Improving the Efficiency of Scientific Research

The Biodiversity Heritage Library and the Hymenoptera Anatomy Ontology

Katja C. Seltmann

The realm of ontology concerns the nature of reality, determining what exists, how it fits within a hierarchy, and how various elements are organized according to similarities and differences. Traditionally a philosophical question within metaphysics, today ontology has a firm application within systems biology as well.

Anatomy ontologies describe the structural and developmental relationships between the various parts of an organism. Defining anatomical ontologies reveals a complete list of distinguishing characteristics for that organism or group of organisms. The act of creating an anatomical ontology requires precise definitions of the terminology used to describe a variety of phenotypes.

Authors that have contributed to the past 250 years of taxonomic literature did not use standardized vocabularies. Katja C. Seltmann (Project Manager for the Tri-Trophic Thematic Collection Network at the American Museum of Natural History) desired to find a way to efficiently analyze this multi-century body of literature to create a single anatomical ontology, specifically for the insect order Hymenoptera. Accomplishing this feat required utilizing the Biodiversity Heritage Library (BHL).

Millions of pages of analog biodiversity literature, spanning the 15th-21st centuries, are digitized and made freely available online by the Biodiversity Heritage Library. Among the over 59,000 titles in the collection is the Journal of Hymenoptera Research (JHR), published by the International Society of Hymenoptera since 1992. Seltmann and a team of four other researchers utilized this publication from BHL to help build the Hymenoptera Anatomy Ontology (HAO).

The Order Hymenoptera contains sawflies, wasps, bees and ants. Find this and other 1807 illustrations of the Order in Nouvelle méthode de classer les hyménoptères et les diptères.

The NSF-funded Hymenoptera Anatomy Ontology is based on a language recognition tool (called the “Proofer”), which can be implemented across biodiversity literature in order to discover domain-specific anatomy terms. Employing the tool across the OCR for JHR resulted in the discovery of nearly 1,200 new terms for HAO. Furthermore, the development of the ontology is iterative. As the “Proofer” is applied to new collections of literature, it finds matches to existing terms as well as proposes new terms to add to the ontology. A human is required to review the proposed terms, selecting those to be added to the growing database.

After creation, this ontology can be applied as a filter to the literature in order to reveal trends in term occurrence within species descriptions, ultimately allowing researchers to analyze hundreds of years worth of scientific publications without having to sift page by page through the texts. The tool is thus instrumental in improving the efficiency of scientific research, and the process and impact was detailed in the 2012 PLoS ONE article “Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology” (Seltmann et al.).*

According to Seltmann, the Biodiversity Heritage Library plays a critical role in modern scientific research, including her own work:

“I am very fond of the BHL. It set a precedent for open access to literature that I feel initiated a cascading of change in our expectations. Sharing information, publications and open access is no longer the suspicious topic it used to be only a few years ago. Now, expectation is that publications, data and otherwise will be readily available. BHL, in my opinion, was truly one of the first examples of an open model becoming successful in the biological community, and, because it was useful, it changed attitudes.” 

The process used to create the Hymenoptera Anatomy Ontology can be applied to other disciplines in order to build any phonotype-relevant ontology. However, as the PLOS article articulates,

“Natural language processing methods for biological data discovery is only possible through open access publications, and efforts such as the Biodiversity Heritage Library to make legacy literature freely available. This exercise to observe trends in the terminology illustrates how the accessibility to literature facilitates anatomy ontology construction.” 

This use case thus provides a clear example of how the BHL is inspiring scientific discovery through free access to biodiversity knowledge.

Interested in telling us about how BHL has helped support your research? Send us feedback or write to feedback@biodiversitylibrary.org.

Grace Costantino
Program Manager | Biodiversity Heritage Library

* Seltmann KC, Pénzes Z, Yoder MJ, Bertone MA, Deans AR (2013) Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology. PLoS ONE 8(2): e55674. doi:10.1371/journal.pone.0055674

The Biodiversity Heritage Library Receives the CBHL Long Award of Extraordinary Merit

The Biodiversity Heritage Library is pleased to announce that it is the recipient of the Charles Robert Long Award of Extraordinary Merit from the Council on Botanical and Horticultural Libraries (CBHL).

The highest honor bestowed by CBHL, the Charles Robert Long Award for Extraordinary Merit was founded to honor outstanding contribution and meritorious service to CBHL or to the field of botanical and horticultural libraries or literature. Since 1988, only 14 people have received this award.

