Since July 2016, the papers of taxonomic botanist John Torrey (1796-1873) have been the focus of a digitization and crowdsourced transcription project at the New York Botanical Garden (NYBG). Digitizing and Transcribing the John Torrey Papers, organized in coordination with the Biodiversity Heritage Library (BHL) and funded by the National Endowment for the Humanities and the Carnegie Corporation of New York, was created in an effort to digitize and make virtually accessible the correspondence of John Torrey and his colleagues, specifically letters received by Dr. Torrey.

Access to the correspondence of Dr. Torrey is particularly useful to natural scientists and natural historians alike as these letters provide a glimpse into the thought process and workflow for many of the 19th century’s greatest botanical minds. These letters are filled with a variety of different content, including commentary on plant taxonomy, personal biographical details, and anecdotal information on the daily lives of these natural scientists. The content within these letters aid in our understanding of the realities faced by these pioneering botanists, including the shift from the Linnaean system to the natural system and the systemic challenges faced by individuals in an emerging profession..

The John Torrey Papers collection contains over 9,500 pages from more than 350 correspondents, including Asa Gray, Amos Eaton, and Joseph Henry. The collection is organized alphabetically by correspondent then chronologically by the date each letter was written. Each page of each letter is scanned as a .tif file and uploaded to Macaw, BHL’s metadata management system, which aggregates the .tif file with a New York Botanical Garden MARC XML record. Once appropriate metadata has been applied in Macaw, the correspondence are uploaded to the Biodiversity Heritage Library Collection in the Internet Archive. The correspondence’s placement in the BHL Collection then allows for BHL to harvest new material from the Internet Archive on a weekly basis.

Digital content management is a crucial aspect of the project, but the heart of the process lies in the crowdsourced transcriptions done by volunteers from the New York Botanical Garden. These volunteers, recruited through citizen science outreach events, workshops, and tabling opportunities at various locations, work on the transcription platform From the Page, which is one of three transcription platforms whose exports are currently accepted by the Biodiversity Heritage Library, allowing the automatically-generated OCR for these items to be replaced with crowdsourced transcriptions, enabling full text search.

The work done by these volunteers is a contribution to the project for two reasons. First, the handwriting, colloquialisms, and personal shorthand of many of Dr. Torrey’s correspondents are exceptionally difficult to read or interpret. With the correspondence of many correspondents containing several hundred pages, it takes a considerable amount of time for our volunteers to develop a proficiency capable of not only accurately deciphering poor handwriting but also of uncovering the intention or context of particular writings.

Second, the transcriptions produced by the Garden’s volunteers coupled with BHL’s new support for transcriptions facilitates full text searching of materials that would otherwise be unavailable. The introduction of full text searching to the world of transcriptions is extremely impactful as it allows researchers to execute a more thorough examination of resources available to them at a faster pace and with higher levels of productivity. A prime example of this is the Biodiversity Heritage Library’s page index of scientific names, as seen in the lower left hand corner of the figure below.

In effect, the Digitizing and Transcribing the John Torrey Paper’s volunteers are the bridge between the content we are looking for and how we look for it.

To date, more than 7,000 pages have been transcribed and more than 6,000 transcribed pages are available for view in BHL, but the goals of the Digitizing and Transcribing the John Torrey Papers project still have not been met.

With less than 1,500 pages remaining, the New York Botanical Garden is in search of new volunteers to help reach our goal and transcribe some of our most interesting correspondents remaining to be done such as William Jackson Hooker, the former Director of the Royal Botanic Gardens, Kew, and New England natural scientist Dewey Chester. While many of our volunteers are drawn to the project due to their interest in botany, many more are captivated by narratives not typically associated with botany, such as Carl Bogenhard’s struggles as an immigrant in the United States or Jacob Whitman Bailey’s experimentation with photography.

If you would like to become a volunteer transcriber for the Digitizing and Transcribing the John Torrey papers project, you can sign up online here or email [email protected] for more information or assistance with the sign up process.

If you would like to learn more about the life of John Torrey, works he published, or plants named after him, please visit out digital exhibit “John Torrey: American Botanist.”

The “Anthropocene Defaunation” and the Lost Florida Zestos Skipper

We are experiencing a “biological annihilation.”

That’s how scientists are describing the biodiversity loss in what is being recognized as Earth’s sixth mass extinction event [1]. Not only are extinctions occurring at a rate 100 times higher than would occur naturally, but overall populations are also shrinking at alarming rates [1,2].

