Special Libraries Associatin

Biodiversity Heritage Library

© 2008 Biodiversity Heritage Library www.biodiversitylibrary.org

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 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



HOW to build this 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 (LC) to a fleet of shuttle craft

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



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



BHL



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?•5,000,000 scanned pages•13,000 volumes•BHL Portal•Sloan, MacArthur, Moore Foundation- funding

•49 full run journals



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



“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



• Information about named groups (taxa) of organisms (taxon-related information)

• Extends back at least 1000 years

• In books, journals, surveys, museum specimens, herbaria….

• In many languages and is distributed

From T.E. Glover, The Fishes of Southwestern Japan, c.1870



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



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



• 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



• 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



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)



uBio

• 10.7 Million+ Name Strings

• Reconciliation Groups

• http://www.ubio.org

• FIND IT – scientific name recognition algorithm

• Training and improving algorithm



uBioRSS Taxonomically Intelligent RSS Feed Aggregator



MBL WHOI Library – Woods Hole authors’ publications



MBL WHOI Library – Woods Hole species publications



Taxonomically intelligent scientific text parsing



• Search• Browse



AcknowledgmentsCatherine NortonPatrick LearyDavid RemsenDiane RielingerDavid PattersonNeil SarkarGerald Weissmann

A.W. Mellon FoundationAlfred P. Sloan Foundation

John D. & Catherine T. MacArthur FoundationInternet Archive

Christopher FreelandTom GarnettMartin KalfatovicGraham HigleyBHL & EOL Teams

Special Libraries Associatin

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