Biodiversity Heritage Library © 2008 Biodiversity Heritage Library Scientific Disciplines From...

Biodiversity Heritage Library

© 2008 Biodiversity Heritage Library www.biodiversitylibrary.org

Scientific DisciplinesFrom Discovery to Delivery

Cathy NortonDeputy Director BHLIAMSLICSeptember 16,2008



This library serves the all of the scientific institutions in Woods Hole

and other scientific groups in the area.

The Library is facing a new dynamic phase



Biodiversity InformaticsEvolving in the Biological Sciences

National Geographic News, 05/21/08 Tuatara

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encyclopedists

Nomencaltor Animalia“Seahorse” Conrad Gesner 1570



encyclopedistsDenis Diderot – 1751Encyclopedie

Precursor to Sematic Web Thinking

• “So great is the power of linkage and order that even the mundane becomes important” DD

• Encyclopedia… the word signifies unity of knowledge



Serine Molecule

BiodiversityHeritage Library

Synthesis CenterField Museum

InformaticsMarine BiologicalLaboratory & MOBOT

Education & OutreachSmithsonian/Harvard

SecretariatSmithsonian



• The Species Sites Group works with contributors and data providers and IP issues

• Biodiversity Informatics Group is responsible for the software development of tools and open access delivery of species information through a single portal

• Education and Outreach Group works to insure widespread awareness of the EOL

• Biodiversity Synthesis Group will facilitate cross disciplinary involvement and will explore integrative topics, including taxonomy, evolution, biogeography, phylogenetics and biodiversity informatics.

• Scanning and Digitization Group led by the Biodiversity Heritage Library, is a consortium of 10 natural history, botanical and research libraries that will scan for the public commons out of copyright and permissioned works.



Encyclopedia of Life

• Major project to create a single Web page for every known species (1.8 million!)

• Total funding will reach at least $50M• EOL needs the literature underpinning in the BHL

project• BHL now key partner in EOL project• Launched on 9th May, 2007

– First 30,000 pages launched at TED Feb 27th, 2008



“The launch of the Encyclopedia of Life will have a profound and creative effect in science… this effort will lay out new directions

for research in Every branch of biology:

– E.O. Wilson





Collaborative Tree of Life distributed semantic

Biodiversity Heritage Library ever evolving TED all information Synthesis Center Oh wow! SpeciesBase ClassificationBank Education and Outreach ANTS index MacArthur Foundation taxonomic intelligence modular software communal ownership user defined AvenueA | Razorfish OBIS MBL free

visualization images WorkBench sounds phylogeny web 2.0 names-based infrastructure Atlas of Living Australia February 2008 Google Marine Biological Laboratory all species Smithsonian FISHBASE Harvard Field Museum Tree of Life E. O. Wilson aggregation / mashup EDIT ScratchPad widgets

MOBOT NHM AMNH NYBotancial Sloan Foundation GBIF llison l NameBank videos National Geographic any classification TDWG/BIS



Biodiversity Heritage LibraryMission:Provide Open Access to Biodiversity Literature

Goals:

Digitize the core published literature on biodiversity and put on the Web

Agree on approaches with the global taxonomic community, rights holders and others





Collaborators:Internet ArchiveInternational Commission on Zoological NomenclatureOpen Content AllianceAmerican Institute of Biological SciencesEuropean Distributed Institute of Taxonomy (EDIT)Global Biodiversity Information Facility (GBIF)BioOneLearned Societies Many more under negotiation



BHL



How to build the BHL enterprise

• Recognition of the importance of all types of material in all formats• Recognition that a single set of rules, a single mechanism, a single

type of discovery tool cannot accomplish everything• Recognition that entities other than libraries can, want to, and will

contribute to the information-finding construct• Recognition that all of us are part of the whole, and that it is an

interdependent relationship, not the relationship of an all-powerful mother ship

• Recognition that the way we have made decisions in the past may no longer serve us well



Boston Scanning Center

Regional Scanning Center

Books are delivered to scanning center where they are processed .

All volumes are on books carts clearly marked with the library’s logo and name. Books are taken off the cart ..scanned… returned to cart.

On the shipping day it is rewrapped and sent back to MBLWHOI Library.



Internet Archive Scribe: Boston



How big is the Biodiversity domain?

•Over 5.4 million books dating back to 1469

•800,000 monographs

•40,000 journal titles (12,5000 current)

•50% pre-1923



Classes of Texts• Public Domain – pre 1923

• Non-profit society journals

• Post 1923 monographs/journals

–Monographs without © renewals

–Commercial journals with permission



Where are we?– 7,046 Titles– 17,945 volumes– 7,431,246 pages– 54 journal or serials titles

permissions obtained– Provisional agreements with

BioOne for rehosting– Working on agreement with

JSTOR



One Year Anniversary MBLWHOI

7354 Books

>3000 Journal volumes

>2.99 Million Pages (standard)

>5280 Foldouts (up to 18” x 24”)

425 Average pages per item

5,346 Miles Traveled

4700 Hours of Staff Time

10¢ Cost per page

$2 Cost per foldout

Statistics as of 9/1/08









Carolus Linnaeus, “father of modern taxonomy”

“Who Knowth not the name

Knowth not the subject”

Linnaeus, 1737,

Critica Botanica n 210.

Royal Science Academy of Sweden, portrait



The challenge for contemporary DIGITAL libraries

Goal:

Use one name to find the content for all names



Names – the only universal metadata for Biology

Names offer a logical way to search for and index content

•Names annotate data objects•All names annotate all data objects

•A compilation of all names ever used is the foundation of a universal index for biology or for a semantic web for biology



LibrariesPublishers

MuseumsFederal Agencies

Who is affected by these problems?



Serious challenges in federated environments

One organism

4 scientific names

4 maps

We want one map



• 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



Taxonomic Intelligence• Lexicon of Scientific Names

• Reconciliation and Disambiguation

• Hierarchical Inclusion

• Integration into Information Retrieval

• Linkage to Other Data Types (e.g., Molecular, Morphological, Phenotype)



uBioRSS Taxonomically Intelligent RSS Feed Aggregator



MBL WHOI Library – Woods Hole authors’ publications



MBL WHOI Library – Woods Hole species publications





What Can the BHL Be?

– One stop shopping for scientific biodiversity texts.– Digital Preservation of the scholarly record in the field

of biodiversity.– A suite of services to facilitate the reuse of the BHL

content especially by the EOL– Embedding of textual content in the emerging

knowledge ecology. Three sets of players – practicing biologists, libraries, publishers.











Questions



AcknowledgmentsNeil SarkarGerald Weissmann

The Gordon and Betty Moore FoundationA.W. Mellon Foundation

Alfred P. Sloan FoundationJohn D. & Catherine T. MacArthur Foundation

Internet Archive

BHL & EOL Teams



www.eol.org

www.biodiversitylibrary.org

www.ubio.org



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