A 2014 Science report termed it the “Anthropocene defaunation”, reflecting humanity’s role in this biodiversity loss [3]. Among the casualties in this “Age of Humans” is one of “the few butterflies known to have become extinct in the United States” [4] — The Florida Zestos Skipper Butterfly Epargyreus zestos oberon (Worthington, 1881) [5]. This butterfly’s story draws forth science, taxonomy, history, and art from the Biodiversity Heritage Library (BHL) for a cutting edge representation of biodiversity in challenging times.

The recorded scientific history of the Zestos Skipper Butterfly extends back to the early nineteenth century. In the 1819 publication Verzeichniss bekannter Schmettlinge [sic], Jacob Hübner first listed the butterfly as Proteides zestos. Hübner later illustrated the P. zestos holotype (type locality “Surinam”, probably in error) via two figures of a female specimen in his Zuträge zur Sammlung exotischer Schmetterlinge (1826). However, as Hübner provided no description to accompany the name and illustration, it was not until 1832, after his death, that his assistant Carl Geyer officially described Proteides zestos as a new species.

Over the next 50 years, this rather unassuming reddish-brown Skipper, with a range from the Florida Keys to the Caribbean, was reclassified and redescribed by various authors. In Dublin, William F. Kirby (1871) assigned it to a new genus (Telegonus zestos) and in Chicago, Charles E. Worthington (1881), examining 31 specimens from Marco Island, Florida, described it as a new species (Endamus [sic] oberon), based on its resemblance to Eudamus tityrus. In 1884, Eugene M. Aaron, after evaluating over 160 specimens of tityrus and zestos, concluded that Proteides zestos, Telegonus zestos, and Eudamus oberon were in fact the same species.

Dr. Marc C. Minno (Insect Ecologist with Eco-Cognizant in Gainesville, FL) began searching for the Florida Zestos Skipper Butterfly in 2006. At his request, Skipper butterfly expert Dr. George T. Austin evaluated Zestos Skipper butterfly specimens in the Florida Museum of Natural History collection with type localities from Florida and the Caribbean. Before his death, Austin concluded that the Florida Zestos Skipper Butterfly actually represents a unique subspecies or sibling species [6]. Based on his own observations and Austin’s comments, Minno believes “oberon” to be the valid name of the Florida Zestos Skipper Butterfly population and has, until he can complete Austin’s study, designated it as Epargyreus zestos oberon (Worthington, 1881) [5].

Over the past 50 years, the Florida Zestos Skipper Butterfly population has been in decline. According to Minno, this butterfly, “once locally common in coastal areas of southern Florida”, had “disappeared from the mainland” by the mid-1980s. The last known sightings of Florida Zestos Skippers occurred in January 2004, at the Key West Tropical Forest and Botanical Garden in Stock Island, Florida [6].

In 2012, Minno et al., concluded a six-year survey looking for declining butterfly species in southern Florida [4]. Because the study failed to produce a single sighting of the Florida Zestos Skipper, in any stage of life, it was recommended that it be presumed extinct. Together with the Rockland Meske’s Skipper, these represent the “first [known] butterfly extinctions in Florida” [4].

The Florida Zestos Skipper exists now only in museums and the pages of historic literature, its memory preserved in natural history collections, libraries, and repositories like the Biodiversity Heritage Library.

Vanity: An Artist’s Story of Extinction and Rediscovery in the “Age of Humans”

The Florida Zestos Skipper Butterfly is just one of the “biological specimens” featured in Vanity, an art installation by Joseph Gregory Rossano. Created for and with the support of the Museum of Glass (MOG) in Tacoma, Washington, Vanity was on display at MOG from March 3 – August 30, 2015. The exhibition tells the story of eleven species and subspecies, presumed extinct, presented through the lens of humanity’s role in their demise.

The installation includes eleven “vanity” cabinets. The cabinet doors, Rossano’s “portrait” of man, are composed of imperfect wood laminate adorned with visual representations of Homo sapiens’ DNA barcode. On the bottom corner of each door, a scientific label hints to the species’ or subspecies’ identity inside the cabinet, beneath these human “fingerprints”. Rossano depicts the species through “faded” pencil portraits and as transparent glass sculptures suspended in clear liquid, inside period specimen jars. The overall effect is of a species vanishing behind the portrait of humanity…just as it has in reality.

