Biodiversity_Next main conference venue, Stadsgehoorzaal, in Leiden, Netherlands. Photo Credit: Grace Costantino.

In October 2019, more than 700 people from over 75 countries gathered in Leiden, the Netherlands for Biodiversity_Next, a joint conference by GBIF, DISSCo, iDigBio, CETAF, TDWG, and LifeWatch Eric. The first conference of its kind to bring together so many major international biodiversity organizations, the conference aimed to promote innovation in biodiversity and geodiversity information management and applications; encourage collaboration across these communities to enhance data standards and management practices; and foster the development of the skill sets necessary to embark on data-intensive scientific research and solutions.

Hosted by the Naturalis Biodiversity Center, a BHL Affiliate, in collaboration with the Netherlands Biodiversity Information Facility, the main conference ran from 22-25 October 2019, with pre-conference workshops occurring 20-21 October, as well as organization-specific meetings for GBIF, CETAF, and TDWG being held in conjunction with the conference.

BHL colleagues from around the world traveled to Leiden for Biodiversity_Next. Eighteen BHL-affiliated representatives from our partner community, representing 13 institutions from nine countries, attended the conference. Dr. Elycia Wallis, Engagement Manager at the Atlas of Living Australia and the BHL Member representative for BHL Australia, served as a key member of the Programme Committee.

Each conference day began with a plenary session featuring diverse speakers ranging from scientists to policy makers and even artists. From the policy perspective, Ana Maria Hernandez Salgar outlined major findings from the recent IPBESGlobal Assessment, while Jorge Soberón described efforts by the Mexican biodiversity agency CONABIO (a BHL Member) to make data useful for politicians and policy makers, and Maxwell Gomera of the UN Environment Program examined the importance of finding solutions that protect both wildlife and people and the value of using storytelling to reach policy makers in profound ways. On the science side, Paul Hebert of the International Barcode of Life Consortium described advances and ambitions in DNA barcoding and global bio-surveillance, while Carrie Seltzer spoke about the diverse and impactful ways that iNaturalist engages people in the biodiversity data system through citizen science.

The plenary sessions also brought in representatives from the world of art and design. Dutch artist Theo Jansen shared his work for the past 30 years creating “beach animals” constructed of PVC pipes that move using wind energy, while Dutch artist Jalila Essaidi described her work to create bio-art, from “bulletproof human skin” created using synthetic spider silk to clothing made from fabric produced from manure.

Beyond the plenary sessions, more than 300 speakers presented over 350 talks as part of over 60 sessions and workshops related to science, policy, standards, and infrastructure. Several major themes emerged across many of the sessions, including the importance of adopting FAIR data principles; the need to link together the many diverse biodiversity data systems; the importance of unique identifiers for data, including DOIs and ORCIDs; and the possibilities of using Wikidata as a source of and way to connect various identifiers.

BHL colleagues were very active in the conference, with 11 BHL-affiliated staff presenting or moderating 16 talks or sessions. See the full list of BHL-affiliated staff presentations at the end of this post. Additionally, members of the BHL Executive Committee (EC), including Constance Rinaldo (EC Chair, Ernst Mayr Library, Harvard University) and Martin Kalfatovic (BHL Program Director, Smithsonian Libraries), as well as colleagues from the Muséum national d’Histoire naturelle, represented BHL at the various organizational meetings, including GBIF, TDWG, and CETAF.

BHL was also highlighted frequently throughout the conference, with many talks discussing the importance of historic literature for science today, the need to integrate BHL data into other biodiversity data services like GBIF and the Catalogue of Life, and the importance of incorporating reciprocal links between BHL and these various data systems. These concepts were distinguished as a high value priority by many of the session presenters.

“Biodiversity_Next was an inspiring and exciting opportunity to hear from more than 700 colleagues representing organizations all over the world,” said Constance Rinaldo, Chair of the BHL Executive Committee. “As a representative to GBIF and TDWG and by leading a symposium, I came away fully understanding the impact of collaboration among biodiversity organizations and data integration: this is the key to the future of biodiversity science.”

BHL Symposium

The Biodiversity Heritage Library organized a Symposium as part of Biodiversity_Next. Entitled Improving Access to Hidden Scientific Data in the Biodiversity Heritage Library, the session featured presentations offering examples of and ideas about how BHL data can be used to empower research and how enhanced data delivery methods can facilitate real-time computing.

