In the face of climate change and environmental challenges, understanding and documenting Earth’s biodiversity is essential. The Global Biodiversity Information Facility (GBIF) serves as a global repository for biodiversity data, playing a pivotal role in this critical mission of safeguarding our planet’s biodiversity. Species occurrence data sourced from the Biodiversity Heritage Library (BHL) provides insights into species distributions, behaviors, and interactions much deeper into time, offering key species baseline data required to effectively address the climate crisis. Without accurate and comprehensive data in GBIF, our collective ability to track environmental changes and make informed decisions is severely hampered.

As a GBIF participant node, BHL is committed to sharing biodiversity data openly, adhering to FAIR (Findable, Accessible, Interoperable, Reusable) and CARE (Collective Benefit, Authority to Control, Responsibility, Ethics) data principles, and collaborating with a global network of biodiversity organizations to bolster and build capacity to strengthen the biodiversity information infrastructure. To honor our commitments, technical staff from BHL are working to establish a scalable data pipeline of occurrence data currently trapped in archival field notes, journals, letters, correspondence, and other primary source materials. The journey has been an arduous one due to poor OCR (optical character recognition) data quality for BHL’s sub-corpus of handwritten materials.

Technical approaches to building a BHL ETL (Extract, Transform, and Load) data pipeline of species occurrence data from BHL’s field notes include machine learning, artificial intelligence (AI), and data extraction through innovative transcription projects like DigiVol, the crowdsourcing citizen science platform collaboration between the Australian Museum and the Atlas of Living Australia.

Now underway, is a global effort to convert centuries of biodiversity knowledge into accessible and actionable data, utilizing advanced AI and technical approaches. BHL Partners now have a stake in supporting international conservation policy aimed at safeguarding Earth’s biodiversity through greater data integration with the global biodiversity data infrastructure.

The Journals of William Brewster

The ornithological papers of William Brewster (1851-1919), held in the Ernst Mayr Library and Archives of the Museum of Comparative Zoology (MCZ) at Harvard University, are a rich source of historical species occurrence data and an ideal use case for building a BHL ETL data pipeline. Brewster’s field notes, journals, diaries, and correspondence comprise over 60,000 pages replete with detailed bird observations spanning 54 years (1865-1919). These records augment and extend his collection of over 40,000 bird specimens, bequeathed by Brewster to the MCZ and considered “one of the largest private collections ever made in this country [United States], and in some respects … by far the most valuable” (Henshaw, 1920). Thanks to a number of projects facilitated by the Ernst Mayr Library over the years, Brewster’s journals have been digitized and later transcribed using DigiVol.

Figure 4 below shows one example of Brewster’s extensive species lists. Brewster fastidiously recorded all essential elements of a species occurrence record and often more such as habitat information and detailed behavioral descriptions. The complexity of this example, featuring Brewster’s unique formatting, use of ornithological symbols, and tiny, crowded handwriting, highlights the value of crowdsourced human transcription by a team of enthusiastic, dedicated volunteers.

Figure 5 shows a portion of the transcription of this species list, produced in DigiVol by one of our long-time transcribers.

Extracting Data via Citizen Scientists and DigiVol

DigiVol, first developed in 2011 to crowdsource the transcription of specimen labels, enables institutions around the world to engage volunteers to extract data of various types, such as text, species identifications, and species traits from images. Each institution is able to upload images and manage their crowdsourcing project through the DigiVol platform. Through a combination of gamification and engagement tools such as a user forum and secure, private emails, institutions can build volunteer skills, a sense of community, and commitment.

Volunteers on the website can contribute any time of day – 24/7, 365 days a year. They can choose from a broad array of “virtual expeditions” on DigiVol, from identifying animals in camera traps located in the Australian “bush” to transcribing specimen labels and field notes from locations around the world.

The DigiVol platform has seen more than 14,000 volunteers contribute 155 equivalent work years (7 hour days, 261 days a year) to the digitisation of over 6 million tasks at an estimated equivalent value of A$12 million.

In terms of the William Brewster project, 352 volunteers have transcribed over 27,000 pages of diaries and field notes, at an average 23 minutes per page. This contribution amounts to more than 5.8 work years at an equivalent cost of A$462,000.

Publishing Data to GBIF

The final output of these recent data pipeline investigations was the deposit of 1,853 species occurrence records at GBIF from the Journals of William Brewster. The data deposit comprises valuable biodiversity records extracted through transcription efforts on DigiVol, transformed into DarwinCore, and subsequently published on GBIF. The species occurrence records span diverse geographical locations, primarily focusing on New England but extending to other regions of the United States, the Caribbean, and Europe. Brewster’s meticulous observations, encompassing species observation, behavioral data, and environmental conditions offer a rich historical perspective on biodiversity dating back over a century.

This deposit of historic biodiversity data demonstrates how valuable BHL’s collection is to global biodata infrastructure, as it plays a crucial role in establishing species base lines, informing climate change studies, tracking key environmental indicators, and contributing to the development of global biodiversity monitoring platforms.

Having the data available in BHL, even as transcribed text is one thing, but it is the human resources to review and reconcile the data that is really required to facilitate the flow of historic biodiversity data into today’s bioinformatics ecosystems. To all the humans involved in this species data project, from the initial observation and recording, to the preservation, digitization, transcription, data extraction and reconciliation, machine-learning, and creation of vital ETL data pipelines, we thank you.

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Related Works

Biodiversity Heritage Library Open Data Collection. (2022, November). Smithsonian Figshare.

Crowley, B., Dearborn, J., Funkhouser, C., Kalfatovic, M., Merriman, K., Iggulden, D., Trei, K., & Herrmann, E. (2023, October). Safeguarding Access to 500 Years of Biodiversity Data: Sustainability Planning for the Biodiversity Heritage Library [TDWG2023]. Biodiversity Information Standards, Hobart, Tasmania, Australia.