Beneath each cabinet are mirrored, almond-shaped glass sculptures and in front of each, a chair with a specimen label: Homo sapiens. These objects accentuate humanity’s role in the loss of each species, for, as Rossano articulates in the exhibition catalogue, “When viewing Vanity from a seated position, we see ourselves reflected in these forms that echo the divine. In our vanity we reflect generations of humans who saw themselves as divine, while the truly divine—our 11 innocent and bygone species, subspecies, and their stories—reflect the truth about us” [7].

Rossano’s use of glass as a medium is equally deliberate: “like our environment, glass is transparent, fragile, and reflective — transparent in that it hides nothing, fragile in that once damaged it may never be repaired, and reflective of how we have impacted it” [8].

Each cabinet also offers a QR code leading to historical accounts of the enclosed species. These accounts summarize the species’ “discovery” (collection date, type locality, collector, scientific illustrations, etc.), humanity’s role in its extinction, and the year it was declared “Extinct”. To produce these species tales, Rossano collaborated with Sandra I. Berríos-Torres, MD. Berríos-Torres served as author of the 11 historical accounts and as Editorial Director of the exhibition catalogue, on behalf of Joseph Gregory Rossano.

The Biodiversity Heritage Library was a crucial resource for Berríos-Torres. Consulting dozens of publications in BHL while conducting research for Vanity, she ultimately cited 16 of them in the historical accounts that were incorporated into the exhibition and catalogue. The Florida Zestos Skipper Butterfly had the highest number of BHL citations in Vanity. Berríos-Torres used BHL to follow the butterfly’s taxonomic journey from its first listing by Hübner in 1819 to Aaron’s evaluation of the species in 1884.

“BHL resources were invaluable in my research for Vanity, in particular for accessing publications with the first collection, scientific description, and illustrations,” affirms Berríos-Torres. “The publications dated from 1819 to 2002, were published in English, German, Dutch, and French, and were contributed to BHL by 10 institutions, including university libraries, museums, government libraries, scientific research institutions, and botanical garden libraries across the USA, Canada, and England.”

From BOLD to Vanity

Berríos-Torres is an orthopaedic surgeon and a Centers for Disease Control and Prevention trained epidemiologist who has conducted laboratory and field research on infectious diseases and had a lead role in public health responses to national and international infectious disease outbreaks. Berríos-Torres was initially introduced to Rossano in the fall of 2009 at the opening of his BOLD exhibit, which examined species identity through art and incorporated Barcode of Life Data Systems‘ (BOLD) DNA barcodes into the installation’s sculptures.

BOLD was inspired by Rossano’s 2008 visit to the Área de Conservación Guanacaste (ACG) in northwestern Costa Rica at the invitation of Bradley Zlotnick, MD. At ACG, Rossano learned about DNA barcoding and met Zlotnick’s mentors, tropical ecologists Dr. Daniel H. Janzen and Dr. Winnie Hallwachs. Their 2004 landmark study on cryptic butterfly species, in collaboration with researchers at Smithsonian’s National Museum of Natural History (John M. Burns) and the University of Guelph, Canada (Paul D. N. Hebert, Erin H. Penton), “…illustrate(d) the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity” [9]. Barcodes offered a “rediscovery” of biodiversity. Concurrently with BOLD, Rossano’s Whitewashed exhibition “…aimed at revealing our own species’ whitewashing of Man’s relationship with nature throughout time” [7].

In 2013, the art critic for the Seattle Stranger drew a parallel between Whitewashed and a blog post about eight animal species and three subspecies reported as “Extinct”, including the Eskimo Curlew, Numenius borealis (Forster, 1772), one of the species highlighted in Whitewashed and also featured in the blog. The post inspired Rossano to imagine a new installation on extinction, and Vanity was born.

Vanity and the Biodiversity Heritage Library

Berríos-Torres first discovered BHL in December 2014 while performing literature searches for the species’ historical accounts in Vanity. It quickly became a daily part of her research process.

“Between December 2014 and March 2015, in the three short months allotted to research and compose the historical accounts of the 11 animals depicted in the exhibition, I used BHL on a daily basis,” shares Berríos-Torres. “In the following months, as Editorial Director of the Vanity exhibition catalogue, I used BHL several times a week, in search of illustrations.”

Tracking down relevant publications required quite a bit of sleuthing. For this, BHL’s various advanced search options proved invaluable.

“In general, the most important aspect of the BHL resources lay in the ability to access first descriptions and early illustrations,” explains Berríos-Torres. “At the onset, the only information I had was the species’ or subspecies’ common and scientific names. A Google search on the scientific names yielded two additional pieces of information: the last name of the person who first described it in the scientific literature and the date of that description. Rarely could I readily find the full name of the person who described it or the original citation. The opportunity to employ varied advanced search strategies in BHL proved indispensable, particularly when starting with such limited information on the subject.”

