An International Cooperative Digital Library for Taxonomic Literature: The Biodiversity Heritage...

MARTIN R. KALFATOVIC :: SMITHSONIAN INSTITUTION LIBRARIES :: AMERICAN LIBRARY ASSOCIATION :: 30 JUNE 2008

Martin R. KalfatovicSmithsonian Institution Libraries30 June 2008

An International Cooperative Digital

Library for Taxonomic Literature


Biodiversity

What is Biodiversity?

Genetic variability within species

Diversity of species Ecosystems and

landscapes


Biodiversity

Wholesome food Drinkable water Breathable air Stable climate for

Forestry Agriculture Fisheries

Waste decomposition Bioremediation Invasive species Pest control Ecotourism

Pharmaceuticals Genomics Proteomics Bioengineering Biotechnology Molecular design Imitating nature Designer organisms Renewable feedstocks Envirofriendly Manufacturing processes


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



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]


The Taxonomic Impediment

“The taxonomic impediment is a term that describes the gaps of knowledge in our taxonomic system”

- Darwin Declaration, 1998


Taxonomic Impediment

Specimen collections Databases Publications Observations ‘Gray’ literature Index cards Field notebooks



• that there is access to information held in national/regional/global collections

• that electronic data is efficiently captured and provided in usable form

• that existing information held in literature and by current experts is made available electronically

• that stability of scientific names of organisms, used to access this information, is promoted

- Darwin Declaration, 1998

The essential requirements for accessing and utilizing this global information are:


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



Biologia Centrali-Americana

0

1

2

3

4

5

6

7

8

US & Canada Europe Mexico & C.America

SouthAmerica

Biologia Centrali-AmericanaEdited by Frederick Ducane Godman and Osbert SalvinLondon : Pub. for the editors by R. H. Porter, 1879-1915

Chart showing distribution in public collections of the complete 63 volume sets held worldwide.2 complete copies in Central America held at the Smithsonian Tropical Research Institute Library


Digital Divide


Henry Walter BatesThe Naturalist on the River Amazons, 1863

Vishwas Chavan travels a lot. An informatician based at the National Chemical Laboratory in Pune, India, he collects data on what types of animal live where in India to enter into a biodiversity database … Much of the information Chavan seeks is in old, out-of-print tomes … To find them, Chavan has spent years trailing around libraries. He dreams of the day when books such as these are scanned and made available as digital files on the Internet.“Science in the Web Age: The Real Death of Print”

by Andreas von BubnoffNature 438, 550-552 1 December 2005

Digital Divide?


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 Timeline


BHL MembersAmerican 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


Encyclopedia of Life…imagine for a moment that all the diversity of the world were finally revealed and then described, say one page to a species. The description would contain the scientific name, a photograph or drawing, a brief diagnosis, and information of where the species if found. If published in conventional book form … this Great Encyclopedia of Life would occupy 60 meters of library shelf per million species … 100 million species of organisms … would extend through 6 kilometers of shelving …

E.O. Wilson (1992)


OH

O

H2N

OH

H

InformaticsMarine Biological Laboratory

Missouri Botanical Garden

Species Pages & SecretariatSmithsonian

Education and OutreachSmithsonian & Harvard

Synthesis CenterField Museum


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


BHL Focus: Literature


Mass Scanning

Mass scanning is a proven technology

Post processing of generated data proven, but evolving


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

day


BHL Scanning Centers

Northeast Regional Scanning Center 10 Scribe machines MBL/WHOI 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 10 Scribe facility at

Library of Congress with Fedlink (operational May2008)


Scanning Stats28 June 20086,153,568 pages15,343 volumes6,049 titles


Automate Discovery

Automated, scalable structural mark-up

Open to schemas for semantic mark-up

Integration of taxonomic intelligence


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


Build Content


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


Successes

• Entomological News• Journal of Hymenoptera

Research

• Herpetological Review

• Publications of the San Diego Natural History Museum

• California Academy of Sciences publications

• And more ...


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 mark-up of backfiles into conformance with NLM DTD (just starting)


Serve Content

Machine to machine communication

Human interfaceable portal

Standard identifiers (proponent of the “yodi” - yet another digital identifier

???


Encyclopedia of Life


Persistent Identifiers Stable URL Handle DOI BICI/SICI ISSN ISBN LSIDs

http://www.biodiversitylibrary.org


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


Search Browse


Infrastructure: Now / Soon / Later

Now: Missouri Botanical Garden development site

Now: Storage; Internet Archive, Missouri Botanical Garden

Soon: Move to Fedora storage model

Later: Move to a distributed Fedora storage model


• 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

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


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 Internationalhttp://tinyurl.com/3hzkax


Thank You ... now, stick around for ... Suzanne


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

An International Cooperative Digital Library for Taxonomic Literature: The Biodiversity Heritage...

Education

Transcript of An International Cooperative Digital Library for Taxonomic Literature: The Biodiversity Heritage...