Data Flows Diagram. (2023, March). BHL Technical Team (BHL-TECH) Biodiversity Heritage Library.

Dearborn, JJ (2023, April). Unifying Biodiversity Knowledge for Life on a Sustainable Planet. Biodiversity Heritage Library. https://bhl.pubpub.org/

deVeer, J. (2021, February 24). Making the Best of Difficult Times: Accelerating the Transcription of William Brewster’s Writings During the COVID-19 Pandemic. Biodiversity Heritage Library.https://blog.biodiversitylibrary.org/2021/02/accelerating-transcription-brewster-covid19.html

deVeer, J. and Rinaldo, C. (2021, February 23). The Life and Work of Robert Alexander Gilbert: Empowering New Insights through Digitization and Transcription of Archival Materials. Biodiversity Heritage Library. https://blog.biodiversitylibrary.org/2021/02/life-work-robert-gilbert.html

Henshaw, Henry W. 1920. In Memoriam: William Brewster, Born July 5, 1851 – Died July 11, 1919. The Auk 37, 1 (1920), 1–23. https://doi.org/10.2307/4072953

Lichtenberg, M. (n.d.). BHL Data Model. BHL Github Repository. https://github.com/gbhl/bhl-us/tree/master/Documentation/DataModel

Mika, K. and Dearborn, J. (2022). [poster] Extracting expedition log data found in the Biodiversity Heritage Library. Through the door and through the web: releasing the power of natural history collections onsite and online, June 5, 2023. Edinburgh, Scotland, United Kingdom: Society for the Preservation of Natural History Collections (SPNHC). https://doi.org/10.5281/zenodo.6593457.

Richard, J. (2022, December 20). OCR Improvements: An Early Analysis. Biodiversity Heritage Library. https://blog.biodiversitylibrary.org/2022/07/ocr-improvements-early-analysis.html

Rinaldo, C. (2021, February 22). Nature Conservation and William Brewster: Insights From a Lifetime of Scientific Observations. Biodiversity Heritage Library. https://blog.biodiversitylibrary.org/2021/02/william-brewster-post-one

Trizna, M., & Dearborn, J. (2023, June). AI models are getting better and better at reading handwriting, but how can we find handwritten text to begin with? [poster]. 7th Annual Digital Data Conference, Leveraging Digital Data for Conservation, Ecology, Systematics, and Novel Biodiversity Research, Tempe, Arizona, United States of America. https://doi.org/10.25573/data.23523495.v1

This post is part of a series from the Ernst Mayr Library exploring the digitization and transcription of ornithologist William Brewster’s archival materials and the insights and scholarship made possible thanks to this work.

Robert Alexander Gilbert (1870-1942) was a Black photographer interested in ornithology and chemistry who worked for ornithologist William Brewster from the mid 1890s until Brewster’s death in 1919 and at various tasks around the Museum of Comparative Zoology (MCZ) at Harvard University beyond 1919. He was an Associate of the American Ornithologists’ Union.

Gilbert was not officially recognized for his photographic work with William Brewster, although Brewster did not claim credit for all the images in his collection. It was assumed that Brewster took all the photographic prints bequeathed to the Ernst Mayr Library and Archives of the MCZ (EMLA) upon his death. However, while conducting research for a book, author John Hanson Mitchell, former editor of the Massachusetts Audubon Society’s (MAS) Sanctuary magazine, discovered over 2000 of Brewster’s glass plate negatives in the attic of a building owned by the MAS. One of the images in particular, a photograph of a young, well-attired Black man standing in front of a rustic cabin in the wilderness, captured his interest. Mitchell was curious as to the identity of this young man. Later, in the mid-1970s, Mitchell had a chance encounter with an Archives Assistant at the MCZ who suggested to him that all of Brewster’s photographs were, in fact, taken by Brewster’s assistant, a young Black man named Robert Gilbert. This piqued Mitchell’s interest and launched his journey to discover more about Gilbert.[1] The quest culminated with the publication in 2005 of Mitchell’s Looking for Mr. Gilbert: the Reimagined Life of an African American. In 2014 an e-book edition was published as well.

Mitchell’s publication helps provide new insight into Robert Gilbert’s life and work. Brewster’s journals and diaries, now digitally available on the Biodiversity Heritage Library (BHL), are also valuable records attesting to Gilbert’s contributions in a variety of areas. While only a handful of Brewster’s photographs in the MCZ collection can be positively attributed to Gilbert, it is clear that Gilbert was with Brewster for photo sessions during the years they worked together. The photographic relationship between Brewster and Gilbert is intriguing. There is new enthusiasm to examine Brewster’s journals and diaries more closely now that they are digitized and being transcribed, to clarify Gilbert’s role in photographic collaboration with Brewster. As a result of identifying connections between the collections in the Museum of American Bird Art at the Massachusetts Audubon Society and the EMLA, a cooperative research project is underway.

Robert Gilbert was born and raised in the rural town of Natural Bridge, Virginia, in the valley of Broad Creek. In 1886, at the age of 16, he moved to Boston, Massachusetts where he would reside for the remainder of his life. Gilbert had an assortment of odd jobs during his first ten years in Boston, including working as a laboratory assistant for Dr. Arthur P. Chadbourne of Harvard Medical School, an amateur ornithologist and acquaintance of William Brewster. The records are unclear as to the actual year, but sometime between 1895 and 1897, work in Chadbourne’s lab slowed down and he recommended Gilbert to Brewster, who was in need of a temporary assistant to help him set up his personal bird museum. Gilbert met with Brewster, who showed him his extensive specimen collection and the tasks at hand, and for the next ten weeks Gilbert helped Brewster establish his new museum on the grounds of his home in Cambridge, MA. Afterward, Gilbert returned to working for Dr. Chadbourne, but shortly thereafter the laboratory experiments were completed whereupon Brewster hired Gilbert as his full-time assistant.[2] Brewster’s first mention of Gilbert in his journals is in his entry for March 31, 1897.