In addition to the Zestos Skipper Butterfly, BHL provided valuable references for several other species featured in Vanity, including a freshwater shrimp from Java Macrobrachium leptodactylus (de Man, 1879a), the Clouded Leopard of Formosa (Taiwan) Neofelis nebulosa (Griffith, 1821), and the Scioto Madtom Catfish Noturus trautmani (Taylor, 1969).

The Scioto Madtom Catfish was first described by Smithsonian scientist Dr. William R. Taylor, former curator of fishes at the National Museum of Natural History, based on a “funny looking catfish” collected by Dr. Milton B. Trautman in 1943, from Big Darby Creek in Pickaway County, Ohio [14]. Using BHL, Berríos-Torres was able to retrieve Taylor’s original description and a photograph of the holotype, a male specimen housed in the Smithsonian collections. Scioto madtom has not been observed since Trautman’s last collected specimen in 1957 [15]. Habitat loss and competition from the Northern Madtom Noturus stigmosus (Taylor, 1969) may have contributed to Scioto Madtom’s extinction [15,16]. In 2013, the IUCN Red List declared Noturus trautmani “Extinct” [17].

Beyond Vanity

The themes in BOLD and Vanity continue to evolve and converge. In 2017, Dr. Jacob J.D. Egge, scientific collaborator on the Vanity exhibition catalogue, championed bringing Vanity to The University Gallery at Pacific Lutheran University (PLU, Tacoma, Washington). There, Rossano expanded the installation to include select biological specimens from Washington state and housed in PLU’s Burton Ostenson Natural History Museum collection. The specimens were displayed atop multiple antique mirrored vanities across from the original installation and included a taxidermied woodpecker alongside Rossano’s clear glass sculpture of the same. Berríos-Torres compiled a supplement to the Vanity exhibition catalogue composed of natural history summaries of the PLU specimens, written by students in Egge’s Natural History of Vertebrates course. The students’ writings were incorporated into the expanded installation through QR codes on the wall, alongside the corresponding museum specimen. In 2018, Egge and Rossano presented on their Vanity collaboration at the University of Puget Sound’s Art|Sci: Art+Science salon.

The La Jolla Historical Society, inspired by Vanity, invited Rossano to create a work that reflected a part of San Diego’s biodiversity for the 2018 La Jolla Canyons: Place, Diversity, Connections exhibition (Wisteria Cottage, La Jolla, California). The Solitary Vireo cryptic species complex [18,19], revealed by DNA sequencing to be three distinct songbird species, includes Cassin’s vireo Vireo cassinii (Xántus, 1858), the only one of the three that migrates through San Diego County. Rossano displayed three morphologically indistinguishable clear glass vireo sculptures, blown in the likeness of museum collection specimens and identified solely through scientific tags or DNA barcodes (as in BOLD), atop an antique mirrored vanity (as in Vanity at PLU).

BHL: Discovery and Rediscovery for Bioliteracy

Vanity asks the viewer to face their own culpability in the loss of our biodiversity heritage. The question is, will we listen? Will we heed the warnings that the tales of species like the Zestos Skipper convey? Or will our own vanity get in the way? As this heritage continues to disappear, do we face a future where the historic literature and museum collections become the only places where we can explore and appreciate these “lost” species? As Dr. Minno wrote in his personal reflection on the Zestos Skipper Butterfly for the Vanity exhibition catalogue:

“[Vanity] gives us a chance to think about our role in this beautiful and vibrant world. The butterflies are telling us that something is wrong with the environment. We must learn to live modestly and to protect our planet if butterflies, as well as humans, are to survive” [20].

From historic literature and museum specimens, to traditional morphological taxonomy and modern DNA barcoding techniques, Vanity and BOLD convey and reflect more than just humanity’s role in this epoch’s loss of biodiversity. Rossano’s installations highlight the “renaissance of taxonomy” [21], the need for continued scientific exploration, and the opportunities that abound in gaining a better understanding Earth’s biodiversity. Mora et al., have predicted that, “In spite of 250 years of taxonomic classification and over 1.2 million species already catalogued in a central database…some 86% of existing species on Earth and 91% of species in the ocean still await description” [22].

As Berríos-Torres’ reflection on her research for Vanity demonstrates, access to historic literature, images, and other library materials are vital to cataloguing, understanding, and communicating Earth’s biological heritage.

