Encyclopedia of Life - the Power of Collaboration

Biodiversity Heritage Library

© 2008 Biodiversity Heritage Library www.biodiversitylibrary.org

The Encyclopedia of Life, Biodiversity The Encyclopedia of Life, Biodiversity Heritage Library, Biodiversity Heritage Library, Biodiversity

Informatics and beyond…..Informatics and beyond…..

MBLWHOI Library

Cathy Norton

Deputy Director, BHL

WebWise 2008

Miami Beach, Florida



“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



EOL Hierarchy

• The EOL Steering Committee is comprised of senior authorities from

Harvard University, Smithsonian Institution, the Field Museum of

Chicago, the Marine Biological Laboratory at Woods Hole, the

Biodiversity Heritage Library consortium, Missouri Botanical Garden,

and the Macarthur and Sloan Foundations.

• The EOL Institutional Council contains more than 25 institutions from

around the world and provides EOL with global perspectives and

outreach capabilities. The Distinguished Advisory Board consists of

13 global leaders from the scientific and policy communities.



Con’t

• 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, a consortium of 10 natural history, botanical and research libraries that will scan for the public commons out of copyright and permissioned works.



Con’t • FishBase (www.fishbase.org), a global information system with data on practically every fish

species known to science. FishBase is serving information on more than 30,000 fish species through the EOL.

• The Catalogue of Life Partnership (CoLp) (www.catalogueoflife.org), an informal partnership dedicated to creating an index of the world’s organisms.. They contain substantial contributions of taxonomic expertise from more than fifty organizations around the world, integrated into a single work by the ongoing work of the CoLp partners. The EOL currently uses CoLp as its taxonomic backbone.

• Tree of Life web project (ToL) (www.tolweb.org), a collaborative effort of biologists from around the world. On more than 9,000 Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics. ToL project illustrates the genetic connections between all living things.

• The Global Biodiversity Information Facility (GBIF) (www.gbif.org), the world’s premiere source for information on biological specimen and observational data, providing on-line access to more than 135 million data records from around the world. GBIF is providing range maps for the EOL species pages.

• AmphibiaWeb (http://amphibiaweb.org), an online system enabling anyone with a Web browser to search and retrieve information relating to amphibian biology and conservation.

• The Solanaceae Source Web site (www.nhm.ac.uk/research-curation/projects/solanaceaesource), The aim of the project is to produce a worldwide taxonomic monograph of the species occurring within the plant genus Solanum (the potato and tomato family), with principal investigators from four research institutions in England and the United States.

Data Partners

http://www.fishbase.org/

http://www.catalogueoflife.org/

http://www.tolweb.org/

http://www.gbif.org/

http://amphibiaweb.org/

http://www.nhm.ac.uk/research-curation/projects/solanaceaesource



“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



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



Data Sharing

Plant Names

Specimens

Plant Names

Plant NamesSpecimensDescriptionsPlant Names

Plant Names

Citations



Data Sharing• Standards • Services



Serine Molecule

BiodiversityHeritage Library

Synthesis CenterField Museum

InformaticsMarine BiologicalLaboratory & MOBOT

Education & OutreachSmithsonian/Harvard

SecretariatSmithsonian



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








•Museums–Field Museum–Natural History Museum (London)–Smithsonian Institution–American Museum of Natural History

•Botanical Gardens–Missouri Botanical Garden–New York Botanical Garden–Royal Botanic Gardens, Kew

•University Libraries–Botany Libraries, Harvard University–Ernst Meyer Library of the Museum of Comparative Zoology, Harvard

University•Research Institute Library

–Marine Biological Laboratory / Woods Hole Oceanographic Institution Library (MBL/WHOI)

All signed MOU’s



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% pre-1923



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



• 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



• 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



• 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

• 2.5 million pages already available

Where are we now?