It is clear from Brewster’s diaries and journals that the tasks performed by Gilbert in Brewster’s employ were many and varied. Glover M. Allen, Curator of Mammals at the MCZ, described Gilbert as “Mr. Brewster’s trusted assistant, looking after innumerable details at his museum or his camp, doing everything from photographic work to preparing and serving meals, and always with a quiet dignity and devotion that never for a moment failed.”[3] Gilbert quickly became Brewster’s right-hand man as evidenced by the innumerable references to him from 1897 to 1919 in his diaries and journals. Here are a few examples:

Journal, June 8, 1897. As a field assistant, note Gilbert’s observational skills and attention to detail as he documents the behavior of a Whistler Duck for Brewster:

“Gilbert who had been to the boat for his breakfast came to relieve me and to keep guard while I had mine. It was arranged between us that if the Whistler began taking out her young while I was absent he would shout a few times to let me know of the fact. I had just finished breakfast when I heard this signal and jumping into the St. Lawrence skiff rowed as hard as I could pull for the nest but as soon as I came in sight of it I knew I was too late for Gilbert was standing up in his boat and paddling slowly towards the tree. Here is his account of what happened during my absence: At 6.45 the old Duck appeared at the entrance (the lower hole) to the nest where she sat for five minutes moving her head continually and looking about in every direction included within her field of vision; then she sank back out of sight reappearing at the end of a minute and looking about as before for another five minutes. At the end of this second period of observation she flew down to the water and swam around the stub three times clucking and calling. On completing the third round she stopped directly under the hole and gave a single loud call or cluck when the ducklings at once began scrambling up to the entrance from the nest and dropping down to the water falling on top of one another. In other words the brood literally poured out of the nest much as shot would fall from one’s hand. One or two hesitated or paused for an instant reaching the mouth of the hole but the greater number toppled out over the edge as soon as they appeared. All used their tiny wings freely beating them continuously as they descended. They did not seem to strike the water with much fear.”

Journal, November 5, 1897. Bird observations reported to Brewster: “Gilbert counted fourteen Chickadees in one flock on Ball’s Hill this morning. With them was a Downy, two Tree Sparrows & two Juncos. He also saw five Black Ducks passing over the meadows at evening.”

Journal, March 24, 1898. Work at Brewster’s cabin in Concord, MA: “Spent the forenoon clearing out the path behind the hill, Gilbert helping me.”

Diary, March 6, 1909. Photographic work: “Lizzy Fuller came over at 8 P.M. She with C. & E.R.S. [Caroline and Elizabeth R. Simmons] spent evening in Museum where I showed them about 100 lantern slides that Gilbert has just made.”

Diary, January 9, 1918. Work in Brewster’s museum: “Gilbert is now going through the collections in search of Anthrinae [Anthrenus] & other insect pests. Thus far he has found traces of them in the cans only.”

In the 1890s Brewster was earnestly transitioning from collecting bird specimens with his shotgun to field observation and photography. He had, in Robert Gilbert, an assistant knowledgeable in ornithology and capable with photography and photographic processing. It is unfortunate that in the Ernst Mayr Library collection of over 1,700 of Brewster’s photographic prints, only six have an inscription on the verso stating that the photograph was taken by Robert Gilbert. Below are two such photographs:

It is possible that many other photographs were taken by Gilbert, but we don’t know for sure. There are a number of occasions recorded in Brewster’s writings where it is clear that Brewster himself was doing the photography. In his journal entry for May 18, 1897, for example, Brewster writes:

“I visited the Hermit’s nest in the Brown clearing taking five photographs of it. The [female] was on the nest and for a Hermit sat very closely allowing me to set up the camera & focus on her at a distance of about 4 ft. but gliding away just as I was about to expose a second plate. She would not return to her eggs, however, while the camera was in position although I waited for her nearly an hour.”

Whether or not Gilbert was taking the picture, it is clear that he played a major role assisting with various aspects of Brewster’s photography. Inscriptions on the verso of photographic prints reveal that Gilbert owned darkroom apparatus and copied glass plate negatives to make prints. In a journal entry dated May 29, 1897 Brewster writes: “In the forenoon I took several photographs (with Gilbert’s help) in the gulf at the head of Great Island and along the western shore of the Sweat Cove.” Though Brewster was taking the pictures, Gilbert was assisting in some fashion.

It is evident that Gilbert was an invaluable assistant and friend who greatly facilitated Brewster’s ornithological accomplishments. Gilbert remained in Brewster’s employ until the latter’s death in 1919. Brewster arranged for the MCZ to hire Gilbert upon his death, another attestation to Brewster’s high regard for him.

There is little on record describing Gilbert’s tasks at the MCZ, but the Annual Report of the Director sheds some light. In the Report of the Director for 1931/1932 Thomas Barbour writes: “Robert Gilbert, aided by several young men, has done excellent work in rearranging some of the exhibition halls.” In the 1933/1934 Annual Report Glover Allen writes in his Report on Mammals: “In the ever-present work of cleaning skulls and skeletal material French and Gilbert have latterly borne a helpful hand, developing some skill.” Were Gilbert doing similar tasks today, he would likely be given the title Curatorial Assistant in the MCZ. Barbour’s report intimates that, among many other skills, supervision and at least familiarity with exhibit design properly belong on Gilbert’s resume. No doubt, Gilbert’s work in Brewster’s museum prepared him well for his tasks in the MCZ.

