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

The Biodiversity Heritage Library Mass Digitizing Project: A Grandeur in this View of Digital Libraries - Presentation Transcript

A Grandeur in this View of Digital Libraries

Martin R. Kalfatovic

Suzanne C. Pilsk

Smithsonian Institution Libraries

LITA Forum

6 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 (10 th 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 violaris Type 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

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

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 19 th 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 it Or

Zea mays L.

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

Title: Species Plantarum

TL2: 4.769

Tropicos Pub_id: 1071

IPNI Pub_id:1071-2

Volume: 2

Start Page: 971

End Page: 972

Year Published: 1753

http:// hdl.handle.net/1234567/9876 http:// www.biodiversitylibrary.org/page/358992

Page turning, multiple views, translations

PDF “Grab-n-Go”

OCR Text Stellaria 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 Intelligence

http://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 Center Field Museum Biodiversity Heritage Library Secretariat Smithsonian Education & Outreach Smithsonian/Harvard Informatics Marine 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