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MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Biodiversity HeritageLibrary Project
“Underway”Taxonomic Intelligence for LARGE Scale
Digitization Projects33rd IAMSLIC Conference
Sarasota, FL
Cathy NortonMBLWHOI Library Director
Oct. 7-11, 2007
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
This library serves the MBL, WHOI, USGS, NMFS, SEA, WHRC,
and other scientific groups in the area.
Facing a new dynamic phase
NMFS - 1871
MBL - 1888
WHOI - 1930
USGS - 1960
SEA - 1971
WHRC - 1985
Woods Hole Scientific Community
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
• Biodiversity Heritage Libraries • Open Content Alliance, Principles • Internet Archive Partner• Northeast Regional Digitizing Center
@Boston Public Library• Taxonomic Intelligence- modernizing the literature
TOPICS
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Vision
Build a Digital Open Access Library for Biodiversity Literature
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Meetings in Colorado,2005
London, 2005 laboratories and libraries
Washington BHL 2006
Simultaneous Meetings in Woods Hole for BHL& EOL 2006
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Members
• American Museum of Natural History• Botany Library- Harvard• British Natural History Museum, UK• Field Museum• MBLWHOI Library• Missouri Botanical Gardens• Museum of Comparative Zoology-Harvard• New York Botanical Gardens• Royal Botanical Gardens @ Kew ,UK• Smithsonian Museum of Natural History
– University of Illinois, contributing member
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
• Legacy Taxonomic Literature available in museums has limited access
• Much of it is rare
• Systematic literature depends on the historic literature
• The cited half-life of natural history is longer than that of any other scientific domain
• 90% of Biodiversity Information is in these libraries
• 90% of Biodiversity is in 3rd world countries like Africa and South America
Why BHL now ?
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
The Open Content Alliance (OCA) represents the collaborative efforts of a group of cultural, technology, nonprofit, and governmental organizations from around the world that will help build a permanent archive of multilingual digitized text and multimedia content.
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Principles of OCA
• The OCA will encourage the greatest possible degree of access to and reuse of collections in the archive, while respecting the rights of content owners and contributors.
INTERNET ARCHIVE• Contributors will determine the terms and conditions under which their collections
are distributed and how attribution should be made.
• IA need not be obligated to accept all content that is offered to it and may give preference to that which can be made widely accessible.
• • IA will offer collection and item-level metadata of its hosted collections in a variety
of formats.
• IA welcomes efforts to create and offer tools (including finding aids, catalogs, and indexes) that will enhance the usability of the materials in the archive.
• Copies of IA collections will reside in multiple archives internationally to ensure their long-term preservation and accessibility to all.
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Name:
BioDiversity Heritage Library
Wiki- for all involved
Web Presence! Where to begin?
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
In the end… simplicity…• http://bhl.si.edu/
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
• BHL invited to be a part of the EOL project.
• EOL - build one web page for each known species… 1.8 million!
• Alfred P. Sloan and Macarthur Foundations
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
QuickTime™ and a decompressor
are needed to see this picture.
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Northeast Digitization Center• Boston Public Library
– Space infrastructure
• 10 Scanning Stations• .10 ¢per page• 50 Books per day• Journals- metadata,foldouts• Transportation
– ILL deliverymoving company15 rolling carts per trip
Photo by lesveilleus 9/20/07
Cathy Norton, Bernie Margolis, Brewster Kale
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Economies of Scale
• North East Regional Digitization Center
• Agreements made with the Boston Public Library to Include the Boston Library Consortium and NE BHL members.
• Smithsonian and Library of Congress
• Field Museum of Ill
• BNH UK and Kew UK*Bernie Margolis- Boston Public Library
Judy Warnement - Harvard Botany Library, Brewster Kale-Internet Archive
Cathy Norton-MBLWHOI Library
Doran Weber- Alfred P. Sloan Foundation
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
10 scribes
BPL
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Biology Digitization Projects Problems, Dilemmas,Puzzles,Difficulties
• Copyright - Pre 1923, 1923-1964, orphan works, out-of-print
– Stanford University Copyright Renewal Database
• Permissions
• Collaboration with publisher, societies, institutions, etc.
• Duplicates, journals 85,000 - 14,000 BID LIST
• Monographs, collection analysis-- Ref Works
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Name Changes over Time
Taxonomic Intelligence
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
“All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has been learned in the past and what we today add to the body of knowledge.”