Gilbert worked at the MCZ until his death in 1942. In his 1941/1942 Director’s report, Barbour provided the following tribute:

“On January 7, 1942 Robert A. Gilbert died. For years before he came to the Museum he had helped Mr. Brewster in many ways and his sterling personal characters of integrity, affection, courtesy, and loyalty made him not only a [sic] honor to his race but one who was proud to do everything which he did as well as he could do it, and who was beloved by us all.”

Robert Gilbert’s many talents as well as his passion, curiosity and integrity enriched Brewster’s life and pursuits. It is evident that he brought these same qualities to his work at the MCZ.

The Ernst Mayr Library is actively transcribing the digitized journals, diaries and correspondence of William Brewster, enabling full-text searching of these resources in the Biodiversity Heritage Library. It is our hope that this will facilitate digital scholarship and further interest in the life and work of Robert Gilbert. In the next blog post we will discuss this transcription work.

References

[1] Mitchell, John Hanson. 2005. Looking for Mr. Gilbert: The Reimagined Life of an African American. Washington, DC: Shoemaker.

[2] Mitchell, John Hanson. 2014 e-book edition. Looking for Mr. Gilbert: The Unlikely Life of the First African American Landscape Photographer. New York, New York : Open Road Distribution.

[3] Allen, Glover M. 1942. Obituaries. Robert A. Gilbert. The Auk 59.3: 467. JSTOR. Accessed on 25 January 2021. https://www.jstor.org/stable/4079251.

This post is part of a series from the Ernst Mayr Library exploring the digitization and transcription of ornithologist William Brewster’s archival materials and the insights and scholarship made possible thanks to this work.

The Ernst Mayr Library and Archives of the Museum of Comparative Zoology (MCZ), Harvard University, holds a unique and extensive collection of photographs, letters, manuscripts and field notes of William Brewster, a prominent ornithologist/naturalist of the late 19th and early 20th centuries. His published work is lauded as providing authoritative and novel additions to ornithology.

Brewster published more than 300 ornithological papers and several books which are widely available in academic and research libraries. He was the first president of the Massachusetts Audubon Society and was a founding member of the Nuttall Ornithological Club, out of which grew the national organization, the American Ornithologists’ Union. Brewster served as President of the American Ornithologists’ Union from 1895 to 1898, and the organization has awarded a medal in Brewster’s name since 1921.

Brewster’s ornithological studies covered the United States, although he worked most extensively in New England. Brewster was a Curator of Ornithology in the Harvard University Museum of Comparative Zoology from 1885 to 1902, continuing to work in the MCZ until his death in 1919. He deposited his bird specimen collection in the MCZ and his associated works such as his journals, diaries, correspondence and some photographic works in the Ernst Mayr Library & MCZ Archives. Brewster’s extensive specimen collection, in combination with his large body of published work, secures his place in ornithological history.

In 2012, the Ernst Mayr Library began digitizing Brewster’s journals, diaries, letters, and photographic prints. Many have been digitized as part of the CLIR-funded BHL Field Notes Project. To date, virtually all of Brewster’s more than 60,000 pages of notes, correspondence and images have been digitized and nearly 10,000 pages of the handwritten notes and diaries have been transcribed. All materials are in the process of being deposited in the Biodiversity Heritage Library, with more than half of the collection, including all of the journals and diaries, now available. The materials have been collated into the William Brewster Papers Collection.

Brewster kept journals and diaries, mostly devoted to his birding activities, for 54 years from the time he was 14 until he died in 1919. These written records afford us a glimpse into the daily inner workings of this scientist’s mind. The Ernst Mayr Library is fortunate to have his full set of journals and diaries, most of his correspondence and some of his photographs and glass negatives. This is indeed a treasure trove of information, now made more accessible as it is digitized and made openly available in BHL. This collection is more than a record of changing landscapes, bird lists, temperature and weather recorded for each day of writing. It shows us how Brewster developed his ideas, how he thought about the world, and how his thinking changed through his life. In his later correspondence with Frank Chapman (a then-young ornithologist that Brewster mentored into a more mature career), they debated about and revised how to do science with less killing of birds.

“This miserable collecting. It is the cause of all higher failing, it lowers a true love of nature through a desire for gain. I don’t mean a specimen here and there, but this shooting right and left, this boasting of how many skins have been made in a day or season. We are becoming pot-hunters. We proclaim how little we know of the habits of birds and then kill them at sight. Sometimes I am completely disgusted with our ways and myself in particular… I long for an outing where the gun will be secondary, recorded observations primary, where I shall be entirely alone or with a companion whose object is my object … The question with me is, how am I going to change this?… Will you embark with me on a novel ornithological expedition, whose aim shall be to really observe birds to learn something of them. Where the gun shall be a servant, not a master, where days may pass without a skin being made, where there will be time to speculate and discuss the habits of birds observed, where systematic observation of certain phaenomena may be attempted.” 15 June 1890, Correspondence, Frank Michler Chapman to William Brewster.

Brewster’s detailed, long-term observations and notes are the key to his published contributions to ornithology and are a unique resource. His diaries, journals and correspondence are a gold mine of unpublished observations, journal notes, sketches, weather reports, specimen lists and travel narratives: these records are primary source data at its most raw and unevaluated. Historical collections of field notes may be the only documentation of a scientist’s thought processes, ideas and observations, particularly if only some of the writer’s material was ever published.

Brewster documented local environmental changes and gradual declines in number and presence of bird species over many years. He was concerned about vanishing wildlife, urbanization and landscape changes. He talked about ecological succession before the concept was officially published.

