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

An International Cooperative Digital Library for Taxonomic Literature Martin R. Kalfatovic Smithsonian Institution Libraries 30 June 2008

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

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

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

The Taxonomic Impediment

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 The Taxonomic Impediment

Biologia Centrali-Americana Biologia Centrali-Americana Edited by Frederick Ducane Godman and Osbert Salvin London : 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 Bates The 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 Bubnoff Nature 438, 550-552 1 December 2005 Digital Divide?

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

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 H 2 N OH H Informatics Marine Biological Laboratory Missouri Botanical Garden Species Pages & Secretariat Smithsonian Education and Outreach Smithsonian & Harvard Synthesis Center Field Museum

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

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 Stats 28 June 2008

6,153,568 pages

15,343 volumes

6,049 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

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

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

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

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