Digitizing Entomology: The Biodiversity Heritage Library @ the Smithsonian

Digitizing Entomology The Biodiversity Heritage Library @ the Smithsonian Martin R. Kalfatovic Smithsonian Institution Libraries 26 November 2007 A Presentation for the Department of Entomology, National Museum of Natural History, Smithsonian Institution

Yet another physical difficulty is the task of assembling the library and indexes which will enable the student to work under proper conditions…. the beginner must now be prepared to spend liberally, or else must establish himself in an institution where a large library exists ; if he work by himself with only a few books, he will have to confine himself to a very narrow specialty indeed. 'The Limitations of Taxonomy' by J.M. Aldrich, Science , April 22, 1927, vol. LXV, no. 1686, p.381

BHL Timeline
2003, Telluride. Encyclopedia of Life meeting
February 2005. London. Library and Laboratory: the Marriage of Research, Data and Taxonomic Literature
May 2005. Washington. Ground work for the Biodiversity Heritage Library
June 2006. Washington. Organizational and Technical meeting
August 2006. New York Botanical Garden. BHL Director’s Meeting.
October 2006. St. Louis/San Francisco. Technical meetings
February 2007. Museum of Comparative Zoology. Organizational meeting
May 2007. Encyclopedia of Life and BHL Portal Launch. Washington DC..

BHL Members
American Museum of Natural History (New York)‏
Field Museum (Chicago)‏
Natural History Museum (London)‏
Smithsonian Institution (Washington)
Missouri Botanical Garden (St. Louis)‏
New York Botanical Garden (New York)‏

Royal Botanic Garden, Kew
Botany Libraries, Harvard University
Ernst Mayr Library of the Museum of Comparative Zoology, Harvard University
Marine Biological Laboratory / Woods Hole Oceanographic Institution
BHL Members

BHL Members
University of Illinois, Urbana-Champaign (contributing member)‏
Scheme for addition of European and Asian partners under consideration
Additional categories of membership under consideration

Structure of the Encyclopedia of Life Serine Molecule

Serine Molecule Synthesis Center Field Museum Biodiversity Heritage Library Secretariat Smithsonian Education & Outreach Smithsonian/Harvard Informatics Marine Biological Laboratory & MOBOT

EOL Species Pages
Built from a variety of new and existing sources
Views available for varying levels of expertise from novice to expert

EOL Species Pages
Legacy literature a key component of the EOL species pages

BHL Focus: Literature

Core literature pre-1923: 400,000 (80 million pages)‏
All pre-1923: 600-750,000 (120-150 million pages)‏
All literature: 1.4-1.6 million (280-320 million pages)‏
Mass. Zoological and Botanical Survey Reports on the fishes, reptiles and birds of Massachusetts , 1839 BHL Focus: Literature

Selection Tools
Combined Serial list for selection of title to scan to avoid duplication of effort
Mongraphic “de-duping” algorithm
OCLC Collection Analysis

1.3 million catalogue records
73% are monographs (remainder are serials at title-level)
63% is English language material
The next most popular language (9%) is German
About 30% of material was published before 1923
BHL Collections

Selection
Marine Biological Laboratory/WHOI
Marine monographs
General Science
Museum of Comparative Zoology
MCZ publications
Herpetology monographs and serials
Ichthyology monographs and serials

Selection
University of Illinois
Fieldiana
Natural history of Illinois
American Museum of Natural History
AMNH publications
Ornithology
Natural History Museum
NHM publications
Major natural history general serials

Selection
Botany Collections
Missouri Botanical Garden, New York Botanical Garden, Harvard Botany Libraries, and Royal Botanic Garden, Kew will cooperatively develop a methodology for botanical publications

Selection
Smithsonian Institution Libraries
Smithsonian publications
Marine mammals
Fishes
Selected special collections materials
Entomology collection

The Internet Archive
501(c)(3) organization
Dedicated to “Universal Access to Human Knowledge”
Founder of the Open Content Alliance
Provides:
Mass scanning
Archival storage of files
Image processing
Technology development

Scribe Scanner
Single Scribe Machine
Custom built by the Internet Archive
Human operated
3,500 page per shift per week

BHL Scanning Centers
Northeast Regional Scanning Center
10 Scribe machines
MBL/WHO (scanning)‏
Harvard
New York Public Library
10 Scribe machines
AMNH
NYBG

University of Illinois
2 Scribe machines
Natural History Museum, London
1 Scribe machine
Missouri Botanical Garden
Non-Scribe operation

Washington, DC
1 Scribe machine at Smithsonian Libraries
Planned 10 Scribe facility in the Washington area (Spring 2008)‏

Scanning Stats
2 million plus total pages scanned
250,000 plus from the Natural History Museum, London
150,000 from the MBL/WHOI library
Fieldiana, 15,000 plus pages

Scanning Stats
Smithsonian Libraries
250,000 pages (non-Scribe scanned, 1996-2007)‏
50,000 Scribe scanned pages (since August 2007)‏
Other libraries (non-Scribe)‏
MOBOT: 780,000
AMNH: 150,000

But what about ...