“Where the road passes through the woods … the roadworkers last May cut away the mountain maples, [cornels] and other shrubs and low trees that made such a beautiful border to the forest clearing in their places a broad belt of bare rocks half covered with the fallen brush wood. This deed of vandalism was performed while I was here and at the time I feared that years must elapse before Nature, with all her diligence, could repair the injury. I underrated her powers for already this thicket of road is, if anything, more beautiful than ever. Fire weed, Eupatorium, Impatiens, Asters, Golden rod and several other tall and rank flowering plants have shot up through and almost perfectly concealed the unsightly brush and stone heaps and I have rarely seen a more brilliant or attractive display of wild flowers.” 15 August 1896, Lake Umbagog, Maine, Journals of William Brewster

Brewster helped develop legislation to discourage excessive hunting and the use of feathers in women’s hats, although at the same time advocating for the continued, but regulated, collection of scientific specimens. His conservation work led him to become the first president of the Massachusetts Audubon Society. The photographs and negatives from the collections chronicle landscape changes through time. Brewster’s growing concerns about the killing of wildlife, even for scientific purposes, can be seen developing in his field notes and correspondence.

“If he would become really familiar with the wood folk and their ways, let him go among them unarmed and in a spirit of peace and loving kindness towards them all. Then he will learn many things which the bearers of guns do not know and cannot be made to believe.” August 1907, Journals of William Brewster.

The availability of Brewster’s notebooks enhances contemporary studies and makes the entire research cycle of this scientist’s work available for analysis by historians of science, scientists, social scientists and humanists or anyone interested in the process of discovery, by creating a richer and more interactive history of science resource. Brewster’s careful observations enable comparisons of his birding lists with contemporary observations (100 years plus later), helping to document environmental changes that might not be evident otherwise.

References

Emmet, Alan. November-December 2007. William Brewster: Brief life of a bird-lover 1851-1919. Harvard Magazine. https://harvardmagazine.com/2007/11/william-brewster-html

Meyer, Elizabeth. April 5, 2018. From ‘Shotgun Ornithology’ to nature conservation: scientific stories and data from the field notes of William Brewster. https://blog.biodiversitylibrary.org/2018/04/from-shotgun-ornithology-to-nature-conservation-scientific-stories-and-data-from-the-field-notes-of-william-brewster.html

Meyer, Elizabeth. April 6, 2017. Notes from William Brewster: The evolving field of zoology. https://blog.biodiversitylibrary.org/2017/04/notes-from-william-brewster-evolving.html

Meyer, Elizabeth. September 9, 2016. Notes from William Brewster: Ecological change in the Maine woods. https://library.mcz.harvard.edu/blog/notes-william-brewster-ecological-change-maine-woods

Mitchell, John Hanson. 2014 e-book edition. Looking for Mr. Gilbert: The Unlikely Life of the First African American Landscape Photographer. New York, New York : Open Road Distribution.

Mitchell, John Hanson. 2005. Looking for Mr. Gilbert: the Reimagined Life of an African American. Washington, D.C. : Shoemaker & Hoard : Distributed by Publishers Group West

Randall, Patrick. June 5, 2014. Transcribing the field notes of William Brewster. https://blog.biodiversitylibrary.org/2014/06/transcribing-field-notes-of-william.html

Rinaldo, Constance, Linda Ford and Joseph deVeer. 2018. Museum, library and archives partnership: Leveraging digitized data from historical sources. Poster presentation at Society for the Preservation of Natural History Collections, August 2018, Dunedin, New Zealand.

Sears, M. 2020. Celebrating Robert Gilbert. Ernst Mayr Library Blog post: https://library.mcz.harvard.edu/blog/celebrating-robert-gilbert

This year, as organizations around the world have done in response to the global COVID-19 pandemic, Biodiversity Information Standards (TDWG) held its annual conference virtually. With a mix of online working sessions, webinar-style symposia, presentations, panel discussions, and recorded presentations, this year’s conference was held across two separate periods—the first dedicated to working sessions during the week of 21-25 September 2020 and the second to symposia and panel sessions the week of 19-23 October 2020.

As the TDWG 2020 Annual Conference website states, the conference “serve two purposes:

• to provide a forum for developing, refining, and extending standards in response to new challenges and opportunities;
• and to provide a showcase for biodiversity informatics – much of which relies on the standards created by TDWG and other organizations.”

You can view the complete list of working session and symposia and discussion session descriptions on the TDWG website. Conference sessions were also recorded and are available for viewing on the TDWG YouTube channel.

BHL Symposium at TDWG 2020

On 20 October 2020 as part of the TDWG 2020 virtual conference, BHL hosted a symposium, “SYM03 Enhancing Connections With the Global Neighbourhood Through Expanding Partnerships”, organized by Constance Rinaldo (Librarian of the Ernst Mayr Library, Harvard and Chair of the BHL Executive Committee) and Colleen Funkhouser (BHL Program Manager, Smithsonian Libraries).

The symposium consisted of four talks, covering topics including building BHL’s technical strategy, digital object identifiers (DOIs), taxonomic name finding services, and BHL’s response to the global COVID-19 pandemic. See more details about the symposium and each talk below.

SYM03 Enhancing Connections With the Global Neighbourhood Through Expanding Partnerships
Abstract: The Biodiversity Heritage Library (BHL) is more than a digital library, it is a key resource for data related to biodiversity. Data such as museum specimens, taxonomic names, environmental and geolocation variables is embedded in the published and unpublished literature found in BHL. Over the past year, BHL has developed a five year strategic plan designed to bring more focus on data, technology and partnerships. BHL is already well-established within the global bibliographical knowledge base. The plan for the symposium is to highlight some new directions and identify synergies and connections with current, new and potential partners in the biodiversity knowledge infrastructure.

