The Biodiversity Heritage Library Mass Digitizing Project: A Grandeur in this View of Digital...

MARTIN R. KALFATOVIC :: SUZANNE C. PILSK :: SMITHSONIAN INSTITUTION LIBRARIES :: LITA FORUM 2007 :: DENVER

BIODIVERSITY HERITAGE LIBRARY

A Grandeur in this View of Digital Libraries

Martin R. KalfatovicSuzanne C. Pilsk

Smithsonian Institution Libraries

LITA Forum6 October 2007

Denver, Colorado



There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved. Charles Darwin, The Origin of Species, 1859



Boutique Scanning Scanning back

cameras All special handling Slow production Expensive



Rare Books Obvious choice “Pretty pictures”



Rare Books Rarely had textual

access (OCR, etc.) Difficult to link to other

materials



Mass Scanning Projects

Google Books MSN Live Internet Archive/Open

Content Alliance



Difficult (impossible?) to repurpose much of the material

Quality of images often questionable

“Frankenbooks” Sketchy / inaccurate

bibliographic data



Content is more re-purposable than Google

Content not fully open Nice search interface Still, no context!



Open Access Hodge-podge of collections Interface hard to use! Still, no, or very little context



United States Exploring Expedition

Biologia Centrali-Americana



Biologia Centrali-Americana Large scale content and

repurposing text Innotaxa



Our Man Sherborn – the Squire Cataloger at heart Slowly went through every

relevant text looking for names Created an index that was

useful as soon as he started Index AND Bibliography of

relevant texts from 1758 through 1850



• Re-keying of data

• Parsing data

• Using tools to harvest out data

• Manually matching data

• Wealth of information locked on the page is being liberated!



Current Uses Look up individual species Batch whole data sets for

comparisons Future Possibilities

Updated species information Accurate images of species Geographic distributions Other databases can link (such as

uBio) Future prioritizing of scans



Demonstration I: Index Animalium and Nomenclature Zoologicus http://www.sil.si.edu/digitalcollections/indexanimalium/http://uio.mbl.edu/NomenclatorZoologicus/



Nomina si nescis, perit et cognitio rerum

Who knoweth not the name, knoweth not the subject

~ Linnaeus, 1737, Critica Botanica n. 210



Over 250 years of systematic description of life

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



Binomial Nomenclature Genus name and

Species epithet or descriptor

Latin or Latin-ized Bill Gates' Flower Fly Eristalis gatesi

Thompson



St. Louis Code of International Code of Botanical Nomenclature

International Code of Zoological Nomenclature

International Code of Phylogenetic Nomenclature



Index Animalium’s Citation:

albimanus Delphinus, T. R. Peale in Wilkes, Expl. Exped. VIII. 1848, 33

On page 33, of volume 8 of Charles Wilke’s 1848 publication:Narrative of the United State Exploring Expedition the Delphinus albmimanus was first named by T.R. Peale.



Agatea violarisType specimen from the U.S. National Herbarium (Smithsonian Institution) collected by the United States Exploring Expedition, 1838-1842



- Specimen- Plate or other visual image- Taxonomic description



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 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



Specimen collections

Databases

Publications

Observations

‘Gray’ literature

Index cards

Field notebooks



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



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



What is Biodiversity? Ecosystems and

landscapes Diversity of species Genetic variability within

species



• 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


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

May 2007. Encylopedia of Life Launch. Washington DC.

September 2007. Missouri Botanical Garden. Technical and Organizational Meeting. St. Louis, Missouri.



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 Mayr Library of the

Museum of Comparative Zoology, Harvard University

Marine Biological Laboratory / Woods Hole Oceanographic Institution



• 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)



Most literature is in the developed world the Northern

Hemisphere

Most Biodiversity is in developing world the Southern

Hemisphere



Most literature is in large libraries

formed in the 19th century



Who has what?

What should we scan and when?

Monographs vs Serials

Series treated as separates

Can it be found and used once scanned?



Initial Metadata Analysis: We have 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.