“BHL is unparalleled and vital in providing worldwide access to a free, publicly available, digital biodiversity repository and reference library,” affirms Berríos-Torres. “For scientists and the public alike, BHL complements the DNA barcode taxonomy reference sequences to discover and rediscover biodiversity. Together they are rich wells of collaboration democratizing global bioliteracy.”

 

Acknowledgements

Berríos-Torres wishes to acknowledge Joseph Gregory Rossano, Museum of Glass, Bradley Zlotnick, MD, C.B. Bell III, and all Collaborating Scientists:

• Franco Andreone, PhD, Museo Regionale di Scienze Naturali, Italy (Cape Verde Giant Skink)
• Neil Burkhead, MS, (Retired) United States Geological Survey (USGS), Southeast Ecological Science Center, USA (Santa Cruz [Monkey Spring] Pupfish)
• Po-Jen Chiang, PhD Formosan Wild Sound Conservation Science Center Co. Taiwan (Clouded Leopard of Formosa)
• Neil Cumberlidge, PhD, Chair, IUCN Freshwater Crustacean Specialist Group, USA (Freshwater Shrimp from Java)
• Jacob J. D. Egge, PhD, Pacific Lutheran University, USA (Scioto Madtom Catfish)
• Robert E. Gill, Jr. MS, USGS, Alaska Science Center, USA (Eskimo Curlew)
• Lonnie I. Grassman, PhD Texas A&M University, USA (Clouded Leopard of Formosa)
• Marc C. Minno, PhD, Eco-Cognizant, Inc. USA (Rockland Meske’s Skipper & Florida Zestos Skipper Butterflies)
• Rohan Pethiyagoda B.Sc., M.Phil, (Retired) Australian Museum, Australia (Sri Lanka Spiny Eel)
• Edwin P. (Phil) Pister, MA – Desert Fishes Council, USA
• Hubert Planton, DVM, Veterinarian and African Wildlife Consultant, France (Western Black Rhino)
• Claudio Soto-Azat, MV, MSc, PhD, Universidad Andrés Bello, Chile (Northern Darwin Frog)
• Raquel Vasconcelos, PhD, University of Porto, Portugal (Cape Verde Giant Skink)

References

[1] Ceballos G., Ehrlich P.R., Dirzo R. (2017). Biological Annihilation via the Ongoing Sixth Mass Extinction Signaled by Vertebrate Population Losses and Declines. Proceedings of the National Academy of Sciences Jul, 114 (30) E6089-E6096; DOI: 10.1073/pnas.1704949114.

[2] Ceballos G., Ehrlich P.R., Barnosky A.D., García A., Pringle R.M., and Palmer T.M. (2015). Accelerated Modern Human–Induced Species Losses: Entering the Sixth Mass Extinction. Science Advances 1(5). e1400253DOI: 10.1126/sciadv.1400253.

[3] Dirzo R., Young H.S., Galetti M., Ceballos G., Isaac N.J.B., Collen B. (2014). Defaunation in the Anthropocene. Science 345(6195): pp. 401-406. DOI: 10.1126/science.1251817.

[4] Minno M. C., Daniels J., Jue D. K. (2012). Statement on the Extinction, Decline, and Loss of Butterflies in South Florida. Available at http://www.bio.miami.edu/horvitz/Plant-animal%20interactions%202013/conservation/required%20readings/Statement%20on%20Species%20Loss%20June%202012%20MC%20Minno.pdf. Accessed on 6 December 2018.

[5] Schweitzer D. F., Minno M. C., and Wagner D. L. (2011). Rare, Declining, and P​oorly Known Butterflies and Moths (Lepidoptera) of Forests and Woodlands in the Eastern United States. U.S. Forest Service, Forest Health Technology Enterprise Team, FHTET-2011-01. USDA Forest Service, Morgantown, West Virginia. 517 pp.

[6] Minno M.C. (2010). Butterfly Extinctions in South Florida. American Butterflies 8(3):17. Available at: http://www.naba.org/pubs/ab183/ab183_extinctions.pdf. Accessed on 6 December 2018.

[7] Rossano, J.G. (2015). Preface. In S.I. Berríos-Torres (Ed.), Joseph Gregory Rossano: Vanity (pp.13-16). Tacoma, WA: Museum of Glass.

[8] Lawrimore S. (2015). Swan Song. In S.I. Berríos-Torres (Ed.), Joseph Gregory Rossano: Vanity (pp.21-26). Tacoma, WA: Museum of Glass.