Receiving two separate nominations highlighting BHL’s global collaboration among libraries, innovative outreach, and exceptional bibliographic and technology standards, this year marks the first time an organization has won the award.

As the award letter articulates, “BHL envisions collaboration among botanical libraries on a scale not attempted previously. It fosters research across borders and disciplines and has made itself indispensible in many areas of the globe where botanical and biological libraries are unavailable to scholars. In an era that is increasingly focused on biodiversity, it has become an indispensible resource for many scholars, scientists and students.”

The award was announced during the CBHL Annual Business Meeting in East Lansing, MI, on May 9. Representatives from the Smithsonian Libraries, Harvard Herbarium Botany Libraries, and the New York Botanical Garden accepted the award on behalf of BHL. As part of the honor, BHL received a certificate and lifelong institutional membership to CBHL.

“We hope this [award] will encourage awareness of and further cross-collaboration between natural history libraries and CBHL,” said Laurie Hannah, Chair of the CBHL Long Award Committee.

About the Council on Botanical and Horticultural Libraries 

The Council on Botanical and Horticultural Libraries, Inc. (CBHL) is an international organization of individuals, organizations and institutions concerned with the development, maintenance and use of libraries of botanical and horticultural literature. The purpose of CBHL is to initiate and improve communication and coordinate activities and programs of mutual interest and benefit to its membership.

See the CBHL Press Release about the award.

Visual Riches of BHL Dazzle those Outside the Biodiversity Domain

Museums and the Web poster. Trish Rose-Sandler.

This spring BHL staff member Trish Rose-Sandler participated in two conferences which were outside of the biodiversity community but whose attendees were very much interested in the natural history illustrations found within the pages of BHL books and journals. These included the Visual Resources Association (VRA) annual conference held in Providence, Rhode Island, April 3-5, and the Museums and the Web (MW) conference held in Portland, Oregon, April 17-20.

Attendees at the VRA conference are image curators, librarians, and archivists who support scholars in arts and humanities departments within universities or museums. Rose-Sandler’s talk at VRA was part of a session on how visual resource collections are reaching out to new audiences through promotion of their content and collaboration with other disciplines. Much in the same way, BHL is reaching out to new audiences through its image content which has a broad appeal among many different fields of research.

MW Demo Table.

The MW conference is attended by folks who work on the technology side of cultural heritage organizations, mostly museums, but also some libraries and historical societies. The story of BHL and its images was told through a one hour demo session that included a poster, one page handouts, and a slideshow of the illustrations. Rose-Sandler and her Art of Life colleague, Kyle Jaebker, explained the challenges BHL faces in identifying the location of millions of images, how we are providing limited access via Flickr, as well as how the Art of Life project is helping scale this effort by automating their identification and crowdsourcing their description. These visually-oriented professionals were enamored of the image content we possess. One visitor at MW, a scientific illustrator from Prague, commented that her students had used images from the BHL Flickr stream for a scientific illustration course she taught. Other visitors were interested in the algorithms we were developing for automatically identifying the location of images within text resources.

Most of the attendees at both conferences were completely unaware of BHL. Those who had heard of BHL were surprised to learn we provided access to natural history illustrations. VRA and MW provide unique opportunities for us to showcase the BHL content to communities who might not have heard of us otherwise. Natural history illustrations provide common ground where the art and scientific communities intersect. If you have any suggestions for other conferences or venues we should be present at, please send us feedback or email us at feedback@biodiversitylibrary.org.

View Handouts from the Museums and the Web Conference:

• The Art of Life Project
• Uploading Images to Flickr
• Tagging Images in Flickr
• The Art of Life Algorithm

Trish Rose-Sandler
Data Analyst | Biodiversity Heritage Library
Missouri Botanical Garden

Refining BHL: New Vision, Mission, and Goal Statements

We are pleased to announce that the BHL Steering Committee has approved new vision, mission, and goal statements for the Biodiversity Heritage Library!

Vision: 

Inspiring discovery through free access to biodiversity knowledge.

Mission: 

The Biodiversity Heritage Library works collaboratively to make biodiversity literature openly available to the world as part of a global biodiversity community.

Goals:

Goal 1: Relevant Content 
Build and maintain the BHL as the largest reliable, reputable, and responsive repository of biodiversity literature and archival materials. 

Goal 2: Tools and Services 
Develop services and tools which facilitate discovery and improve research efficiency of BHL content. 

Goal 3: User Engagement 
Increase global awareness about the BHL through outreach, learning and education, and branding through engagement and collaboration with existing and new user communities. 