• Building the Biodiversity Heritage Library’s Technical Strategy — Elisa Herrmann (Museum für Naturkunde Berlin)
  • Presentation Slides
• Discovering the Platypus: From Its Scientific Description to Its DOI — Nicole Kearney (BHL Australia, Museums Victoria)
  • Presentation Slides
• Improving Taxonomic Name Finding in the Biodiversity Heritage Library — Joel Richard (Smithsonian Libraries)
  • Presentation Slides
• The Biodiversity Heritage Library Response to the Global COVID-19 Pandemic — Delivered by Martin Kalfatovic (BHL Secretariat, Smithsonian Libraries). Co-authors: Constance Rinaldo (Ernst Mayr Library, Harvard); Jane Smith (Library and Archives, Natural History Museum, London); David Iggulden (Library, Art & Archives at the Royal Botanic Gardens, Kew); Colleen Funkhouser (BHL Secretariat, Smithsonian Libraries).
  • Presentation Slides

The symposium was well-received, with approximately 100 people attending. The talks sparked interesting discussions, with questions around such topics as opportunities for Wikidata integration; supporting annotations as part of a future IIIF integration; strategies for improving optical character recognition (OCR); development of visualizations using BHL data; identification of additional useful data access points, such as collection and specimen codes and locality names; and potential strategies for supporting third-party application development using BHL data, such as through researcher prizes and challenges.

You can view a recording of the symposium on YouTube and all session presentation files in this Google folder.

The Biodiversity Heritage Library (BHL) has added functionality to allow BHL Partners to upload transcriptions in place of the automatically-generated OCR (Optical Character Recognition) for archival materials digitized in BHL. This functionality supports transcriptions generated as part of Partner crowdsourcing projects on Smithsonian Transcription Center, DigiVol, and From the Page.

Optical Character Recognition (OCR), also called text recognition, translates text characters in scanned documents into code that can be used for data processing and enables searching of document text. Handwritten archival materials like correspondence and field notes are notoriously problematic for OCR software. Full-text searching of these materials is significantly hampered by poor OCR output.

Crowdsourcing the transcription of archival materials has become a popular way to generate machine-readable text that enables searching and discoverability. Several BHL Partners are using crowdsourcing platforms (e.g. Smithsonian Transcription Center, DigiVol, and From the Page) to transcribe field notes, correspondence, and other archival materials that they have digitized in BHL.

With this new functionality, these transcriptions can now be uploaded in place of the automatically-generated OCR for these items, allowing them to be full-text searchable and enabling our taxonomic name recognition software to index scientific names within their pages. Since the transcribed text can be viewed alongside the digitized page image, users can also more easily read materials with difficult-to-decipher handwriting. Thus, this new functionality makes it easier for researchers and the public to explore these valuable primary source materials and access specific information from their pages.

Participating Partners have begun uploading transcriptions to BHL. To date, transcriptions have been uploaded from Partner crowdsourcing projects with BHL Australia, Ernst Mayr Library of Harvard University, The New York Botanical Garden, and Smithsonian Institution Archives. This is an ongoing process, and more transcriptions will be uploaded to the Library over time.

Interested in transcribing archival materials? Several BHL Partners have active transcription projects on various crowdsourcing platforms. Follow the links below to explore the opportunities and get involved:

• Ernst Mayr Library of Harvard University on DigiVol
• The John Torrey Papers from The New York Botanical Garden on From the Page
• Smithsonian Institution Archives on the Smithsonian Transcription Center

As Chair of the BHL Members’ Council, I had the privilege of attending the 25th Meeting of the GBIF Global Governing Board convened in Kilkenny, Ireland, 15-18 October 2018. I represent BHL in its capacity as an Associate Participant in GBIF at the governing board meeting. BHL has been a participant since 2014.

The Global Biodiversity Information Facility (GBIF) operates through a network of global nodes to develop and maintain an open data infrastructure for sharing digital biodiversity data.

GBIF Governing Board Chair Tanya Abrahamse (former CEO South African National Biodiversity Institute) and Donald Hobern (GBIF Executive Secretary), along with the host, Liam Lysaght (National Biodiversity Data Centre, Ireland) led the meeting. Abrahamse and Hobern provided an overview of GBIF activities over the past year, including a discussion of the GBIF Strategic Plan Goals and Work Program updates. The various GBIF Committee chairs (Science, Nodes, Budget) all reported the past year’s activities. Around 4 July 2018, GBIF reached the one billion record mark. The GBIF 26 Governing Board meeting will be part of the Biodiversity_next joint conference in Leiden, The Netherlands.

Results of the Governing Board elections with terms ending in 2020:

• 1st Vice-Chair, Governing Board: Christoph Hauser, Deputy Director General, Museum fur Naturkunde, Berlin
• 3rd Vice-Chair, Governing Board: Leonard Krishtalka, Director University of Kansas, Biodiversity Institute and Natural History Museum
• Nodes Committee Chair: André Heughebaert, Belgian Biodiversity Platform
• Nodes Committee 1st ViceChair : Anders Telenius, Swedish Museum of Natural History
• Nodes Committee 2nd Vice-chair : Hulda Gideon, Tanzania Commission for Science and Technology
• Science Committee 1st ViceChair: Gregory Riccardi, iDigBio/Institute of Scientific Data, Florida State University

Public Session of GBIF Governing Board. GBIF applications and relevance: progress and next steps.

All GBIF delegates and others from the greater biodiversity community in Ireland were invited to the public session. Many of the talks focused on data discovery and mobilization, improving functionality and relevance to policy.

Presentations were introduced by Tim Hirsch (GBIF).