[9] Hebert P.D.N., Penton E.H., Burns J.M., Janzen D.H., and Hallwachs W. (2004). Ten Species in One: DNA Barcoding Reveals Cryptic Species in the Neotropical Skipper Butterfly Astraptes Fulgerator. PNAS 101(41): 14812-14817. www.pnas.org/cgi/doi/10.1073/pnas.0406166101. Accessed on 6 December 2018.

[10] Buckley-Beason V.A. et al. (2006). Molecular Evidence for Species-Level Distinctions in Clouded Leopards. Current Biology 16(23):2371-2376. Available at: http://www.cloudedleopard.org/Documents/Val_CB_2006.pdf. Accessed on 6 December 2018.

[11] Grassman L., Lynam A., Mohamad S., Duckworth J.W., Bora J., Wilcox D., Ghimirey Y., Reza A. & Rahman H. (2016). Neofelis nebulosa. The IUCN Red List of Threatened Species 2016: e.T14519A97215090. http://dx.doi.org/10.2305/IUCN.UK.2016-1.RLTS.T14519A97215090.en. Accessed on 6 December 2018.

[12] De Grave S., Smith K.G., Adeler N.A., Allen D.J., Alvarez F., Anker A., et al. (2015). Dead Shrimp Blues: A Global Assessment of Extinction Risk in Freshwater Shrimps (Crustacea: Decapoda: Caridea). PLoS ONE 10(3): e0120198. doi:10.1371/ journal.pone.0120198. Accessed on 6 December 2018.

[13] Berríos-Torres S.I. (2015). Freshwater Shrimp from Java. Macrobrachium leptodactylus (de Man, 1879a). In S.I. Berríos-Torres (Ed.), Joseph Gregory Rossano: Vanity (pp.52-56). Tacoma, WA: Museum of Glass.

[14] U.S. Fish and Wildlife Service (USFWS). (1976). National Digital Library. Milton B. Trautman Oral History Transcript. Interview with Milton B. Trautman. Interviewer Michael Smith. “Audio Cassette Dub from Reel-to Reel”. July 1976. Available at: http://digitalmedia.fws.gov/cdm/ref/collection/document/id/1031. Accessed on 6 December 2018.

[15] Scioto madtom (Noturus trautmani) 5-Year Review: Summary and Evaluation. U.S. Fish and Wildlife Service, Midwest Region, Ohio Ecological Services Field Office, Columbus, Ohio. Available at: http://www.fws.gov/midwest/endangered/recovery/5yr_rev/pdf/scma5yr2009.pdf. Accessed on 6 December 2018.

[16] King C.C. (1981). Prairies of the Darbie Plains in West-Central Ohio. Stuckie & Reese. Ohio Biological Survey Biology Notes 15:108-127. Available at: http://images.library.wisc.edu/EcoNatRes/EFacs/NAPC/NAPC06/reference/econatres.napc06.cking.pdf. Accessed on 6 December 2018.

[17] NatureServe. Noturus trautmani. The IUCN Red List of Threatened Species 2013: e.T14908A19032932. http://dx.doi.org/10.2305/IUCN.UK.2013-1.RLTS.T14908A19032932.en. Accessed on 6 December 2018.

[18] Murray B. W., McGillivray W. B., Barlow J. C., Beech R. N., and Strobeck C. (1994). The Use of Cytochrome B Sequence Variation in Estimation of Phylogeny in the Vireonidae. The Condor 96:1037-1054. https://sora.unm.edu/sites/default/files/journals/condor/v096n04/p1037-p1054.pdf. Accessed on 17 December 2018.

[19] Johnson N.K. (1995). Speciation in Vireos. I. Macrogeographic Patterns of Allozymic Variation in the Vireo Solitarius Complex in the Contiguous United States. The Condor 97:903-919. https://sora.unm.edu/sites/default/files/journals/condor/v097n04/p0903-p0919.pdf. Accessed on 17 December 2018.

[20] Minno, M.C. (2015). Reflections on the Rockland Meske’s Skipper Butterfly and the Zestos Skipper Butterfly. In S.I. Berríos-Torres (Ed.), Joseph Gregory Rossano: Vanity (pp.52-56). Tacoma, WA: Museum of Glass.

[21] Miller S.E. (2007). DNA Barcoding and the Renaissance of Taxonomy. Proc Natl Acad Sci USA 104(12): pp. 4775-6. Epub 2007 Mar 15. https://www.pnas.org/content/104/12/4775. Accessed on 17 December 2018.