Constance Rinaldo introducing the BHL Symposium at Biodiversity_Next. Photo Credit: Grace Costantino.

The Symposium was moderated by Constance Rinaldo (Chair, BHL Executive Committee) and included the following presentations:

• “Introduction to the Symposium: Improving Access to Hidden Scientific Data in the Biodiversity Heritage Library” (Presented By: Constance Rinaldo — Ernst Mayr Library, Harvard University). Abstract | Slides
• “BioStor Next (a.k.a. Text-Mining BHL: Towards New Interfaces to the Biodiversity Literature” (Presented By: Roderic Page — University of Glasgow | BioStor). Abstract | Slides
• “It’s Not Always FAIR: Choosing the Best Platform for Your Biodiversity Heritage Literature” (Presented By: Nicole Kearney — BHL Australia, Museums Victoria). Abstract | Slides
• “Finding Scientific Names in Biodiversity Heritage Library, or How to Shrink Big Data” (Presented By: Dmitry Mozzherin — University of Illinois, Champaign). Abstract | Slides
• “Extracting Data From Legacy Taxonomic Literature: Applications for Planning Field Work” (Presented By: Francisco Andres Rivera-Quiroz — Naturalis Biodiversity Center). Abstract | Slides
• “BHL and Specimen Collection Data: The Needle in the Festuca Stack” (Presented By: Martin Kalfatovic — Smithsonian Libraries). Abstract | Slides

Nicole Kearney presenting during the BHL Symposium at Biodiversity_Next. Photo Credit: Grace Costantino.

Topics covered within the Symposium presentations included exploring the types of data—from scientific names and geographic localities to species treatments and specimen codes—that can be extracted from the literature; methods to extract that data, including recent work to improve the speed and effectiveness of the Global Names algorithm for identifying taxonomic names in the BHL corpus; applications for that data, including helping to inform field work; recent work by BHL to improve access to the content in its collection, including full text search and the utilization of transcriptions for archival materials; the value of linking BHL literature collections with other databases like GBIF; and the importance of and the role BHL can play in the assignment of DOIs for historic literature.

You can explore more details about each of the presentations in this @BioDivLibrary Twitter thread.

Beyond the Conference

Beyond the sessions and workshops, there were several opportunities for networking and tours around the conference.

BHL colleagues gathered for the informal get-together at a local Leiden venue. Left to Right: David Iggulden (Library, Art & Archive, Royal Botanic Gardens, Kew); Clément Oury (Muséum national d’Histoire naturelle); Jiří Frank (National Museum, Prague); Chloé Besombes (Muséum national d’Histoire naturelle); Jana Hoffmann (Museum für Naturkunde Berlin); Constance Rinaldo (Ernst Mayr Library, Harvard University). Photo Credit: Martin Kalfatovic.

On Monday, 21 October, the day before the start of the main conference, BHL colleagues gathered for an informal get-together at a local Leiden venue. The gathering was an excellent opportunity for colleagues—some of which had never met in person—to connect.

Attendees at the Biodiversity_Next reception hosted in the Naturalis Biodiversity Center. Photo Credit: Grace Costantino.

Biodiversity_Next also hosted a reception the evening of the first conference day at the newly-opened Naturalis Biodiversity Center. Hundreds of attendees had a unique opportunity to explore the museum’s exhibits and network with representatives from around the world.

The Library of the Naturalis Biodiversity Center, a BHL Affiliate, also arranged tours of the general and special collections for several BHL colleagues. Godard Tweehuysen, Librarian and Information Specialist at Naturalis, showcased several special and unique items from the collection, including a copy of Les Pigeons (1808) by Coenraad Jacob Temminck (the first director of Rijksmuseum van Natuurlijke Historie—today Naturalis) with the original artwork by Pauline Courcelles and a special proofprint copy of Malacostraca Podophthalmata Brittanniae (1815-1875), which Naturalis has digitized for BHL and featured on the BHL blog.

Original artwork from Les Pigeons (1808) in the Naturalis Library collection. Photo Credit: Grace Costantino.

Proofprint copy of Malacostraca Podophthalmata Brittanniae (1815-1875) in the Naturalis Library collection. Photo Credit: Grace Costantino.

