Global Library of Life: The Biodiversity Heritage Library

MARTIN R. KALFATOVIC :: SMITHSONIAN INSTITUTION LIBRARIES :: BOSTON LIBRARY CONSORTIUM ::18 MARCH 2008

A Global Library for Life

Martin R. KalfatovicSmithsonian Institution Libraries18 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]


Over 250 years of systematic description of life

Systema naturae (10th 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



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 accessTom Moritz



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 Timeline


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)

BHL Members


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

GoldenGATEThe 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 ...


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

Funding



Structure of the Encyclopedia of Life

Serine Molecule


Serine Molecule

Synthesis CenterField Museum

BiodiversityHeritageLibrary

SecretariatSmithsonian Education &

OutreachSmithsonian/Harvard

InformaticsMarine 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




• 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

Looking Forward


• 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


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

The Long Now Strategy


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

A Global Library for Life




Thank You ... for sticking around!


Biodiversity Heritage Libraryhttp://www.biodiversitylibrary.org/

Biodiversity Heritage Library Bloghttp://biodiversitylibrary.blogspot.com

Encyclopedia of Lifehttp://www.eol.org/

Smithsonian Institution Librarieshttp://www.sil.si.edu/

Universal Biological Indexer and Organizerhttp://www.ubio.org/

Biologia Centrali-Americana http://www.sil.si.edu/digitalcollections/bca/

LINKS


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

CREDITS