[22] Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B. (2011). How Many Species Are There on Earth and in the Ocean? PLoS Biol 9(8): e1001127. doi:10.1371/journal.pbio.1001127. Accessed on 17 December 2018.

As I am wrapping up a short 10-week virtual internship with the Biodiversity Heritage Library, I believe that I will look back on this experience as one of those pivotal opportunities that impact the course of life.

The internship was made possible by the LIS Education and Data Science for the National Digital Platform (LEADS-4-NDP) fellowship program through Drexel University and funded by the Institute of Museum and Library Services, in collaboration with BHL. LEADS-4-NDP has a mission to improve library services by providing LIS (Library and Information Science) educators and researchers with data science skills.

BHL offered an ideal data science challenge for a future LIS scholar like me to explore: a huge dataset of documents spanning five centuries, along with an engaged community of users and researchers interested in extracting new knowledge from these fascinating texts!

In particular, the summer internship focused on exploring methods of identifying references to geographic places within the text of BHL collections, along with ways to visualize these references. This project envisions eventual new library services – perhaps a browse-able map interface where BHL users could locate complex information spatially, as well as generating new biodiversity data for conducting research on distribution of species over time.

As a PhD student at the University of Arizona’s School of Information, I am currently working on a dissertation extracting information from astronomy literature. Although I study data curation from a social science perspective and am particularly focused on astronomy, I wanted to enhance my technical skills in order to contribute to the evolution and relevance of LIS, and to accomplish my own research. LEADS-4-NDP and BHL provided a crash-course and hands-on learning opportunity, and by participating in this program I was able to pull my eyes from the cosmos for awhile and focus on the incredible biodiversity here on Earth.

Through this internship, I attended a two-day data science bootcamp, which was a priceless opportunity to quickly learn valuable techniques with a cohort of 9 other LEADS Fellows. I was also introduced to relevant researchers and projects associated with BHL. After a summer of investigation and experimentation, I created a report with recommendations for a full-scale geoparsing effort based on strategies and resources I examined. I also used Python programming tools to map and compare place names extracted from BHL text using several different human and automated methods. I evaluated and annotated a test corpus of BHL documents that could be used to develop customized Named Entity Recognition for a much larger set of documents. And I configured a software environment for future human annotators.

Although this was a virtual internship and I did not visit Smithsonian in person – unfortunately sweltering in Tucson, Arizona instead – my supervisor Carolyn Sheffield was extremely supportive. I looked forward to our weekly Skype conversations, where we shared ideas and brainstormed. Carolyn has been an ideal mentor, making connections with other projects and frequently sending along helpful information. I am grateful to Carolyn and to Martin Kalfatovic, along with the LEADS faculty and other Fellows, as well as everyone who kindly met with me this summer.

Overall, the internship has illuminated that this is an exciting time to be involved in library science, as our knowledge of the universe – and the technology to research it – rapidly expand. It is fascinating to view printed words as a source of new insight, and when you think of it that way – the library itself is actually an observatory for collecting data and deciphering the mysteries of the natural world!

As part of BHL’s mission to ‘improve research methodology by making biodiversity literature openly available to the world as part of a global biodiversity community’, the BHL Secretariat and Partners regularly participate in meetings and initiatives centered on collaborating with other biodiversity organizations throughout the world. One such recent event was the 2nd Global Biodiversity Informatics Conference (GBIC2) held in Copenhagen from 24-27 July 2018.

Organized by the Global Biodiversity Information Facility (GBIF), the meeting convened stakeholders from across the biodiversity informatics community to explore a model for coordinating across geographic and political boundaries to share and link data managed by various biodiversity infrastructures. GBIC2 was organized to build on outcomes and recommendations from the first GBIC meeting held in 2012. The Global Biodiversity Informatics Outlook (GBIO) framework (pictured below), developed as part of that first GBIC meeting, served as a foundation for exploring various considerations–from the cultural to the technological–involved in managing and sharing resources related to biodiversity data, evidence, and understanding.

The meeting kicked off with three plenary presentations followed by an interactive exercise to illustrate some of the key components of the current biodiversity informatics landscape. The presentations provided various perspectives from within and beyond the immediate biodiversity informatics. Topics covered experiences in other scientific domains on coordinating international collaboration, perspectives of funding agencies, and background on the GBIO framework and the high-level vision for a coordinating mechanism that would help guide discussions through the rest of the meeting. Speakers included Robert Hanisch, Director of the Office of Data and Informatics in the Material Measurement Laboratory at NIST; Maria Uhle, Program Director for International Activities at the National Science Foundation; and Donald Hobern, Executive Secretary of GBIF.

