:04 -- grungle

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.

Research Spotlight: October 2016

Wed, 2016-09-21 11:53 -- grungle

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.

Research Spotlight: September 2016

Tue, 2016-08-23 10:40 -- grungle

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.

iDigBio Hosts Workshop on Biodiversity Research Methods at Botany 2016 in Savannah, GA

Mon, 2016-08-15 10:38 -- grungle

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 (

Researchers Use MyCoPortal to Track Down Specimens Lost for Over 100 Years

Thu, 2016-08-11 10:23 -- maphillips

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

Research Spotlight: August 2016

Wed, 2016-07-27 08:18 -- grungle

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.

 

iDigBio at Flora Malesiana 10

Sun, 2016-07-17 09:25 -- grungle

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.

Research Spotlight: May 2016

Wed, 2016-04-27 14:13 -- grungle

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.

Can iDigBio be my research data repository?

Fri, 2016-04-01 11:30 -- grungle

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.

Software Carpentry: an iDigBio staff perspective

Wed, 2016-03-30 14:54 -- grungle

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.

Research Spotlight: June 2016

Tue, 2016-03-29 15:17 -- grungle

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.

PHOIBOS2 at Biosphere 2 - practical hacking on identifiers

Thu, 2016-02-18 12:10 -- grungle

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,

Call for Abstracts for iDigBio Symposium at the Pacific Science Congress 2016

Mon, 2016-02-15 09:24 -- grungle

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.

Call for student abstracts for iDigBio workshop at Island Biology 2016

Fri, 2016-02-12 10:27 -- grungle
Are you a student attending the Island Biology 2016 International Conference on Island Evolution, Ecology and Conservation, to be held on Terceira Island, Azores, from 18-22 July 2016? Do you have a research project which involves the digitization of vouchered natural history collections data from island communities, or utilizes published natural history collections data to better understand island ecosystems?
 

Research Spotlight: Using Museum Specimens to Refine Models of Species Distribution

Wed, 2016-01-13 12:47 -- maphillips

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.

The Inaugural WeDigBio Event: Global Event Advances Digitization and Science Literacy

Thu, 2015-11-19 10:10 -- maphillips

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

iDigBio and the EMu NHSIG in Philadelphia

Wed, 2015-10-14 10:57 -- joanna

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:

A summer learning R to clean up data with the iDigBio portal recordset correction feature

Sun, 2015-10-11 00:30 -- dpaul

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.

mcollins's picture

Exploring unique values in iDigBio using Apache Spark

Thu, 2015-09-10 16:55 -- mcollins

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.

Tales from the iDigBio Booth: American Society of Mammalogists Conference

Fri, 2015-06-26 10:15 -- maphillips

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!).

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The Results of the 2015 iDigBio Community Survey are In!

Wed, 2015-06-17 08:02 -- maphillips

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!

SPNHC 2015: Sowing the Seeds of Digitization

Mon, 2015-06-01 15:49 -- maphillips

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”.

Sustainability and Social Media Conference Report

Wed, 2015-04-29 15:33 -- maphillips

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.
   

Field to Database (F2DB): field-data collecting trends and 21st century data skills

Mon, 2015-04-20 02:33 -- dpaul

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.

Call for Participation: Hackathon on iDigBio APIs/Services and Interoperability

Thu, 2015-02-05 10:26 -- ammatsun

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.