Global Library of Life: The Biodiversity Heritage Library

A Global Library for Life Martin R. Kalfatovic Smithsonian Institution Libraries 18 March 2008

The cultivation of natural science cannot be efficiently carried on without reference to an extensive library Charles Darwin, et al (1847)‏ Darwin, C. R. et al. 1847. Copy of Memorial to the First Lord of the Treasury [Lord John Russell], respecting the Management of the British Museum. Parliamentary Papers, Accounts and Papers 1847, paper number (268), volume XXXIV.253 (13 April): 1-3. [Complete Works of Charles Darwin Online]

Taxonomic Literature
Over 250 years of systematic description of life
Systema naturae (10 th ed. 1758) by Carl von Linné

Taxonomic Literature
Taxonomic descriptions must be published for the name to be valid
Publications must be available to the public through trusted sources
Libraries have been the traditional place

Taxonomic Literature The cited half-life of publications in taxonomy is longer than in any other scientific discipline * * * The decay rate is longer than in any scientific discipline ~ Macro-economic case for open access Tom Moritz

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 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. February 2008. Launch of EOL species pages and associated BHL literature

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 way
Additional categories of membership under consideration

BHL Focus: Literature

Cost low – 10-19 cents a page
Other projects funded recently – Microsoft and Google
Tractable, well-defined scientific domain
Supports GBIF and other international initiatives – including CBD, ABS, Darwin Declaration

Core literature pre-1923: 100 million pages (?)‏
All pre-1923: 120-150 million pages
All literature: 280-320 million pages
Over 5.4 million books dating back to 1469
800,000 monographs
40,000 journal titles (12,5000 current)‏

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

BHL Tools
Serials Bid List
Allows institutions to “bid” on titles for scanning
Helps avoid duplication of scanning of large serial runs
Allows for partial “bidding” so that other members can fill in runs of titles

BHL Tools
Mongraph De-duping tooll
Separate accounts for each institution
Designed to ingest packlists in excel (.xls) format
Ability to track your institution’s packing list upload activity
If duplicates are found, you’ll be able to see which institution scanned it, and when

BHL Tools
WonderFetch
Allows institutions to pass additional information to the metadata that is not included in a MARC record
Intellectual property
Due diligence
Other identifiers
Enumeration and chronological information (for serial volumes)‏

BHL Tools
OCLA Collections Analysis Tool
Allows for gross analysis of collections of the member libraries to help in selection

So how do we get from this ...

... to this?

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

BHL Scanning Centers
New York City
10 Scribe facility at New York Public Library
Boston
10 Scribe facility at Boston Public Library
Other
1 Scribe, 2 shifts, London
2 Scribes at UIUC

BHL Scanning Centers
Washington, DC
1 Scribe machine at Smithsonian Libraries
10 Scribe facility at Library of Congress with Fedlink (operational Spring 2008)‏

BHL Scanning Centers ... what Robert said!

Scanning Stats
5.5 million plus total pages scanned (IA and non-IA)‏
Going full speed in Boston
Productive smaller operations in Urbana-Champaign and London
Operations ramping up in Washington and New York

But what about ...

BHL Google (the difference between)‏
Bibliographic accuracy for all materials
Ability to re-purpose and reuse all data as needed
Congruence of original printed materials to digital versions

BHL Add-ons
Identifiers added at a variety of levels
Structural markup for re-purposing of data in other systems
Semantic markup for re-purposing of data in other systems
Taxonomic Intelligence

Persistent Identifiers
Stable URL
Handle
DOI
BICI/SICI
ISSN
ISBN
LSIDs
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
California Academy of Sciences publications
And more ...

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

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
Legacy literature a key component of the EOL species pages

Looking Forward
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

Quick ramp-up high early costs – development, mass scanning, etc.
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.
Looking Forward

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

A Global Library for Life 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. Charles Davies Sherborn, Epilogue to Index Animalium , March 1922

Thank You ... for sticking around!

LINKS
Biodiversity Heritage Library http://www.biodiversitylibrary.org/
Biodiversity Heritage Library Blog http://biodiversitylibrary.blogspot.com
Encyclopedia of Life http://www.eol.org/
Smithsonian Institution Libraries http:// www.sil.si.edu /
Universal Biological Indexer and Organizer http://www.ubio.org/
Biologia Centrali-Americana http://www.sil.si.edu/digitalcollections/bca/

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

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Global Library of Life: The Biodiversity Heritage Library

by Martin Kalfatovic on Mar 18, 2008

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Global Library of Life: The Biodiversity Heritage Library — Presentation Transcript