An International Cooperative Digital Library for Taxonomic Literature Martin R. Kalfatovic Smithsonian Institution Libraries 6 June 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 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 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

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

Over 250 years of systematic description of life

Systema naturae (10 th ed. 1758) by Carl von Linné

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

University of Illinois, Urbana-Champaign (contributing member)‏

Scheme for addition of European and Asian partners underway

Additional categories of membership under consideration

BHL Focus: Literature

BHL Focus: Literature

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

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 day

Single Scribe Machine

Custom built by the Internet Archive

Human operated

3,500 page per shift per day

BHL Scanning Centers Northeast Regional Scanning Center 10 Scribe machines MBL/WHOI Harvard New York Public Library 10 Scribe machines AMNH NYBG

Northeast Regional Scanning Center

10 Scribe machines

MBL/WHOI

Harvard

New York Public Library

10 Scribe machines

AMNH

NYBG

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

University of Illinois

2 Scribe machines

Natural History Museum, London

1 Scribe machine

Missouri Botanical Garden

Non-Scribe operation

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

Washington, DC

1 Scribe machine at Smithsonian Libraries

10 Scribe facility at Library of Congress with Fedlink (operational Spring 2008)‏

Scanning Stats: Now 5.5 million plus total pages scanned (and growing daily)‏ <90,000 Fieldiana (via UIUC)‏ >100,000 pages each Harvard, New York Botanical Garden, 225,000+ pages from the American Museum of Natural History 400,000+ from Smithsonian Libraries 500,000+ from the Natural History Museum, London 800,000 Missouri Botanical Garden Library 1,000,000+ from the MBL/WHOI library

5.5 million plus total pages scanned (and growing daily)‏

<90,000 Fieldiana (via UIUC)‏

>100,000 pages each Harvard, New York Botanical Garden,

225,000+ pages from the American Museum of Natural History

400,000+ from Smithsonian Libraries

500,000+ from the Natural History Museum, London

800,000 Missouri Botanical Garden Library

1,000,000+ from the MBL/WHOI library

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

Bibliographic accuracy for all materials

Ability to re-purpose and reuse all data as needed

Congruence of original printed materials to digital versions

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

Stable URL

Handle

DOI

BICI/SICI

ISSN

ISBN

LSIDs

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>

<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)

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

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

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

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)‏

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 ...

Entomological News

Journal of Hymenoptera Research

Herpetological Review

Publications of the San Diego Natural History Museum

California Academy of Sciences 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

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

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

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

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 Herbaria and museum specimen databases

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

Herbaria 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

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

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

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

Midrange estimate: 25% of 5 million species = 1.3 million species, or roughly 1 every 20 minutes Low estimate: 15% of 4 million species = 0.6 million species, or roughly 1 every 44 minutes. High estimate: 50% of 6 million species = 3 million species, or roughly 1 every 9 minutes Conservation International http://tinyurl.com/3hzkax

Midrange estimate: 25% of 5 million species = 1.3 million species, or roughly 1 every 20 minutes

Low estimate: 15% of 4 million species = 0.6 million species, or roughly 1 every 44 minutes.

High estimate: 50% of 6 million species = 3 million species, or roughly 1 every 9 minutes

Conservation International http://tinyurl.com/3hzkax

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/

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

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