Looking ahead, during the Biodiversity_Next closing ceremony, conference organizers made an exciting announcement. A follow-up to the Biodiversity_Next conference will be held in Arlington, Virginia, USA in September 2020. The Biodiversity Summit is a joint meeting organized by iDigBio, GBIF, TDWG, and the Smithsonian’s National Museum of Natural History. Scheduled for 20-25 September 2020, the Summit will be an excellent opportunity to reconnect, continue the momentum fueled by Biodiversity_Next, and further strengthen collaborations to advance biodiversity information science and offer real, innovative, and attainable solutions to tackle today’s climate and environmental challenges.

We were privileged to be a part of such an exciting, constructive, and collaborative opportunity as Biodiversity_Next and look forward to coming together again in 2020 for the Biodiversity Summit! Until then, we’ll continue to work with the biodiversity community to incorporate data from the literature into the broader network of systems and services supporting the work of researchers, policy makers, citizen scientists and beyond.

Presentations and Moderated Sessions by BHL-Affiliated Staff from BHL Consortium Institutions

• “The European Journal of Taxonomy: Enhancing Taxonomic Publications for Dynamic Data Exchange and Navigation” (Presented By: Laurence Bénichou — Muséum national d’Histoire naturelle). Abstract
• “People of Collections: Facilitators of Interoperability?” (Presented By: Chloé Besombes — Muséum national d’Histoire naturelle). Abstract
• “Hazards and Disasters in the Geological and Geomorphological Record: A Key to Understanding Past and Future Hazards and Disasters and Their Impact on Life” (Presented By: Jiří Frank — National Museum, Prague). Abstract
• BHL Presentation as part of “Biodiversity Informatics 101: Preparing for Biodiversity_Next and Beyond” (Presented By: David Iggulden — Library, Art & Archives, Royal Botanic Gardens, Kew). Abstract
• “BHL and Specimen Collection Data: The Needle in the Festuca Stack” (Presented By: Martin Kalfatovic — Smithsonian Libraries). Abstract | Slides
• “It’s Not Always FAIR: Choosing the Best Platform for Your Biodiversity Heritage Literature” (Presented By: Nicole Kearney — BHL Australia, Museums Victoria). Abstract | Slides
• “If Wikipedia Is the Gateway to Biodiversity Knowledge, How Do We Open the Gate?” (Presented By: Nicole Kearney — BHL Australia, Museums Victoria). Abstract | Slides
• “Mesoamerica’s Crop Wild Relatives: A New Approach for Conservation Planning” (Presented By: Patricia Koleff — CONABIO). Abstract
• “Planning Landscape Connectivity in Mexico Under Global Change” (Presented By: Patricia Koleff — CONABIO). Abstract
• “Biodiversity Data Management: Regional Challenges” (Presented By: Lawrence Monday — National Museums of Kenya). Abstract
• “Introduction to the Symposium: Improving Access to Hidden Scientific Data in the Biodiversity Heritage Library” (Presented By: Constance Rinaldo — Ernst Mayr Library, Harvard University). Abstract | Slides
• “Lessons Learned From Managing Millions of Records to Create the World Flora Online” (Presented By: William Ulate — Missouri Botanical Garden). Abstract
• “Sharing Species Pages in the Atlas of Living Costa Rica Using Plinian Core” (Presented By: William Ulate — Missouri Botanical Garden). Abstract
• “Building a Global Infrastructure for Biodiversity Data. Together” — Plenary Panel Discussion (Moderated By: Elycia Wallis — BHL Australia, Atlas of Living Australia). Abstract
• “A Fireside Chat – Reflections on the Conference” — Closing Ceremony Panel Discussion (Moderated By: Elycia Wallis — BHL Australia, Atlas of Living Australia). Abstract
• “Contributed Papers: Data Extraction, Literature and Collections” (Moderated By: Elycia Wallis — BHL Australia, Atlas of Living Australia). Abstract

Passenger pigeon (Ectopistes migratorius). The Birds of North America. 1903. Contributed in BHL from Smithsonian Libraries.

The passenger pigeon’s demise is one of the most infamous examples of human-caused extinction. Once the most abundant bird species in North America, it was hunted relentlessly, with large-scale commercial hunting facilitated by railroad distribution placing excessive pressure on the species. The population declined from billions to none in less than one hundred years.

The last passenger pigeon, Martha, died at the Cincinnati Zoological Garden at about 1pm on September 1, 1914.

While stories of passenger pigeon flocks blackening the skies underscore the species’ once staggering abundance, its distribution was concentrated in the eastern United States. But could there have been resident populations in the western U.S.?

