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Tuesday, February 25, 2014

Helping Out with Diverse Interests in Biodiversity: Taxonomy of Molluscs and Birds

Prof. Hamish Spencer (right) and his long-time 
collaborator, Prof. Jon Waters (left) examining the 
holdfast of a brown alga, Durvillaea poha, a species 
they and a student of theirs described after showing
 it was genetically distinct from the widespread D. antarctica.  
The holdfasts pictured are the habitat for a number of 
interesting invertebrates (e.g., molluscs, crustaceans). 
One of these, the gastropod mollusc Diloma durvillaea
was also described by them.

New Zealand is an exciting place to study biodiversity for a number of reasons. First, its unique set of plants and animals, evolving in the context of an active geologic history, results in several model systems that are ideal for testing ideas about how evolution works. Second, the country still has areas of its natural environment that are relatively undisturbed, something of which the wider public is very proud and which means that many people are interested in and aware of many native species. And, third, New Zealand is still in an “age of discovery” with undescribed species turning up in numerous studies across almost all habitats.

Hamish Spencer has had the good fortune not only living in such an amazing location but has also pursued a very rewarding career in preserving and improving understanding of the rich biodiversity found here. He currently serves as Director of the Allan Wilson Centre, a cross-institutional group of evolutionary biologists working on various aspects of New Zealand’s biodiversity.  He is also a Professor in the Department of Zoology at the University of Otago, in the city of Dunedin, known as the Edinburgh of the South.  

As part of our regular BHL and Our Users series, Professor Spencer has graciously agreed to answer some questions about how BHL has impacted that work.

When did you first discover BHL?

A while ago! Not sure.  Maybe 6 years?

What is your opinion of BHL and how has it impacted your research? 

It is fantastic! What is more important, even: it is getting better.  I am amazed at the breadth of its material, especially from the 19th Century. I work on the phylogenetics of a variety of groups (so far, molluscs, birds, trematodes, brown algae, polychaetes, crustaceans), usually as model systems to answer a question about the way evolution works. For example, I have been interested in the importance of long-distance dispersal in marine environments, especially the Pacific and Southern Oceans. With my collaborators, I have used brown algae, molluscs and crustaceans to investigate various questions about dispersal and sometimes venture into the taxonomy of these groups when the phylogenetic work reveals new species or clades. In order to do that properly, I like to consult original descriptions and, although Otago is New Zealand’s oldest university, with a good library dating back well over 130 years, sometimes that literature is simply unavailable.  That is where BHL comes in.

How often do you use BHL?

It is very sporadic.  Sometimes not for weeks at a time and then intensively for a week or so.

How do you usually use BHL? 

Usually I want a whole article from an ancient journal, so I download that.  I find that if I just read online, I inevitably need to check some detail and so I have to go back and look at I again. Sometimes, if I want some part of a book, I download just the relevant pages.

What are your favorite features/services on BHL?

I am amazed and impressed by the breadth of material available.  It is a real tribute to the many people who have gone to the effort of producing high-quality scans of so much material. It is seldom, now, that I am wanting to read something from the 19th century that is not there.  As a consequence BHL is becoming my first port-of-call for such items.  It is a bookmark I use frequently.

If you could change one thing about BHL, what would it be, or what developmental aspect would you like the BHL team to focus on next?

The one thing that does not work very well is the downloading of parts of an item.  Selecting a large number of pages and then finding a number of them are blank can waste quite a bit of time.  (I think you know this is an issue, already, though!)

If you had to choose one title/item in BHL that has most impacted your research, or one item that you prefer above any other in BHL, what would it be and why?

That’s hard, since I work on a range of groups, but I suppose the early issues of Proceedings of the Malacological Society of London would be up there (even though it is 20th century!).  More recently the (19th-century) Transactions of the Royal Society of South Australia have been very useful.

We send our deepest thanks to Hamish Spencer for his participation in this series.  We’re always excited to learn more about how people are using BHL and the impact it has had on their work.  Gathering feedback on what our users would like to see changed or improved also helps us guide future development so that we can continue to improve and transform BHL to meet the needs of our users.  Have a story of how BHL has impacted your work?  We would love to hear from you! Send us an email to feedback@biodiversitylibrary.org.

Thursday, February 20, 2014

BHL Day at the Melbourne Museum, opening event for the 5th Global BHL meeting

Ely Wallis (left) and Tim Hart
BHL Australia and the Melbourne Museum hosted "BHL Day" at the museum on 31 January 2014. Representatives of all the global BHL nodes (with the exception of BHL Egypt) were in attendance. BHL members were joined by staff and volunteers from BHL Australia as well as from the Atlas of Living Australia.