Scalable Mass Scanning Contracts Firewalls Bathrooms Security Loading docks Trucks



Mass Scanning Workflow Pick lists Packing lists Serials management Monographic management Stickers for books



Demonstration II: Workflow Tools



Stable URL Handle DOI BICI/SICI ISSN ISBN

http://www.biodiversitylibrary.org



Biologia Centrali-Americana :zoology, botany and archaeology

Mammalia Aves v. 1 … Aves v. 4 Reptilia and Batrachia

Biologia Centrali-Americana : Aves v. 1 Introduction -- Subclass Aves Carinate. Order

Passeres. v. 2 Subclass Aves Carinate. Order[s]: Passeres

(contd.), Macrochires, Pici, Coccyges, Psitta

Is itOr



Zea mays L.

Sp. Pl. 2: 971-972. 1753.

Title: Species PlantarumTL2: 4.769Tropicos Pub_id: 1071IPNI Pub_id:1071-2

Volume: 2Start Page: 971End Page: 972Year Published: 1753

http://hdl.handle.net/1234567/9876

http://www.biodiversitylibrary.org/page/358992



Page turning, multiple views, translations PDF “Grab-n-Go”

OCR TextStellaria ongipes ? Goldie. Cornwallis Island.Silene acaWlis, L. Woman Islands.Sawfraga oppositifolia, L. Kakkidlarn, Greenland; Cornwallis Island.Sa4mfraga cerua, De Cand. Ukaari; Cornwallis Island.Sairaga csepitosa, L. Wolstenholme, Greenland; Cornwallis Island.Saxfraga rimdaris, De Cand. Whale Fish Island.Sad~ raga nivalis, L. Cornwallis Island.Ptentilla emarginata? Pursh. Wolstenholme.Dipena Lapponica, L. Whale Fish Island.Pyrola rotndifolia, L. Whale Fish Island.Casiope tetragona, Don. Ichauti.Vaccinium uliginosum, L.Loiseleuria procumbens, L. Whale Fish Island.



<genus>Polygonum</genus>

<species>viviparm</species>,

<author>L.</author>

<locality>Bushnan Island.</locality>

Created via automated or

semi-automated means.

Machine-readable literature



10.3 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



Demonstration III: Taxonomic Intelligencehttp://www.ubio.org



Search Browse



Demonstration IV: BHL Portal http://www.biodiversitylibrary.org



Funding from the MacArthur and Sloan Foundations

Part of the larger Encyclopedia of Life project



Structure of the Encyclopedia of Life

Serine Molecule



Serine Molecule

Synthesis CenterField Museum

BiodiversityHeritageLibrary

SecretariatSmithsonian Education &

OutreachSmithsonian/Harvard

InformaticsMarine Biological

Laboratory & MOBOT



Let us … rejoice in the fact, that we have realised what no other kingdom can boast of, and that such vast and harmoniously related accumulation of knowledge is gathered together around a library

Charles Darwin, et al, 1858



Thanks to: Chris Freeland, Missouri Botanical Garden Neil Thomson, Natural History Museum, London David Remsen, Global Biodiversity Information Facility Neil Sarkar, Marine Biological Laboratory/Woods Hole

Oceanographic Institution Anna Weitzman, National Museum of Natural History Chris Lyal, Natural History Museum, London The staff at the Internet Archive

Images from The Galaxy of Images, Smithsonian Libraries (

www.sil.si.edu/imagegalaxy) NASA, Visible Earth Project Martin R. Kalfatovic

Diane Rielinger



Biodiversity Heritage Library http://www.biodiversitylibrary.org/ Encyclopedia of Life http://www.eol.org/ Smithsonian Institution Libraries http://www.sil.si.edu/ Universal Biological Indexer and Organizer http://www.ubio.org/ Sherborn’s Index Animalium http://

www.sil.si.edu/digitalcollections/indexanimalium/ Neave’s Nomenclator Zoologicus http://

www.ubio.org/NomenclatorZoologicus/ United States Exploring Expedition http://

www.sil.si.edu/DigitalCollections/usexex/index.htm Biologia Centrali-Americana

http://www.sil.si.edu/digitalcollections/bca/ Botanicus http://www.botanicus.org/

The Biodiversity Heritage Library Mass Digitizing Project: A Grandeur in this View of Digital...

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