• Legal issues - BHL organisational structure, content licensing, contracts being developed by EFF

• BHL will take responsibility for long-term sustainability of the scanned material

• Blackwell Publishing/Wiley back-files possibly available through the BHL

• Zoological Record will provide their index as route to BHL articles

• OCR and name recognition tools identified and linked to project - Taxonomic Intelligence



• BHL is US/UK focused. • Plans to engage European partners – through projects such

as EDIT and SYNTHESYS – in a similar attempt to capture the non-English language publications

• G8+5 Environment Ministers identified need for ‘Global Species Information System’ – first EU meeting to address response endorsed the BHL as the way forward

• Positive discussions have already taken place with the Chinese Academy of Sciences

• Australian Government likely to fund scanning as part of Atlas of Australian Life

Where are we now? Europe, Rest of the World



Classes of texts

Public Domain – pre-1923Non-profit society journalsPost-1923 monographs

some with copyright renewalssome 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.



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 to 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 intaxonomy is longer than in any other scientific discipline.

The decay rate is longer than in most scientific disciplines.

-Macro-economic case for open accessTom Moritz

Current taxonomic literature often relies on texts and specimens >100 years old.



Georges Louis Leclerc, comte de BuffonHistoire 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. –Interoperability is the key.. Repository islands will sink

The Long NOW Strategy



Biologia Centrali-American

0

1

2

3

4

5

6

7

8

US & Canada Europe Mexico & C.America

SouthAmerica

Physical Distribution…

Now… you can virtually

Parse data, harvest out data, Wealth of information locked on the pages are now liberated!



Henry Walter BatesThe Naturalist on the River Amazons, 1863

Most literature is in the developed worldthe Northern Hemisphere

Most Biodiversity is in the developing worldthe 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 LiteratureLondon, February 2005Eighty 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 ScanningContractsFirewallsSecurityLoading DocksTrucks180 mile round trip!



Ernest Ingersoll Hand-book to the National Museum … Smithsonian Institution, 1886

Mass Scanning WorkflowBid ListsPick ListsPacking ListsSerials ManagementMonographic ManagementStickers for Media and cartsRare Books-vaults



It began and begat

Reptilia and Batrachia. (1885-1902) by Albert C.L.G. Günther

Open Access: all content can be reused, repurposed, reformatted, sliced, diced, scraped, harvested, integrated.

2003 Telluride . Encyclopedia of Life Meeting2005 London. Library and laboratory: the

Marriage of Research, Data, and Taxonomic Literature.June 2006 Washington. Organization and Technical MeetingOctober 2006 St Louis/San Francisco Technical Meeting



Reptilia and Batrachia. (1885-1902) by Albert C.L.G. Günther

February 2007 MCZ Harvard Organizational MeetingMay 2007 Encyclopedia of Life Launch. Washington DCSept 2007 Missouri Botanical Garden Technical MeetingMarch 2008 MCZ Harvard Organizational Technical Meeting



Collaborators

Sanborn TenneyNatural History of Animals . . .1868. Internet Archive

Set up scanning centers in London, New York, Washington, Boston, etc.High-quality, non-destructiveScanning.Image files and text derived from OCR.

Internet ArchiveInternational Commission on

Zoological NomenclatureOpen Content AllianceEuropean Distributed Institute

of TaxonomyGlobal Biodiversity Information

Facility (GBIF)Many more under negotiation

Sanborn TenneyNatural History of Animals . . .1868.



Jacob Christian SchäfferElementa entomologica . . . 1766.

BHL Portalhttp://www.biodiversitylibrary.org

Serve image and test files: create volume, Part, piece, metadata; ingest page level Metadata at scanning level; apply GloballyUnique Identifiers (GUIDs) for linking to Other taxonomic services.

http://www.biodiversitylibrary.org/



AcknowledgmentsPatrick LearyDavid Remsen

Diane RielingerDavid Patterson

Neil Sarkar

A.W. Mellon FoundationAlfred P. Sloan Foundation

John D. & Catherine T. MacArthur FoundationInternet Archive

Christopher FreelandTom Garnett

Dr. James Edwards

Martin KalfatovicGraham HigleyBHL & EOL Teams

Encyclopedia of Life - the Power of Collaboration

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