The day began with Caroline Martin, Bunjilaka Manager at the Melbourne Museum who welcomed the group with a traditional welcome from the indigenous people of Australia. Tim Hart, Acting CEO of the Melbourne Museum gave a welcome to the day's events. The Global BHL delegates also received a special tour of the First People exhibition by multimedia designer (and BHL Australia scanning coordinator) Joe Coleman.

Fenghong Liu (BHL China)
The morning session consisted of presentations from each of the attending nodes.

  • Nancy Gwinn, Chair, Biodiversity Heritage Library
  • Ely Wallis, Biodiversity Heritage Library Australia
  • Jinzhong Cui and Fenghong Liu, Biodiversity Heritage Library China
  • Jiri Frank, Biodiversity Heritage Library Europe
  • Abel Packer and Fabiana Montanari Lapido, Biodiversity Heritage Library SciELO (Brazil)
  • Anne-Lise Fourie, Biodiversity Heritage Library Africa

Joe Coleman, Connie Rinaldo,
 and Anne-Lise Fourie
After the presentations, three "provocative" questions were presented to the audience (which consisted of a number of Melbourne Museum, CSIRO, and Atlas of Living Australia staff (including ALA Director John La Salle). The questions posed were:

"Recent Literature" by John La Salle (Atlas of Living Australia). What are the questions and concerns about BHL more actively engaging in the acquisition of in copyright material?

"Topic Based Reprint Collections" by Robin Wilson (Senior Curator, Marine Invertebrates, Museum Victoria). Many scientists hold extensive reprint collections around their subject area of expertise. What provision can we make for incorporating such collection into digital repositories without inadvertently infringing copyright laws? How do we strike a balance?

"Archival Materials" by Martin Kalfatovic (Smithsonian Libraries / BHL). How can, and should, BHL proceed on expanding its collections of non-print materials (e.g. field notes, art work, etc.)?

The questions engendered lively and useful discussion and input for BHL writ large.

Abel Packer and
Fabiana Montanari Lapido
BHL SciELO
There was also a tour of the Melbourne Museum rare book collection and scanning center where the group met with the volunteer scanning staff.

A reception and opportunity to catch-up with colleagues ended the evening.

The Global BHL members wish to give Ely Wallis (Museum Victoria/BHL Australia) special thanks for organizing the event which was one of the most productive at a Global BHL meeting.

Thursday, February 13, 2014

The Collector Connection: United States Geological Survey

This is the final post of a joint blog series by the Field Book Project (FBP) and the Biodiversity Heritage Library (BHL), showcasing examples of digital connections between collectors, field book catalog records, and the resulting publications of collecting events.

In 1878 the United States Congress was investigating rivalries between four surveys (Powell, Hayden, King, and Wheeler Surveys) that had been sent west to study the nation’s resources and search for a potential route for a railroad to the west coast. The investigation made it clear to Congress that the current system was not working. So Congress turned to the National Academy of Sciences (NAS) for guidance. NAS approached experts across the country for input, including survey leaders John Wesley Powell and Clarence King. Their subsequent recommendations, sent to Congress, provided the main structure for the legislation that created the United States Geology Survey (USGS).

In 1879, the USGS was established with the mission to provide: “reliable scientific information to describe and understand the Earth; minimize loss of life and property from natural disasters; manage water, biological, energy, and mineral resources; and enhance and protect our quality of life."

William H. Dall, c. 1910.  Smithsonian Institution Archives. RU 000095, Box 6, Folder 42.  SIA2009-4237.
The USGS had a mission, but now they needed the people with the vision to make it happen. King was named director, but left in 1881. Powell became the second director (1881-1894) and was an important force in shaping the new agency.

The USGS began sending staff into the field shortly after its creation. Staff surveyed and collected in national parks as well as local neighborhoods, like the DC-Maryland-Virginia environs. Their field books show a dizzying variety of collecting. The agency’s earliest field staff included individuals who would make important contributions to the fields of geology and paleontology. People like Charles Walcott, known for his discovery of the Burgess Shale, worked for the USGS 1879 – 1907 (eventually becoming its director in 1894), and conducted field work in the Grand Canyon among many other locations in the country. William Healey Dall worked for USGS 1884-1925, conducting research and spending significant time in Alaska for the Agency as well as the US Coast and Geodetic Survey; the work helped establish him as a well-respected expert in the geology of the state.