Difficult (impossible?) to re-purpose much of the material
Quality of images often questionable
“ Frankenbooks”
Sketchy / inaccurate bibliographic data
But what about

Persistent Identifiers
Stable URL
Handle
DOI
BICI/SICI
ISSN
ISBN
http://www.biodiversitylibrary.org

Structural Markup
<article>
<title> A BRIEF CONSIDERATION OF CERTAIN POINTS IN THE MORPHOLOGY OFTHE FAMILY CHALCIDID^E.*. </title>
<author> L. O. HOWARD. </author>
<volume> 1 </volume>
<issue> 2 </issue>
<start_page> 65 </start_page>
<end_page> 86 </end_page>
<start_count_page> 85 </start_count_page>
<end_count_page> 106 </end_count_page>
<start_page_image_file> 3908800908001101smthrich_0085.djvu </start_page_image_file>
<end_page_image_file> 3908800908001101smthrich_0106.djvu </end_page_image_file>
</article>

Semantic Markup
GoldenGATE The intention of the GoldenGATE editor is to build a bridge between NLP components and XML markup of natural language text according to arbitrary XML schemas. It allows the deployment of NLP components to marking up the bodies of literature they were designed for. In this way, it enables transforming the texts into XML content according to an XML schema that was designed to gain maximum benefit from the knowledge provided in them.
Integrated Open Taxonomic Access (INOTAXA)

10.7 million name strings in NameBank
Uses sophisticated algorithm (TaxonGrab) to locate likely name strings in OCR text
Iterative processing of BHL texts will both increase the number of name strings in NameBank and increase the accuracy of name string recognition
Taxonomic Intelligence

BHL & Publishers

Permissions
Seek permissions from copyright holders
Opt in Copyright Model: The BHL will actively work with professional societies and associations to integrate their publications into the BHL in a way that serves the societies’ missions and goals
BHL will digitize learned society backfiles and mount them through the BHL Portal at no cost.
Will provide a set of files to the publishers for reuse as they see fit.

BHL Advantages
Use of the articles will increase as evidenced by citation upsurge
Long-term management of the digital assets is provided by the BHL at no cost
Publishers’ content is embedded in the emerging knowledge ecology that is sweeping biology in this century
Structural markup of backfiles into conformance with NLM DTD (just starting)‏

Successes
Entomological News
Journal of Hymenoptera Research
Herpetological Review
Publications of the San Diego Natural History Museum
University of Kansas natural history publications
And more ...

BHL Portal
Library catalog-like interface to BHL literature
Enhanced structural analysis to provide volume/issue/article page access to the literature
Iterative development based on feedback from user community
Provide access to two key audiences:
Humans
Machines

Page Delivery

Taxonomic Intelligence

Web 2.0 Features
Search
Browse

Discovered Bibliographies

Funding & the Future
Initial grant from the MacArthur and Sloan Foundations (as part of the Encylopedia of Life grant)‏
Additional support from parent institutions
Additional grants being actively pursued by BHL and individual members

Co-evolving bioinformatics resources produce a rich information ecology:
Consortium for the Barcoding of Life (CBOL) with gene sequences deposited in GenBank.
GBIF’s Electronic Catalog of Taxonomic Names
Hebaria and museum specimen databases

Financial Sustainability Strategy
Quick ramp-up high early costs – development, mass scanning, etc. Drive long-term costs down the asymptote toward zero.
Derive some long-term costs from the operating budgets of the member institutions. (examples under consideration: acquisitions budget, staff positions, etc.)‏
Integrate functions/tasks with wider efforts where appropriate, e.g. mass storage.
Clear roles for staff who wear multiple hats. Two full-time grant funded positions currently but >15 staff who make substantive contributions.

The Long Now Strategy
Institutions that are creating the BHL exist to persist through time. That’s an important part of their business. Use them!
The future is uncertain, the technology landscape changes, people pass on. So create consortial structures that are low-overhead, flexible, and can respond quickly

In any well-appointed Natural History Library there should be found every book and every edition of every book dealing in the remotest way with the subjects concerned. One never knows wherein one edition differs from or supplements the other and unless these are on the same table at the same time it is not possible to collate them properly. Charles Davies Sherborn, Epilogue to Index Animalium , March 1922

Thank You

CREDITS
Thanks to:
Chris Freeland, Missouri Botanical Garden
Tom Garnett, The Biodiversity Heritage Library Project
Suzanne C. Pilsk, Smithsonian Institution Libraries
The staff at the Internet Archive
Images from
The Galaxy of Images, Smithsonian Libraries ( www.sil.si.edu/imagegalaxy )‏
Martin R. Kalfatovic
Keri Thompson
Bernard Scaife

Digitizing Entomology: The Biodiversity Heritage Library @ the Smithsonian

by Martin Kalfatovic

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