Goal 4: Membership and Partnerships 
Grow BHL consortia membership and partnerships while fostering cross-institutional collaboration that continues to serve as a model for digital library development. 

Goal 5: Financial Sustainability 
Ensure sustainability and relevance by being flexible, adaptable, and financially sound while the content and services remain openly and freely available.

Work on revising BHL's vision, mission, and goals began at the September 2012 BHL Staff and Technical Meeting. During the meeting, BHL staff dedicated several hours to pinpointing exactly what the BHL project is about and translating that into elements for a BHL vision statement. Staff also dissected BHL's existing goals, paring them down to simple statements outlining the most important objectives of the project.

Following the meeting, two staff subcommittees worked to take the resulting suggestions and mold those into draft vision and goal statements for BHL. The BHL Secretariat, including the BHL Program Director, Program Manager, and Collections Coordinator, then took all of the recommendations provided by staff and produced final draft vision, mission, and goal statements.

These statements were presented at the 2013 BHL Institutional Council Meeting, May 6-7, in Woods Hole, MA, where the BHL Steering Committee applied final revisions to the statements before approving them as BHL's new official vision, mission, and goals!

You can now see BHL's vision and mission on the homepage of our website, and our goals are clearly articulated on the BHL About page. We hope you find them as inspiring as we do!

2013 BHL Institutional Council Meeting

Attendees at the 2013 BHL Institutional Council Meeting. Back Row, Left to Right: Martin Kalfatovic (BHL Program Director); Marty Schlabach (Mann Library, Cornell University); Judy Warnement (Harvard University Herbarium); William Ulate (BHL Technical Director); Diane Rielinger (MBL-WHOI); Tom Baione (American Museum of Natural History). Front Row, Left to Right: Bianca Crowley (BHL Collections Coordinator); Susan Fraser (the New York Botanical Garden); Nancy Gwinn (Smithsonian Libraries); Connie Rinaldo (Harvard Museum of Comparative Zoology); Grace Costantino (BHL Program Manager); Jane Smith (Natural History Museum, London).

The seventh annual BHL Institutional Council Meeting occurred at the Marine Biological Laboratory and Woods Hole Oceanographic Institute Library (MBL-WHOI) in Woods Hole, MA, on May 6-7, 2013.

The BHL Institutional Council is composed of the directors (or designated alternative representatives) of the BHL member libraries. The annual meetings serve as an opportunity for council members to provide updates about BHL activities at their institutions, discuss governance issues, make funding decisions, and strategize about the future of BHL. It also allows BHL Administrative Staff to inform council members about developments in their areas of expertise.

Representatives from eight member libraries were able to attend the meeting in person, and, for the first time in IC Meeting history, those who could not be present physically were able to virtually join the meeting using video conference software available within the MBL-WHOI library. Representatives from California Academy of Science, the Field Museum Library, and our newest BHL member, The Library of Congress, participated in a virtual capacity throughout the meeting. As part of the meeting, each representative gave updates on the BHL activities that occurred at their institutions over the past year.

Hard at work at the 2013 BHL IC Meeting!

Day one of the meeting began with a BHL Program Director update, provided by Martin R. Kalfatovic, discussing project developments and achievements.

Also during day one, William Ulate, BHL Technical Director and Global Coordinator, detailed BHL's work in the past year, highlighting the implementation of the new user interface, work to date on the Art of Life  project, and the status of BHL's six global nodes. BHL Program Manager, Grace Costantino, also provided an update on BHL's outreach activities, including the presentation of a new BHL Outreach and Communication plan. Finally, Bianca Crowley, BHL Collections Coordinator, outlined her recent work and that of the BHL Collection's Committee, including an overview of collection analysis needs and a new Permissions Plans which proposes a strategy for obtaining and fulfilling agreements with publishers to scan in-copyright content for BHL.

The BHL Business Meeting occurred on day two. Topics covered included approval of the 2013 budget, discussion of a new proposed member library organizational structure for BHL, and brainstorming about fundraising options to achieve financial sustainability. One final topic of discussion was a review of a proposed revision to BHL's vision and mission statements:

Vision

"Inspiring discovery through free access to biodiversity knowledge."

Mission

"The Biodiversity Heritage Library works collaboratively to make biodiversity literature openly available to the world as part of a global biodiversity community."

As always, these meetings serve as a valuable opportunity to bring together BHL's geographically dispersed leadership in order to make important decisions about BHL's future. The decisions reached at this meeting promise to ensure continued positive growth and prosperity. We look forward to the ninth annual meeting next spring.

