The Encyclopedia of Life, BioDiversity Heritage Library, Biodiversity Informatics MBLWHOI Library Cathy Norton Deputy Director, BHL Massachusetts Library Association May 7, 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

“ 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

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

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 9 th May, 2007 First 30,000 pages launched at TED Feb 27th, 2008

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 9 th May, 2007

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

Serine Molecule Biodiversity Heritage Library Synthesis Center Field Museum Informatics Marine Biological Laboratory & MOBOT Education & Outreach Smithsonian/Harvard Secretariat Smithsonian

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

Digitize the core published literature on biodiversity and put on the Web Agree on approaches with the global taxonomic community, rights holders and others Mission: 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

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% pre1923

Over 5.4 million books dating back to 1469

800,000 monographs

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

50% pre1923

Why now? Cost low – 10-19 cents a page Other projects funded recently – BL/Microsoft /Google big ten Tractable, well-defined scientific domain Taxonomic information has exceptionally longevity Supports GBIF and other international initiatives – including CBD, ABS, Darwin Declaration

Cost low – 10-19 cents a page

Other projects funded recently – BL/Microsoft /Google big ten

Tractable, well-defined scientific domain

Taxonomic information has exceptionally longevity

Supports GBIF and other international initiatives – including CBD, ABS, Darwin Declaration

Taxonomists and other scientists will have access to biodiversity literature - globally Will provide the developing world with access to the historical literature Scientists working in many biological domains – and other areas like meteorology, geology, ecology, genomics, etc – will get access Advance objectives of the Convention on Biological Diversity Benefits

Taxonomists and other scientists will have access to biodiversity literature - globally

Will provide the developing world with access to the historical literature

Scientists working in many biological domains – and other areas like meteorology, geology, ecology, genomics, etc – will get access

Advance objectives of the Convention on Biological Diversity

Less space needed for Library collections In Lillie – space freed for other uses % material can be stored off-site in ‘dark storage. FTP Our scientists will get access at their desk or in the field Library focus will shift to informatics Virtual web library will increase public access Library staff will change – Benefits to the MBLWHOI Library

Less space needed for Library collections In Lillie – space freed for other uses

% material can be stored off-site in ‘dark storage. FTP

Our scientists will get access at their desk or in the field

Library focus will shift to informatics

Virtual web library will increase public access

Library staff will change –

Key partner of Encyclopedia of Life Working Groups have agreed technical plan , metadata standards and image standards Internet Archive to be technical partner – scanning and hosting ‘ Scribe’ scanners now installed in NHM NYC and in Boston 4.1 million pages already available Where are we now?

Key partner of Encyclopedia of Life

Working Groups have agreed technical plan , metadata standards and image standards

Internet Archive to be technical partner – scanning and hosting

‘ Scribe’ scanners now installed in NHM NYC and in Boston

4.1 million pages already available

Classes of texts Public Domain – pre-1923 Non-profit society journals Post-1923 monographs some with copyright renewals some without copyright renewals Commercial journals

Classes of texts

Public Domain – pre-1923

Non-profit society journals

Post-1923 monographs

some with copyright renewals

some without copyright renewals

Commercial journals

BHL Seeks Permissions BHL will digitize learned society backfiles and mount them through the BHL Portal at no cost. Will provide a set of files to the learned society for reuse as they see fit. Will index the issues using Taxonomic Intelligence increasing their usability.

BHL Seeks Permissions

BHL will digitize learned society backfiles and mount them through the BHL Portal at no cost.

Will provide a set of files to the learned society for reuse as they see fit.

Will index the issues using Taxonomic Intelligence increasing their usability.

Benefits Use of the articles will increase as evidenced by citation upsurge. Long-term management of the digital assets is provided by the BHL at no cost so it’s contributors Content will be integrated into EOL project through TI nomenclatural linking.

Benefits

Use of the articles will increase as evidenced by citation upsurge.

Long-term management of the digital assets is provided by the BHL at no cost so it’s contributors

Content will be integrated into EOL project through TI nomenclatural linking.

Levinus Vincent Elenchus tabularum, pinacothecarum, 1719 The cited half-life of publications in Taxonomy is longer than in any other Scientific discipline. The decay rate is longer than in most scientific disciplines. Maco-economic case for open access Tom Moritz Current taxonomic literature often relies on texts and specimens> 100 years old.

The cited half-life of publications in

Taxonomy is longer than in any other

Scientific discipline.

The decay rate is longer than in most

scientific disciplines.

Maco-economic case for open access

Tom Moritz

Current taxonomic literature often relies

on texts and specimens> 100 years old.

The Long NOW Strategy Georges Louis Leclerc, comte de Buffon Histoire naturelle : générale et particulière (Oiseaux) , 1799-1808 Convention on Biological Diversity: Article 17 Institutions that are creating the BHL exist to persist through time. The future is uncertain, the technology landscape changes, people pass on. So create consortial structures that are low-overhead, flexible, and can respond quickly. Interoperabilty is the key.. Repository islands will sink

Institutions that are creating the BHL exist to persist through time.

