Botanicus.org: Applying ermerging technology to historic scientific literature

Botanicus.org: Applying emerging technology to historic scientific literature Chris Freeland Doug Holland Missouri Botanical Garden

Published literature is the foundation on which biological science is based
Botany & systematics are sciences built on accumulated knowledge

Taxonomic Literature
Over 250 years of systematic description of life
Systema naturae (10 th ed. 1758) by Carl von Linné

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

How historic literature is used

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

www.botanicus.org
A freely accessible, Web- based encyclopedia of digitized botanical literature, sponsored by the Missouri Botanical Garden Library
650,000+ pages of text
1,300 volumes, 200 titles
145,000 linked protologues
~10TB of data

Workflow Selection Preparation Post Production Publication Metadata Enhancement Digitization Conservation

Selection

Preparation
Review bibliographic metadata in MOBOT library catalog
Clean up, if needed
Extract MARC
Transform to MARCXML
Parse into Botanicus DB
Review title & determine which scanning device to use
Possible trip through Conservation

Digitization 5 Full time scanners 3 Indus 5002 book scanners 1 Kodak i280 Sheet feed scanner

Post Production – Custom Apps
PageConvert
JPEG2000 (*.jp2) creation
Thumbnail creation
Moves derivative images to server
Updates item records to prepare for publishing
Runs on each scanning workstation
PagePublish
Looks for items ready to publish
Creates or updates page records
Guesses page “types” text or illustration
Triggers OCR generation and PDF creation
Updates titles and item records to “publish ready”
Runs centrally

Post Production – Packaged Apps
PrimeOCR
6 voting engines
Multi-language support
Character coordinates
Outputs ASCII text, other formats
LuraTech PDF Compressor
2GB of TIF page images -> 30MB PDF
PDF/A
OCR (ABBY FineReader)

Enhancement - Paginator

Web 2.0 Features
AJAX interface
JPEG2000 (Image compression with zoom)
Web Services
uBio TaxonFinder and NameBank Taxonomic Intelligence
RSS feeds
Volumes added and news
Mash Ups
Geocoded Subject headings plotted on Google Maps
Tag Clouds

9. Page View

Distributed taxonomic indexing
Public-resource computing application that identifies name-like strings in OCR text
Bundles of text pages sent to volunteer computers for indexing & results reporting
Runs as a screensaver
Open source framework behind SETI@Home

TIF Image from Scanner Converted to text via PrimeOCR Name finding via bTaxonGrab Extract names Submit to TaxonFinder SOAP response SciLINC in action…

Taxonomic Impedectomy Prof. Newton wrote me that he is extremely excited about your digitization project. At the moment he and his graduate botany students in Kenya have access to very few resources . He spends his summer terms at Kew doing his research for the next year's teaching and writing, but he tells me that now, because of what is already on your site, he will not have to carry so much back to Kenya for his research and his students but can download and work with your resources right there. -- excerpt re: Botanicus from email August 2006

The Future
User Accounts
User defined views
MyBookshelf – favoriting & sharing
Wiki-type editing & tagging
Metadata enrichment
OCR correction by users
Bibliographic Intelligence
Improved “click through” citations
Citation finding & linking
Increased geospatial extraction and visualization

Biodiversity Heritage Library
American Museum of Natural History (New York)
Field Museum (Chicago)
Natural History Museum (London)
Smithsonian Institution (Washington)
Missouri Botanical Garden
New York Botanical Garden
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

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)
Biodiversity Heritage Library

www.biodiversitylibrary.org

Botanicus.org brought to you by:
Andrew W. Mellon Foundation
2000-2004
Wm. Keck Foundation
2005-2007
Institute of Museum and Library Services (IMLS)
2006-2008

Botanicus.org
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Botanicus.org: Applying ermerging technology to historic scientific literature

by Chris Freeland on Aug 08, 2008

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