Charles Walcott's field notes from October 15 - November 3, 1879, Page 19.  Smithsonian Institution Archives. RU 007004, Charles D. Walcott Collection, 1851-1940 and undated; Box 32, Folder 1.  SIA2012-9643.

Other staff may not be so well known, like Lester Ward (1841-1913), but their field books document important routine field work with a specificity of detail that is fascinating. Specimen location information and interviews with individuals who found them sometimes list neighborhoods or street intersections. We encourage you to take a look at and compare the field books and the publications, the field work and the conclusions drawn from them.

Field Books:
Publications:

In November of 2011, the USGS Library joined the BHL consortium. Describing themselves as "one of the world’s largest libraries dedicated to the earth and natural sciences," they have contributed over 15,000 pages of digital content to the BHL collection.

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

Monday, February 10, 2014

Inspiring discovery through free access to biodiversity knowledge...



On March 2013, with support from the National Science Foundation's Advance in Biological Informatics program and in collaboration with our Australian colleagues at Museum Victoria, BHL updated its website architecture to include the possibility of accessing and displaying article and chapter metadata.  


Our APIs and Data Exports were also modified to include this available information.  The BHL book viewer was updated to allow users to view multiple columns of pages on screen at once and more easily navigate to a specific page within a book. Users can also view OCR text alongside page images, and, where the books have been indexed, users can navigate directly to the articles or chapters within using a Table of Contents feature.   The custom PDF creation process was also modified to allow users to select pages for their PDF while in the book-viewer mode and more easily review the PDF before creation. Also, other important biodiversity informatics initiatives like ZooBank and The International Plant Names Index (IPNI), are now linking directly and more closely to BHL journals and pages using BHL’s citation disambiguation service, based on the OpenURL standard.


Now BHL is expanding the data model for its portal to be able to accommodate references to content in other well-known repositories. This is highly beneficial to end users as it allows them to search for articles, alongside books and journals, within a single search interface instead of having to search each of these siloes separately. BHL is strategic about the content providers it chooses to partner with and works with trusted organizations that provide relevant quality materials, technical know-how, resource support, and sustainability of content links. The improved BHL User Interface enables users to search among the 81,000 articles and chapters harvested and indexed from BioStor. So far, most of these articles have been identified from within BHL corpus of books and journals. But now, BHL has included metadata information provided by three well-known and trusted repositories of freely available biodiversity literature: Biblioteca Digital del Real Jardin Botanico (CSIC), Pensoft Publishers and the SciELO Network.



The Real Jardín Botánico Digital Library (RJB) from Madrid is an online bibliographic information service that aims to become the go-to reference for the Iberian Peninsula, Baleares, Macaronesia, north of Africa, Mediterranean region and Latin America and offer the biggest collection possible of classic works, periodic publications and other botanical works (historical, floristical and taxonomical) cryptogams and phanerogams).  RJB's Digital Library's objective is to become a work tool for researchers, environmental technicians, teachers, historians, amateurs, etc; providing also detailed bibliographic records and detailed descriptions of the contents and pagination of publications.  More than 6,000 book references from RJB have been added to BHL since January 2014.

Pensoft is well known in the academic community worldwide as a book and journal publisher, and as one of the pioneers of open access and data publishing. Starting in 1994, Pensoft has become one of the leading academic publishers in the field of natural history with more than 800 books and e-books published so far. The company is actively developing new tools and methods for dissemination of scientific information, including semantic technologies to enrich the article content and to export it to global data aggregators. The flagship open access journal of Pensoft, ZooKeys, is currently recognized as a technology leader in biodiversity publishing. Their latest innovation, namely the Pensoft Writing Tool and the Biodiversity Data Journal, present the first ever workflow to put manuscript authoring, community peer-review, publishing and dissemination within a single online collaborative platform. At the end, it comes to an integrated narrative and data publishing model which ensures that content is harvestable and re-usable by both humans and computers. BHL Users can find now almost 2,500 articles from Pensoft.


The SciELO Network's major objective is to contribute to the progress of academic research by improving the communication of research results in national quality journals. National journals fulfill an important function which is to complement international journals as far the communication of research undertaken nationally is concerned. The specific objective of SciELO is to increase in a sustainable way the visibility, quality, use and impact of the journals it indexes. In addition, it contributes to the development of national capacity and infrastructures for information and scholarly communication. The principal functions undertaken by SciELO have been the indexing of academic journals based on strict quality control measures, the online open access publication of full text on the Web, the measurement of performance with regard to downloads and citations and Web interoperability with indexes, and the products and services used for the indexing of scholarly content.  Users will find references to almost 9,000 biodiversity articles from the first 14 SciELO biodiversity journals harvested so far of a total of 38 available.