The future is uncertain, the technology landscape changes, people pass on. So create consortial structures that are low-overhead, flexible, and can respond quickly.

Interoperabilty is the key.. Repository islands will sink

Biologia Centrali-American Physical Distribution… Now… you can Parse Date, harvest out data, Wealth of informaiton locked on the pages are now liberated!

Henry Walter Bates The Naturalist on the River Amazons , 1863 Most literature is in the developed world the Northern Hemisphere Most Biodiverstiy is in the developing world the Southern Hemisphere

Progne subis- Purple Martin Illustrations of the nest and eggs of birds of Ohio , 1879-1886 Library and Laboratory: the Marriage of Research, Data and Taxonomic Literature London, February 2005 Eighty participants from 22 countries gathered to discuss the status and future of access to the taxonomic literature and to propose an agenda for actions that would improve the research environment for taxonomy. The participants were taxonomists; librarians; publishers; representatives of learned and professional societies, private foundations and government agencies; and specialists in information and communications technology. Scalable Mass Scanning Contracts Firewalls Security Loading Docks Trucks 180 mile round trip!

Internet Archive Scribe: Boston

Ernest Ingersoll Hand-book to the National Museum … Smithsonian Institution , 1886 Mass Scanning Workflow Bid Lists Pick Lists Packing Lists Serials Management Monographic Management Stickers for Media and carts Rare Books-vaults

Jacob Christian Schäffer Elementa entomologica . . . 1766. BHL Portal http://www.biodiversitylibrary.org Serve image and test files: create volume, Part, piece, metadata; ingest page level Metadata at scanning level; apply Globally Unique Identifiers (GUIDs) for linking to Other taxonomic services.

Biodiversity Heritage Library

Biodiverstiy Informatics

“ 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

Who knowth not the name, knoweth not the subject Linnaeus, 1737, Critica Botanica n 210 .

Information about named groups (taxa) of organisms (taxon-related information) Extends back at least 1000 years Books, journals, surveys Museum specimens, herbaria In many languages and is distributed From T.E. Glover, The Fishes of Southwestern Japan, c.1870

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

Extends back at least 1000 years

Books, journals, surveys

Museum specimens, herbaria

In many languages and is distributed

The challenge for contemporary DIGITAL libraries Goal: Use one name to find the content for all names related to “that” species.

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

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

Who is affected by these problems? Libraries Publishers Museums Federal Agencies

Serious challenges in federated environments One organism 4 scientific names 4 maps We want one map

Reuse, don’t rebuild

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

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

data from various sources may be merged red dots on the map link back to the website that provided the geographical co-ordinates Specimen distribution data from remote sources

data from various sources may be merged

red dots on the map link back to the website that provided the geographical

co-ordinates

uBio Programmers BHL Taxonomic Intelligence Tool Georges Louis Leclerc, comte de Buffon Histoire naturelle : générale et particulière (Oiseaux) , 1799-1808

uBio 10.7 Million+ Name Strings Reconciliation Groups http://www.ubio.org

10.7 Million+ Name Strings

Reconciliation Groups

http://www.ubio.org

Training and Improving the Algorithm

uBioRSS Taxonomically Intelligent RSS Feed Aggregator

uBioRSS Taxonomically Intelligent RSS Feed Aggregator

MBL WHOI Library – Woods Hole authors’ publications

MBL WHOI Library – Woods Hole species publications

Taxonomic intelligence works miracles! It will benefit any initiative that uses distributed and heterogeneous information about biology Distributed content on the same species can be drawn together because different names will be standardized through reconciliation We can read documents, find names, catalog and taxonomically index documents Produce a framework around which we can organize and assemble remote and local content

It will benefit any initiative that uses distributed and heterogeneous information about biology

Distributed content on the same species can be drawn together because different names will be standardized through reconciliation

We can read documents, find names, catalog and taxonomically index documents

Produce a framework around which we can organize and assemble remote and local content

Taxonomically intelligent scientific text parsing

Search Browse

Search

Browse

“ It is exciting to anticipate the scientific chords we might hear once 1.8 million notes are brought together through this instrument. Potential EOL users are professional and citizen scientists, teachers, students, media, environmental managers, families and artists. The site will link the public and scientific community in a collaborative way that’s without precedent in scale.” Jim Edwards, Executive Director, EOL

“ It is exciting to anticipate the scientific chords we might hear once 1.8 million notes are brought together through this instrument. Potential EOL users are professional and citizen scientists, teachers, students, media, environmental managers, families and artists. The site will link the public and scientific community in a collaborative way that’s without precedent in scale.”

Jim Edwards, Executive Director, EOL

Acknowledgments Catherine Norton Patrick Leary David Remsen Diane Rielinger David Patterson Neil Sarkar A.W. Mellon Foundation Alfred P. Sloan Foundation John D. & Catherine T. MacArthur Foundation Internet Archive Christopher Freeland Tom Garnett M artin Kalfatovic Graham Higley BHL & EOL Teams

www.biodiversitylibrary.org www.eol.org www.ubio.org