See presentations from the meetings by:

• Martin Kalfatovic, BHL Program Director: Presentation
• Grace Costantino, BHL Program Manager: Presentation One | Presentation Two
• Bianca Crowley, BHL Collections Coordinator: Presentation One | Presentation Two

* Photo Credits: Martin Kalfatovic, BHL Program Director

Documenting Scientific Knowledge One Handwritten Note at a Time

Connecting Content: The Wonderful World of Field Books

The California Academy of Sciences and our partners (all of whom are also BHL member institutions) are in the midst of a 3 year IMLS National Leadership Grant titled "Connecting Content: A Collaboration to Link Field Notes to Specimens and Published Literature." This project aims to digitize published scientific findings, their related field books and specimens, and metadata for these items, link all of these resources, and make them available for harvesting, reuse, and repurposing without cost. At this point, the bulk of the field books selected for this project have been digitized and made available through the Biodiversity Heritage Library. (*You can see the sixty-one titles digitized for this project by searching for “Connecting Content” in the BHL search box.) You can download a selection of these field book for free via the latest BHL iTunes U Collection: Connecting Content through Archival Field Notes.

Field books (or field notes) are the original documents which chronicle specimen collection and the events and observations that led to scientific discovery.  Field books are unique unto the creator and vary greatly from book to book. Here are a selection of highlights from the collection which demonstrate the wealth of information and styles found throughout the selection of field books:

William Whitman Bailey and the USGS Exploration of the 40th Parallel

Page One. A diary of a journey in California and Nevada. William Whitman Bailey.

Portuguese Man of War. Bailey.

Riccinus communis. Bailey.

William Whitman Bailey’s life story reads like a blockbuster movie plot. When young William was just nine years old, he and his family took an ill fated boat trip aboard the 198 foot side-wheeler, the Henry Clay. On this fateful day, the Henry Clay was involved in a minor collision with another vessel, but pressed onwards as it seemed that the ship has sustained little damage. However, about an hour outside of its final New York destination, the ship beached itself on shore near Yonkers as a result of a fire that had been burning unnoticed since the collision. The lucky passengers on the bow of the ship were either thrown or able to jump onto land, but the Baileys were not so fortunate. Separated from land by 140 feet of water and a wall of fire, the Baileys had no choice but to jump into the water as the fire approached. William’s mother and sister succumbed to the depths and his father barely survived. William managed to grab hold of a floating wicker chair and was eventually picked up by a passing ship, but the experience would leave him with permanent health problems.

However, this tragic setback did not lessen Bailey’s enthusiasm for adventure and curiosity about the natural world. Bailey would eventually study under Dr. Asa Gray at Harvard University and at 24 years old, he became the botanist for the United States Geological Exploration of the 40th Parallel. The field book for this expedition chronicles Bailey’s journey through California and Nevada in a flowing prosaic style with beautiful illustrations and photographs of Bailey’s observations. The very first page of Bailey’s journal opens with a beautiful demonstration of his illustrative pen and ink style. Bailey’s rich descriptions are paired with exquisite drawings that seem to jump off the page whether he is waxing poetic about the Portuguese Man of War or closely observing the leaf of the Riccinus communis. Bailey’s flowing narrative style and gorgeous illustrations make this field book a charming and informative look at the exploration of the 40th parallel that will surely captivate readers.

Washington H. Ochsner and the Galapagos Islands

Charles Island. Ochsner.

In 1905, the California Academy of Sciences sent 11 men off for a year and a day on an eighty-five foot schooner destined for the Galapagos Islands. While the expedition was underway, the California Academy of Sciences would fall into ruin during the great San Francisco earthquake of 1906. The specimens gathered during the Galapagos expedition would come to form the crux of the new California Academy of Sciences’ collections. Of the young men on that voyage, 26 year-old Washington Henry Ochsner travelled as the expedition’s geologist. His journals are more technical than Bailey’s in what they intended to capture and often included geological survey information, as well as inferences about how the geological features were formed. Ochsner also drew detailed surveys of the island terrains like this map of Charles Island. Ochsner’s field books have a scientifically focused structure and tend to be not-so-much a diary but a close and careful record of his scientific observations.

The Diaries of William Brewster, 1865- 1919

Eggs and Nests. Brewster.