Note that, although freely and openly available, an important difference of this type of content from trusted repositories is that the text shown is not being hosted at the BHL's Internet Archive collection, like the rest of the BHL corpus, but rather on their respective external repositories.  This means that, even when BHL still allows discovery and access to the full-text from its Portal, and that BHL will benefit from all new additions and corrections to the content, we are not able to provide the exact same services of taxa name finding and showing the content in our own book viewer... just yet!  But to help clarify any confusion, our User Interface and RSS Feeds clearly indicate whenever you will be leaving our site to open a new window and access the external content from our partners.


Take a look at some of the examples that Pensoft: (biodiversitylibrary.org/part/98901), Real Jardín Botánico (biodiversitylibrary.org/bibliography/74811) and the SciELO Network (biodiversitylibrary.org/part/107970) have provided us with and tell us here, through the feedback form, what you think about this new way to discover and access more biodiversity content through the Biodiversity Heritage Library Portal.


William Ulate
BHL Technical Director

Monday, February 3, 2014

Happy Lunar New Year from BHL and Equus Caballus!

Album of celebrated American and English running horses.
New York: Kinney Bros. [1888?]
biodiversitylibrary.org/page/24788565

From agriculture to transportation to war, Equus caballus has held a prominent and highly respected position in cultures across the world for thousands of years.  With the Lunar New Year celebrations underway for the next several days, we're ushering in the year of the horse with some highlights on horse biodiversity from the literature in BHL!
The new book of the horse.  London: Cassell and Co., 1911.
biodiversitylibrary.org/page/254311803
  • So you've always wanted to learn to ride a horse but weren't sure where to start?  For some turn- of-the-century tips on trotting, walking, and galloping, look no further than the 1881 treatise How to Ride and School a Horse by Edward L. Anderson.  As a bonus, Anderson has also included some tips on horse gymnastics! 
The analysis of the hunting field. London: Methuen, 1904.
biodiversitylibrary.org/page/20389207
  • Which modern horse can't be ridden?  Considered the last truly wild horse, Equus przewalskii Poliakov, 1881, more commonly known as Przewalskii's horse, is the only extant horse to never be tamed.  Nearly extinct by the late twentieth century, it has been reintroduced into the wild in places like China and Mongolia and its status has been updated to endangered.  Populations have seen some increases but threats such as disease, habitat destruction, and climate change remain.  BHL and our partners at EOL work hard to provide open access to information about species, including habitat and behavior, so that informed conservation decisions can be made, especially for those that been threatened or endangered.  Learn more about Przewalskii's horse in BHL:  http://www.biodiversitylibrary.org/name/Equus_przewalskii.

The Evolution of the Horse Family,
as illustrated in the Yale Collections.
American Journal of Science, 1907.
biodiversitylibrary.org/page/40226990
  • How do modern horses differ from their earlier counter-parts?  Many of you may already know that pre-historic horses were generally smaller than modern horses but you may be surprised to learn that one of the key differences was the number of toes.  That's right, toes.  While the modern horse has one-toed hooves, many pre-historic horses had three or more toes as shown in the illustration to the right.  Find out about how these changes may have benefitted horses as they evolved and discover other changes as described in Richard S. Lull's 1907 article The Evolution of the Horse Family, as illustrated in the Yale Collections in the American journal of science.

Horses are documented in over 400 pages of open access literature in BHL, with a significant portion focusing on the modern Equus caballus: http://www.biodiversitylibrary.org/name/Equus%20caballus.
BHL relies on donations from individuals to support scanning of the biodiversity literature held in some of the world's most renowned natural history and botanical libraries.  The examples below highlight the ways your donation can make a meaningful and lasting impact:

$25 - Creates Flickr sets of our images which are popular with educators and artists

$50 - Promotes biodiversity education through social media, such as our blog

$100 - Scans 1,000 pages to be made available for free and open access

$250 - Helps us support marketing interns who circulate biodiversity content worldwide

$500 - Improves existing methodology and helps develop new tools for biodiversity research

Help make the year of the horse a lucky and prosperous year for BHL and our users by making a donation to support our continued growth!  https://donate.sil.si.edu/v/DonateBHL.asp