Following the presentations, the professional consultant firm Taylor + Tyler conducted an exercise with Donald Hobern, Executive Secretary of GBIF, to identify overarching goals, key stakeholders, and the connections as well as challenges between those, all through an interactive use of various toys and bits and other representative figurines. The resulting candidate model was used as a starting point for discussions on global coordination of biodiversity knowledge management, notably in ways that might help inform decisions and policies to protect biodiversity, particularly as related to Aichi Targets and Sustainable Development Goals (SDGs).

On the second day, conference attendees broke out into four groups and held parallel sessions, each organized around one of the following four GBIO components: Biodiversity Knowledge Network; Published Materials; Integrated Occurrence Data; Trends and Predictions. Each of these four groups was co-facilitated by GBIF staff with an invited representative. BHL’s Program Manager, Carolyn Sheffield, worked with GBIF Science Communications Coordinator, Daniel Noesgaard, to facilitate the Published Materials group. Approximately twenty attendees participated in this group, including several of our BHL colleagues from BHL Partner institutions including Patricia Koleff (CONABIO/BHL Mexico), Nicole Kearney (Museums Victoria/BHL Australia), and Lawrence Monda (National Museums of Kenya/BHL Africa). In addition, other participants also hailed from BHL Partner institutions (e.g., Harvard University and Museum National d’Histoire Naturelle), and while they themselves may not be directly involved in BHL, it was a pleasure to have the opportunity to meet and work with them.

The four groups participated in a series of exercises throughout the day to identify challenges facing the component areas, define sample investments for addressing those challenges, and then rank those investments according to criteria such as cost and value. Breakout groups were encouraged to consider not just technical challenges but also social and cultural challenges.

Some themes that emerged in the Published Materials Group included connecting taxon names to literature, assigning and appropriately managing DOIs for historic literature, and enabling more robust linkages between the literature and other biodiversity resources. The day concluded with a discussion of the process as a potential operating model for a coordinating mechanism for globally collaborative initiatives around sharing and linking about biodiversity data.

On the third day, all participants reconvened to debrief. Paul Taylor (of Taylor + Tyler) facilitated a discussion with the session leads to reflect on the experiences of the four groups. All told, the consensus seemed to be that while there were undoubtedly elements that couldn’t be addressed in a day-long exercise, the overall model was one that could be expanded and scaled up.

The report-outs were followed by two plenary presentations on governance models adopted by the intergovernmental organization ELIXIR and the Apache Software Foundation. Jerry Lanfear, Chief Technology Officer of ELIXIR, presented on their collaborative infrastructure and governance for coordinating life science resources across Europe. Ismaël Mejía, Member of the Apache Software Foundation, presented on the values that underlie the distributed network of programmers that form Apache. Specifically, he highlighted the commitment to open source development and merit-based opportunities. The day concluded with open discussions on the models presented and their potential applications for coordinated efforts across the wider biodiversity community.

The final day of the conference provided opportunities for further discussion on the proposed establishment of a coordinating mechanism. Participants reflected on the types of goals that might be achieved—and the types of coordination that might be required—by establishing a coordinated approach to biodiversity data sharing and linking. The group revisited the significance of extending beyond short-term, locally-based project initiatives to seek more globally coordinated opportunities in order to contribute to high impact outcomes such as those outlined in the Aichi Targets and Sustainable Development Goals (SDGs). All told, participants reached consensus on the value of establishing a “light weight coalition” and called on GBIF to take the lead.

The GBIC2 Organizing Committee is now in the process of producing consultation documents outlining a path forward and plans to make these available in multiple languages, including the 6 UN languages. In addition, information from the meeting has already been shared via two sessions at the recent SPNHC-TDWG 2018 Conference in Dunedin, New Zealand:

• W05 – Developing a mechanism to coordinate planning and investment in biodiversity informatics. Organiser – Donald Hobern.

• W05 – Developing a mechanism to coordinate planning and investment in biodiversity informatics. Organisers – Donald Hobern, Rebecca Snyder and Thomas Orrell. Moderator – Rebecca Synder Castle B (32)

We look forward to the forthcoming report and continued developments and opportunities for working with our colleagues across the global biodiversity informatics landscapes. Learn more about GBIC2.