Passenger pigeon bones uncovered from the La Brea Tar Pits in Los Angeles, California inspired Dr. Libby Ellwood to ask this very question and embark on a research project empowered by the Biodiversity Heritage Library’s collections.

Dr. Libby Ellwood. Photo credit: Deborah Paul, Florida State University.

Ellwood has been studying ecology, and its intersection with climate change, conservation, and citizen science, for ten years. For the past year, she has been engaged as a Research Fellow at the La Brea Tar Pits & Museum. She first discovered BHL several years ago during her postdoc at iDigBio, a national resource for digitizing natural history collections and associated information. Since then, the Library has had a significant impact on her research.

“It may sound like hyperbole, but BHL truly is an invaluable resource,” lauds Ellwood. “I have used BHL to fill in datasets with historical data, to research foundational information, and, let’s be honest, just to look at the beautiful images. I have crossed paths with BHL staff and affiliates at conferences near and far and appreciate not only their digitization work, but equally their work to engage the online community in their efforts.”

When working on a research project, Ellwood sometimes accesses BHL daily for months at a time, reading publications online, taking notes and citation information as she goes, and downloading custom PDFs as needed. The Library has saved her precious time during these research projects.

“I know firsthand that weeks of travel to various libraries and special collections is resource and time-intensive,” shares Ellwood. “I have painstakingly used texts that have later been digitized by BHL. Had I to do it again, a good portion of that time and energy would be saved by using information available through BHL. All in all, I have a deep appreciation for BHL’s contributions to the digital landscape.”

Since BHL has proven to be such a valuable source of information for her research, it was the natural place for Ellwood to turn with questions surrounding the possibility of western passenger pigeon populations. In fact, as Ellwood shares, “In this particular case, the text and images in BHL have not only improved my research but have even driven it.”

Ellwood shared her preliminary research findings at the 2018 BHL Annual Meeting during an evening reception hosted by the Natural History Museum of Los Angeles County.

What did she find?

Read on to explore Ellwood’s account of her research to date and topics for further investigation.

Passenger pigeons of the western US – accident or resident?

By Dr. Libby Ellwood

Soon after starting my current position, I learned of the passenger pigeon bones we have in our collections at La Brea Tar Pits. While I might normally have considered this just another in a long list of cool fossils that we have in our collections, the relatively recent extinction of passenger pigeons got me thinking a little more deeply about it. More specifically, were there resident populations of passenger pigeons in southern California, or were these birds accidental visitors?

Three of the passenger pigeon bones found at La Brea Tar Pits, Howard, Hildegarde. “A Pleistocene record of the Passenger Pigeon in California.” The Condor 39.1 (1937): 12-14.

The La Brea Tar Pits fossils inform us that tens of thousands of years ago passenger pigeons were in what is now Los Angeles, California, though the extent of their range and population size at that time remain unknown. Passenger pigeons are a species that was so abundant in the eastern U.S. that their flocks would darken the skies…at least that was the case until we hunted them to extinction just over a hundred years ago.

While I might not be able to reconstruct tens of thousands of years of passenger pigeon abundance data in the western U.S., just how much information is out there about western populations of passenger pigeons? Is there information from the near historical past that could provide more information about this species’ distribution?

Enter BHL.

To cut to the chase, using documents accessed through BHL, I found numerous accounts of passenger pigeons west of the Rocky Mountains in the 1800s. Some accounts point to numerous birds, perhaps even resident populations of the species, while other accounts portray sightings of a lone individual, likely far from its intended route. My research using BHL has not yet been able to solidly answer whether or not passenger pigeons were ever residents of the western U.S., but it does open the possibility more widely.

Map of passenger pigeon localities from a variety of sources. The western BHL points are the ones added through this current research. Image credit: Libby Ellwood.

With BHL, I added five additional points to the passenger pigeon range map. Where only one poor data point of modern-day western passenger pigeon sightings existed in the past, now there are six. And with this we now have an even more compelling reason to keep digging into this story. If in fact passenger pigeons lived in the western U.S. in some abundance, how far back do those populations go? Or, looking at it from the opposite direction, if there’s a possibility that the La Brea Tar Pits fossil specimens represent resident populations, for how long did those populations persist?

From here, I will continue this investigation by compiling more information about passenger pigeon fossil specimens as well as the more recent historical information to see if I can more deeply piece together a timeline of occurrence and abundance of this once common species.

