biodiversity heritage library: cornerstone of the encyclopedia of life

Martin R. KalfatovicSmithsonian Institution Libraries

BHL @ Smithsonian Libraries @ ALA25 June 2007

The BiodiversityHeritage Library


A Cornerstone of the Encyclopedia of Life



Biodiversity Heritage Library



Structure of the Encyclopedia of Life



OH

O

H2N

OHH

Serine Molecule



Education &Outreach

Smithsonian/Harvard

InformaticsMarine Biological

Laboratory

SecretariatSmithsonian

Synthesis CenterField Museum

BiodiversityHeritageLibrary



Biodiversity Heritage Library• 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



Biodiversity Heritage Library• 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 Meyer Library of the Museum of

Comparative Zoology, Harvard University• Marine Biological Laboratory / Woods

Hole Oceanographic Institution

James Dwight DanaZoophytes. Atlas, 1849



Taxonomic Literature• Over 250 years of

systematic description of life

• 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– Tom Moritz



Literature Repatriation

0

1

2

3

4

5

6

7

8

US & Canada Europe Mexico & C.America

SouthAmerica

Biologia Centrali-Americana. Edited by Frederick Ducane Godman and Osbert Salvin. London : Pub. for the editors by R. H. Porter, 1879-1915



Digital Divide?



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?

Henry Walter BatesThe Naturalist on the River Amazons, 1863



Narrowing the Divide



• Core literature pre-1923: 400,000 (80 million pages)

• All pre-1923: 600-750,000 (120-150 million pages)

• All literature: 1.4-1.6 million (280-320 million pages)


Mass. Zoological and Botanical SurveyReports on the fishes, reptiles and birds of Massachusetts, 1839



Changing Priorities

• Open Access for scientific literature

• Encourage re-use and re-purposing of the data in multiple and diverse systems

• Work with non-commercial publishers to provide access



Changing Priorities

• BHL has had discussions with various society publishers as well as:– BioOne– JSTOR

T.H. Huxleyby Leslie Ward (“Spy”)



Digital Book Creation

• Automated structure detection – vital for serials

• Taxonomic Intelligence• Digital Identifiers• Scalable mass scanning

(outside of the Google environment)

Richard Owenby Leslie Ward (“Spy”)



BHL Structural MetadataFirst Ingest

Internet Archive

39088834745632

39088834645632

39088834545632

39088834445632

39088834345632

Sub-elementBarcodeBib #



BHL Structural MetadataSub-Element Map

Internet Archive

539088834345632

439088834345632

339088834345632

239088834345632

139088834345632




BHL Structural Metadata

139088834345632


Page Structure Map

Internet Archive

0005

0004

0003

0002

0001

Image Number

XML structure map that delineates the relationships of the images created automatically



Taxonomic Intelligence



Taxonomic Intelligence• 9.4 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

Georges Louis Leclerc, comte de BuffonHistoire naturelle : générale et particulière (Oiseaux), 1799-1808



Digital Identifiers

• Digital Object Identifiers (DOI)

• Handles• Life Science Identifiers

(LSID)• URIs• Etc.

Telespiza palmeriAvifauna of Laysan, 1893-1900



Digital Identifiers• Factors:

– Cost per identifier– Community

acceptance– Scalability

• BHL is working with TDWG and others to come up with the best scheme(s)

Moho bishopiAviafauna of Laysan, 1893-1900



Scalable Mass Scanning



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



Internet Archive Scribe Scanner

• Single Scribe Machine– Human operated– 200 volumes per

shift per week– ~ 70,000 pages from

a single machine per week

– Cost: $100,000 / year



Internet Archive Scribe: Boston• Cooperative facility

with the Boston Library Consortium (19 New England Libraries)

• BHL Members MBL/WHOI and Harvard Libraries will use the facility

• Status: In production



Internet Archive Scribe: Boston



Internet Archive Scribe: London

• Single Scribe in place

• Projected 5 unit pod to be located at The Natural History Museum




Internet Archive Scribe: London



Internet Archive Scribe: Washington

• Single unit arrived May 5• Funded by Smithsonian

Libraries• Projected 5 unit BHL pod in

National Museum of Natural History

• Projected 10-15 unit pod shared by Smithsonian/BHL and regional Washington libraries



Internet Archive Scribe: Washington



Internet Archive Scribe:New York

• Current BHL plans focus on sharing a 10 unit pod located at the New York Public Library

• American Museum of Natural History and New York Botanical Garden will use this facility

• Status: in planningCarl von Linné (1707 - 1778)



Internet Archive Scribe: Illinois• Two machines funded

by State of Illinois• UIUC scanning

Fieldiana (all series)• Arrangement

coordinated by Michael Godow, Bryan Heidorn (UIUC/GSLIS), Betsy Kruger (UIUC/Library)




Internet Archive Scribe: Illinois



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



www.biodiversitylibrary.org



BHL Literature Online

1,291,485 pages657,310 pages via BHL Portal

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

biodiversity heritage library: cornerstone of the encyclopedia of life

Technology

taxonomic literature

digital divide

digital files

digital identifiers

priorities bhl

biodiversity database

scientific literature

bhl directors meeting