• org at 1 billion records: trends in data publication and research use
  Kyle Copas, Communications Manager, GBIF Secretariat | presentation
• Encouraging a data citation culture
  Daniel Noesgaard, Science Communications Coordinator, GBIF Secretariat | presentation
• Shining a light on ‘dark taxa’: naming and discovering DNA-based biodiversity data, Part 1
  Dmitry Schigel, Scientific Officer, GBIF Secretariat | presentation
• Shining a light on ‘dark taxa’: naming and discovering DNA-based biodiversity data, Part 2
  Urmas Kõljalg, University of Tartu Natural History Museum & Botanic Garden, Estonia
• Shining a light on ‘dark taxa’: naming and discovering DNA-based biodiversity data, Part 3
  Dmitry Schigel, Scientific Officer, GBIF Secretariat
• Improved information on invasive and alien species, Part 1
  Shyama Pagad, IUCN Invasive Species Specialist Group (via video), New Zealand
• Improved information on invasive and alien species, Part 2
  Tim Hirsch, Deputy Director, GBIF Secretariat | presentation
• Improved ecological data capture and Essential Biodiversity Variables
  introduced by Donald Hobern, Executive Secretary, GBIF Secretariat
• Improved ecological data capture and Essential Biodiversity Variables Laetitia Navarro, GEO BON: Group on Earth Observations – Biodiversity Observation Network, Germany | presentation
• Overcoming the taxonomic challenge Olaf Bánki, Species 2000| Catalogue of Life, Netherlands | presentation
• Biodiversity data for national reporting Liam Lysaght, National Biodiversity Data Centre, Ireland | presentation

The winners of the 2018 Young Researchers Award and Ebbe Nielsen Challenge were presented at the end of the public session. The Young Researchers Award honors projects that foster innovative research and discovery in biodiversity informatics and provides financial support for winners.

• Raquel Gaião Silva, University of Algarve, Portugal: Raquel is a Master’s student in International Science/ Marine Biodiversity Conservation. She has used GBIF mediated data in her work on climate-driven changes in seaweed distribution in Atlantic Iberian marine forests.
• Kate Ingenloff, University of Kansas Biodiversity Institute is a doctoral student who used GBIF mediated data along with time-specific environmental and behavioral data to develop better niche models for highly mobile species such as pelagic birds.

The Ebbe Nielsen Challenge annual prize honors the memory of Dr Ebbe Schmidt Nielsen, a principal founder of GBIF and leader in biodiversity informatics. The six recipients shared prize money, some provided by the Swedish Research Council.

• Checklist recipe: a template for reproducible standardization of species checklist data Lien Reyserhove, Damiano Oldoniand Peter Desmet, INBO: Research Institute for Nature and Forest, Belgium First prize
• Ozymandias: a biodiversity knowledge graph Roderic D. M. Page, University of Glasgow, United Kingdom First prize
• The bdverse. Tomer Guetaand Yohay Carmel, The Technion – Israel Institute of Technology, Israel, Vijay Barve, Florida Museum of Natural History, United States, Thiloshon Nagarajah, Informatics Institute of Technology, Sri Lanka, Povilas Gibas, Vilnius University, Lithuania, Ashwin Agrawal, Indian Institute of Technology (BHU), India Second prize
• GBIF Issues Explorer. Luis J. Villanueva, Smithsonian Institution, United States Second prize
• Smart mosquito trap to DwC pipeline. Connor Howingtonand Samuel Rund, VectorBase, United States Second prize
• Taxonomy Tree Editor. Ashish Singh Tomar, University of Granada, Spain | BIG4 Second prize

Videos of the public sessions of the meeting are available on the GBIF website.

Other Explorations

I had some productive, informal meetings with BHL partners and potential partners providing opportunities to explore new partnerships or deepen existing ones. During the reception and other networking events, I learned about GBIF’s Biodiversity Open Ambassador program, a chance to promote the principles of open data sharing in presentations, whether or not the work is about GBIF. GBIF will provide slides and information or you can develop your own to add to appropriate presentations. Discussions with Ana Casino of the Consortium of European Taxonomic Facilities (CETAF), Donald Hobern and Dmitry Shigel (GBIF), Dmitris Koureas (TDWG) and Patricia Koleff (BHL México), among others, determined that BHL’s future plans will augment interoperability in the biodiversity community and that BHL is a critical resource for many GBIF participants.

William Brewster (1851-1919) was a renowned American amateur ornithologist, serving as a co-founder of the American Ornithologists’ Union, the first president of the Massachusetts Audubon Society, and a curator at Harvard’s Museum of Comparative Zoology (MCZ). As a part of the CLIR-funded BHL Field Notes Project, MCZ has been digitizing Brewster’s journals, diaries, letters, and photographic prints, which are held in Special Collections at the MCZ’s Ernst Mayr Library.

Most of Brewster’s observations are based in New England, where he split his time between two homes in Cambridge and Concord, Massachusetts. Brewster would stay in a cabin by the Concord River to study nature and escape city life in Cambridge. He also took notes when travelling: his notebooks document trips to the southern USA, the Caribbean, and Europe.

Brewster’s writings contain a wealth of information, from data on temperature and weather conditions to descriptions of animal behavior and personal musings. Some of the extensive Brewster collection is already available to view on BHL – here’s a sampling of the kinds of information you’ll find.