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Thank you, Dr. Ellwood, for sharing your research findings at our 2018 Annual Meeting and as part of our BHL User series! We look forward to learning more as your research progresses, and are thrilled to know that BHL is helping to paint a fuller picture of the passenger pigeon’s story.

May we learn from our past to make better decisions in the future and support a healthy, biodiverse planet.

Learning lessons from the CITScribe Hackathon participation

Two members of BHL’s Technical Advisory Group (TAG), BHL Technical Director William Ulate from Missouri Botanical Garden and Joe deVeer, Head of Technical Services of the Ernst Mayr Library at the Museum of Comparative Zoology, Harvard, “virtually” attended the CITSCribe Hackathon in Gainesville, Florida from Dec. 16 to 20, 2013.

The hackathon was co-organized by iDigBio (www.idigbio.org) and Zooniverse’s Notes from Nature Project (www.notesfromnature.org). Led by the co-organizers Rob Guralnick (University of Colorado, Boulder) and Austin Mast (Florida State University), the objective of the hackathon was to further enable public participation in the online transcription of biodiversity specimen labels and to produce new functionality and interoperability for Zooniverse’s Notes from Nature and similar transcription tools.  The event started by focusing on four areas of development, progressively addressed throughout the week: (1) interoperability betweenpublic participation tools and biodiversity data systems, (2) transcriptionquality assessment/quality control (QA/QC) and the reconciliation of replicatetranscriptions, (3) integration of optical character recognition (OCR) into thetranscription workflow, and (4) user engagement.

The LI LI Hackathon subgroup working on the integration of OCR.

For a while now, the BHL Technical Advisory Group (TAG) has been participating in the events of iDigBio, particularly on the Augmenting OCR Working Group, under Deb Paul and Bryan Heidorn’s guidance.  One of our BHL colleagues and TAG members, John Mignault from New York Botanical Garden, also participated last year at iDigBio’s previous hackathon which primarily focused on parsing OCR output to standard darwin core.

This time, we had a presentation by Cody Meche, an Agile trainer who gave some useful directions and tips on how to approach our hackathon to use our time as efficiently as possible while following an agile development process.  Alex Thompson, from iDigBio, presented on the digital resources that could allow programmers to run a copy of the web interface of Notes for Nature on their local machines using Vagrant and Virtualbox.  Paul Kimberly also presented the Smithsonian transcription project (transcription.si.edu) and Yonggang Liu talked about iDigBio’s image ingestion tool, useful for getting images into the iDigBio cloud.  Laura Whyte, Director of Citizen Science at Adler Planetarium joined us virtually at the Hackathon to talk about Zooniverse and citizen science.

I also had a chance to present shortly about our approach to OCR and Transcription with in our Purposeful Gaming project funded by the Institute of Museum and Library Services (IMLS). Basically, we intended to leverage iDigBio’s knowledge while tackling the challenge of improving the existing BHL OCR through Purposeful Gaming.  Our interest was mainly two-fold: on one side we wanted to learn from the amazing cumulative experience and skills that iDigBio comprises and the tools that are being adapted, built and used to generate the OCR and transcribe the text of their specimen labels; a challenge very similar to our own issues with OCR of books and journals in BHL.  On the other hand, we wanted to learn from their workflow definition to improve the OCR generation process, the incorporation of their transcription outputs and the reconciliation of the existing versions into a single one (for example, read about using sequence aligning methods on this recent blogpost by Rob Guralnick), while at the same time taking advantage of the citizen scientists’ help in an efficient manner that copes with the scale of the challenge.

High level workflow proposed for the Purposeful Gaming project

Specifically, our short term goals include incorporating recommendations and adapting existing tools developed by many of the participants in the past two hackathons: Jason Best’s DarwinScore, Ben W. Brumfield’s work on QC for Collaborative (Crowdsourced) Manuscript Transcription, the QA/QC track developments to take outputs from the citizen science transcription products and assure the highest quality end result, are just some among many other outputs and suggestions from these activities that can be incorporated to our process of improving the OCR texts in BHL.  And if you have more ideas, I would definitely like to hear about them…

For more information on the recent CITScribe Event read this iDigBio’s blogpost, Austin Mast’s detailed blog post or consult directly the Hackathon wikipage.

You can access all information and results about iDigBio in their home page and follow our own BHL developments from the webpage of the Purposeful Gaming project, made possible in part by the Institute for Museum and Library Services [Grant number LG-05-13-0352-13].