Renowned ornithologist William Brewster mused over his daily observations in a personal and often humorous way. William Brewster’s love of ornithology blossomed early, and he kept careful records of the birds he observed throughout his life. These journals begin when Brewster was 14 years old, and it is interesting to see how his hand, knowledge, and confidence all develop over time.  In his later journals, Brewster takes care to write in a colloquial manner, and these notes provide unique insight into the daily life of a researcher over a 54 year span. This collection of journals also provide an enticing perspective on the detrimental changes to the environment and bird populations as a result of industrialization and the growth of urban centers.

All of the field books digitized for the Connecting Content project offer inimitable insight into how scientific data is gathered, synthesized, and extrapolated. It is the hope that by sharing these unique resources, researchers can better understand scientific findings and that the insights gained from this will promote further inquiry and the spirit of discovery.

Yolanda Bustos
Connecting Content Project Manager | Archives and Digital Collections Assistant Librarian
California Academy of Sciences

Want more Field Book Content?
View 61 field books digitized by the Connecting Content grant in BHL
Download a selection of these books for free on iTunes U
Find out more about the link between expeditions, field books, and publications in our previous blog posts with Smithsonian's Field Book Project: Post One | Post Two | Post Three

The Expedition Documentation Trifecta: Harriman Alaska Expedition (1899)

This is the third in a 4 part joint blog series by the Field Book Project (FBP) and the Biodiversity Heritage Library (BHL), showcasing examples of digital connections between museum specimens, field book catalog records, and the resulting publications.

View post one | View post two

In 1899 Edward Harriman, President of the Union Pacific Railroad, turned a family vacation into a two month foray into Alaska. Originally proposed as a hunting expedition, it was transformed into a scientific exploring expedition on the advice of Clinton Hart Merriam, Chief of the Bureau of Biological Survey. Harriman and his family, accompanied by 126 researchers, traveled to Alaska aboard the S.S. George W. Elder. In the end, the work of the many researchers resulted in vast amounts of valuable scientific data, including the discovery of a new glacier and an array of floral and faunal specimens.

Reid Inlet, Glacier Bay 1899. Photographed by Edward S. Curtis.    

Harriman and the Washington Academy of Sciences collaborated to fund the entire expedition, and Harriman chose researchers with diverse scientific backgrounds in order to collaborate on all fields of plant, animal, and earth science. After the expedition had ended, the scientists published a multi-volume Harriman Alaska Series, sometimes simply known as Alaska, of which vols. 6-7 were never published.

The Harriman Expedition is a particular favorite, because among the field documentation at Smithsonian Institution Archives, are two photograph albums of images from during the trip. Many of these images are available to view on Smithsonian Collection Search Center.

For such a large expedition with participants from across the Institution, you would think the field notes would be numerous and comprise their own collection. There are only as few as 6 field books from the Harriman Expedition found across the National Museum of Natural History (NMNH) and Smithsonian Institution Archives (SIA).

The photograph albums mentioned above reside in SIA; field notes of A. K. Fisher are in NMNH, Division of Mammals; T. H. Kearney’s journal is in the Department of Botany’s field book collection housed in the Main NMNH Library. Additionally there is item “Walpole, paintings, 1899 – 1904” whose abstract explains it may contain illustrations from the Harriman Expedition. One would only know this by the abstract or reading the field book content. Additionally these various field notes were cataloged by the Field Book Project, November 2011 - July 2012.

Specimens are equally difficult to track down. Though US National Museum received a collection of mollusks, birds, and plants, many of these specimens do not state they came from the expedition. One must know the collector, location, and/or time period.

Publications resulting from the expedition are a bit easier to locate, given the close relationship between Harriman and the Washington Academy of Sciences. In addition to the Harriman Alaska Expedition series linked above, the Biodiversity Heritage Library provides the following publications:

C. Hart Merriam papers : including correspondence, papers relating to career with the United States Biological Survey. http://www.biodiversitylibrary.org/bibliography/60472 Proceedings of the Washington Academy of Sciences, vol. 2 http://www.biodiversitylibrary.org/item/35745 Proceedings of the Washington Academy of Sciences, vol. 3 http://www.biodiversitylibrary.org/item/35746 Proceedings of the Washington Academy of Sciences, vol. 4 http://www.biodiversitylibrary.org/item/35272

Whether an expedition is large or small, its resulting natural history documentation can lose its connections and become increasingly difficult to locate. Cataloging and digitization efforts by Smithsonian and consortiums like the Biodiversity Heritage Library offer researchers increasingly better odds of rediscovering those connections. Stay tuned for the fourth and final blog post in the series.

By Lesley Parilla, Field Book Project, with contributions from Bianca Crowley, BHL Collections Coordinator