~ Grimaldi & Engel, 2005, Evolution of the Insects
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
The challenge for contemporary DIGITAL libraries
Goal:
Use one name to find the content for all names
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Names are even misspelled, such as Loligo pealei
Loligo pealeiiLoligo pealiiLoligo pealei
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Peranema – the fern
One name can refer to more than one organism
Peranema – the euglenid
Yet, despite this, taxonomists have used names and hierarchies to manage
information about organisms very effectively for 250 years
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
LibrariesPublishers
MuseumsFederal Agencies
Who is affected by these problems?
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Serious challenges in federated environments
One organism
4 scientific names
4 maps
We want one map
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Reconciliation – linking alternative names for the same organism
A query initiated with any name, can be expanded to all names and will unify data associated with each
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
• All names & all Classifications ClassificationBank • Alternative names reconciled
• Similar names disambiguated
• Exploit hierarchies to browse and search, build a comprehensive classification
• Improve performance with federated systems
• Read documents, web sites, databases and taxonomically indexing the content
• Create a unified portal to information about organisms on the internet
Taxonomic intelligence is the inclusion of taxonomic practices, skills and knowledge within informatics services to manage information about organisms
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
• There are many resources out there, but no single comprehensive resource for species information
• Rather than building another big database, we can create a new way to link existing information using an aggregation portal
• This places little or no burden on data providers
• Protecting ownership and diversity of initiatives
Taxonomically intelligent aggregation technology builds portals to distribute information about
organisms
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Alternative names
Vernacular names
Expert view
More or less specific
Suggestions & corrections
Indexing power from NameBank
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Results from an array of resources
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
• data from various sources may be merged
• red dots on the maplink back to the website thatprovided the geographical co-ordinates
Specimen distribution data from remote sources
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
FindIT - uBio’s Scientific Name Recognition Algorithm
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Training and Improving the Algorithm
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
uBioRSS Taxonomically Intelligent RSS Feed Aggregator
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
uBioRSS Taxonomically Intelligent RSS Feed Aggregator
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI Library – Woods Hole authors’ publications
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
MBL WHOI Library – Woods Hole species publications
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Taxonomically intelligent scientific text parsing
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
• Documents go to Internet Archive for OCR and storage
• The documents are added to the BHL collection
• uBio checks the BHL collection for new documents
• The documents are scanned for names
• TaxonFinder adds new strings to Namebank
• Document markup with anchors
• TaxonFinder adds all namebankIDs to Taxonomic Index
• This index is called upon by various applications...
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Biological Data Revolution
Biomedical Knowledge
Biodiversity Knowledge
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Scientific Names
No Complete List of Scientific Names
Published Variants
Escherichia coli
112,133 741,872
49,382
Objective Synonyms
Bacterium coliBacillus coli
Mis-spellings
Escheria coli
*
*Scientific Names ≠ Species
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Taxonomic Knowledge
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
BHLVision Information coming from Everywhere
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
What role will librariesplay once the scanning is done?
Will you be negotiators like you are now with serials?
Public domain publications restricted FOREVER by contract…. or open?
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Road map• US libraries -- 12 billion per year ( OCLC)
• Acquisitions--- 3-4 billion per year• 1% - could scan 1 million BKS/vols per year• Librarians will create informatics tools that will
enhance indexing and organizing for not only their users but world wide
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
Acknowledgments
A.W. Mellon FoundationAlfred P Sloan Foundation
Macarthur Foundation
Martin KalfatovicTom GarnetGraham HigleyConnie Rinaldo
Neil SarkarDavid RemsenDavid PattersonDiane RielingerLesveilleux.com
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
URLSwww.biodiversitylibrary.org
www.eol.org
www.collections.stanford.edu/copyrightrenewal
www.ubio.org
The Public Domain: How to Find & Use Copyright-Free Writingsk Music, Art & More by Attorney Stephen Fishman
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
MBL WHOI LibraryMarine Biological Laboratory
Woods Hole Oceanographic Institution
© 2007 MBLWHOI Library www.mblwhoilibrary.org
BHL Bid List for Serialshttp://obsidian.nhm.ac.uk/test/library/bhlseriallist/
Taxa Toy