In the warmer months, Brewster often camped at Lake Umbagog (north of the White Mountain National Forest, straddling Maine – New Hampshire border), where he spent his days tracking the progress of bird nests around the lake and making other general observations. Here’s a typical example of one of Brewster’s bird lists, recorded at Lake Umbagog in 1907. The larger numbers are dates, with superscripts indicating the number of individuals counted that day. Asterisks tell us that the bird was heard vocalizing. Some additional details are also penned in (for example, he notes that Dendroica pensylvanica, the Chestnut-sided Warbler, was in an apple tree). [1]

Beginning in the 1890s, Brewster’s journals document a transition of focus from mainly specimen-collecting to photography and documenting behaviors. (His journals reveal an interesting story about his increasing ethical conflict and desire to study wildlife without contributing to its decline. You can read more about this in a previous BHL blog post found here.) Earlier in Brewster’s career, his journals list and provide details on species collected – data that is similarly useful to the list above in that it gives an indication of species distribution and abundance. It also corresponds with existing specimens and documents the impact made by scientific collectors of the era.

The kinds of data in these journals diversifies as Brewster started devoting more time to documenting animal behaviors. In many ways, this work seems to have been harder than getting a good shot at a bird. Even with today’s apps and audio libraries, figuring out bird calls can be a challenge. Equipped with just pencil, paper, field glasses and ears, studying bird vocalizations is much trickier, as shown by Brewster’s notes below from 1902. [2] Today, we can represent bird vocalizations visually using spectrograms. In order to translate sounds to text, Brewster listened diligently to invent mnemonics, describe patterns, and make comparisons to other more familiar sounds.

It’s worth mentioning that Brewster’s animal observations weren’t limited to birds, and that a lot of his animal encounters made for interesting stories. Below is a sketch of a moose from Lake Umbagog, observed in August 1869. [3] His impression: “He seemed like some long-forgotten antedeluvian creature which, arousing from a sleep of thousands of years, was wandering aimlessly about in a land so changed that it no longer had any place for such strange monsters.”

As though telling the story to a friend, he recounts following the moose through the wetland in his canoe – sometimes ending up way too close for comfort. After talking to a local guide, he learned that the moose that he’d seen was a mid-sized female, and concluded, “If she was not really a very large one I have no wish to be equally near to a big bull!”

Because he returned to Lake Umbagog year after year, Brewster was able to notice longer-term changes in familiar ecosystems. Increasingly, these changes were man-made disturbances: the clearing of woods, the creation of new roads, and other urbanizing changes. He also recorded how local communities of animals and plants responded after these disturbances. The following passages from Brewster’s field notes document some changes that he saw in the Maine woods as a consequence of logging for paper mills, and include some of his own predictions.

“Where the road passes through the woods … the roadworkers last May cut away the mountain maples, cornels and other shrubs and low trees that made such a beautiful border to the forest clearing in their places a broad belt of bare rocks half covered with the fallen brush wood. This deed of vandalism was performed while I was here and at the time I feared that years must elapse before Nature, with all her diligence, could repair the injury.

“I underrated her powers for already this thicket of road is, if anything, more beautiful than ever. Fire weed, Eupatorium, Impatiens, Asters, Golden rod and several other tall and rank flowering plants have shot up through and almost perfectly concealed the unsightly brush and stone heaps and I have rarely seen a more brilliant or attractive display of wild flowers. The fire weed is especially tall and fine and the jewel weed grows in solid beds yards in extent. Of course the Humming birds had not overlooked such a feeding ground. There were at least three of them there at once including an adult male with blazing ruby throat at which I fired an ineffectual shot.” [4]

In this instance, Brewster noticed that one year was enough time to see plant growth after the woods had been cleared, that the colonizing plants were different from the ones that characterized the location before, and that they had impacted animal life. He penned these observations on ecological succession just a few years before the first scientific paper on this concept was published (“An Ecological Study of the Sand Dune Flora of Northern Indiana”, Henry Chandler Cowles, 1898.). [5]

The following year, he wrote:

“The Lake shore has been sadly marred … by the lumbermen who last winter cut all the spruces and many of the fine, tall white pines all the way from this landing to the deep cove near the Tidswell place. […] Lumbering is a very different business now from what it was twenty years ago. Then only the larger trees were taken; now the pulp mills devour everything and nothing is spared thicker at the base than five inches! […] These changes in the character of the forests must make speedy & considerable changes in the bird fauna. The shore near Crocker’s camp, for instance, has been one of the chief breeding grounds for the Bay breasted Warbler. They will breed there no longer, now that all the spruces are gone.” [6]

Knowing now that local extirpations and even total extinction can occur (this was the decade when the passenger pigeon disappeared from the wild), he would have penned this prediction with heavy heart. To help preserve an area he cared about – his familiar stomping grounds along the Concord River in Concord, Mass. – over time, Brewster purchased 300 acres of the riverfront. His ‘October Farm,’ across the river from Great Meadows National Wildlife Refuge, is now protected land with trails recently opened to the public – while his writings, notes and photographs preserve the region for us as he knew it in the 19th and early 20th centuries.

(If you’re interested in learning more, I write an ongoing series of blog posts on the Brewster collection on the Ernst Mayr Library blog. You might like to see archival and modern photos of October Farm, Brewster’s property in Concord.)

References

[1] July and August 1907. Journals of William Brewster, 1871-1919 (inclusive). Find this journal on BHL.

[2] June 1, 1902. Journals of William Brewster, 1871-1919 (inclusive). Find this journal on BHL.

[3] August 27, 1896. Journals of William Brewster, 1871-1919 (inclusive). Find this journal on BHL.

[4] August 15, 1896. Journals of William Brewster, 1871-1919 (inclusive). Find this journal on BHL.

[5] ‘Henry C. Cowles’. The University of Chicago Centennial Catalogues. Web accessed: https://www.lib.uchicago.edu/projects/centcat/fac/facch14_01.html

[6] May 15, 1897. Journals of William Brewster, 1871-1919 (inclusive). Find this journal on BHL.