Biodiversity Heritage Library © 2011 Biodiversity Heritage Library Scientific Disciplines From Discovery to Delivery Cathy Norton

Biodiversity Heritage Library

© 2011 Biodiversity Heritage Library www.biodiversitylibrary.org

Scientific DisciplinesFrom Discovery to Delivery

Cathy NortonDeputy Director BHLPrincetonJanuary 18, 2011



“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



http://tagcrowd.com/That's a service that will make word clouds from arbitrary text or a URL

• Clouds– Building word clouds

• Count how many times a word appears• Decide on font large to small



Serine Molecule

BiodiversityHeritage Library

Synthesis CenterField Museum

InformaticsMarine BiologicalLaboratory & MOBOT

Education & OutreachSmithsonian/Harvard

SecretariatSmithsonian

Missouri Botanical Garden



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 Working groups

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



Con’t • 2008: 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.. 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.

• 2011 Now over 120 partners! See them at:

• http://www.eol.org/content/partners.

Data Partners



Encyclopedia of Life

• Major project to create a single Web page for every known species (1.9 million!)

• Total funding will reach at least $50M by 2012• EOL needs literature Hence the BHL project• BHL key partner in EOL project• Launched on 9th May, 2007

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



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






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 DCFrom then on at least one Annual Meeting per year for Institutional Council and One/Two Technical Meetings per year. Next one in March in Washington



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.



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



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.





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– BL/Microsoft

/Google big ten, BLC• Tractable, well-defined scientific domain• Taxonomic information has exceptionally

longevity • Supports GBIF and other international

initiatives –



• 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

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, Boston, Library of Congress, Univ. Ill ,China, Egypt

• 33 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

• Blackwells 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



• GLOBAL BHL– BHL Europe – 47 libraries– BHL China – National Academy of China– BHL Australia- Atlas of Living Australia– BHL South America – Brazil– BHL- Egypt



Global Coordinating Committee

BHL-China

BHL-Egypt

BHL-Australia

BHL-South America

BHL-Europe

BHL-US/UK



Classes of texts

Public Domain – pre-1923 US Pre 1955 Australia, all different

Non-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 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 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

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 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 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



Internet Archive Scribe: Boston



US/UK PROCESS: multiple institutions

•American Museum of Natural History •Botany Libraries, Harvard University•Ernst Mayr Library, Museum of Comparative Zoology, Harvard University•Field Museum•Marine Biological Laboratory / Woods Hole Oceanographic Institution Library•Missouri Botanical Garden•Natural History Museum (London)•New York Botanical Garden•Royal Botanic Gardens, Kew•Smithsonian Institution Libraries•Academy of Natural Science (Philadelphia)•California Academy of Science US

PROCESS: communication•Telephone conversations•Email strings•Working documents•bhl.wikispaces.com•Face to face meetings•Presentations•Articles•Going beyond self expectations was the norm



The Work-Flow Process

• Select Book ~Pull from Shelf

• Review Physically, • and check Metadata• Establish viability and

create pick/pack list / Wonderfetch

• Send to IA scanning center





THE TITLE:

•Requested by patron/curator?

•EOL need?

•Gap fill?

Is the title a serial? …need to bid in scanlist

Is the title a Monograph?

…need to run through deduper

THE SCANNING:

Picklist creation

Metadata check

Physically move volumes from stacks to scanning area/building/off campus

Are pages torn?-what are parameters for rejection?

POST SCANNING:

Volumes returned post scanning

QA/QC checking – what are parameters for quality?

Where will volumes be viewed?

Integration with ILS

Integration with web, tools



PROCESS –

Documentation,Feedback

Tweaking, Completing

Process

is a continual process!

; - )



Biodiversity Informatics



Period of explosive growth• NCL Centre for Biodiversity Informatics (India)--2000• Speciation event: Biodiversity Informatics--2004• Ocean Biodiversity Informatics conferences--2004, 2007• Species-bases sites: FishBase, AntWeb, AmphibiaWeb, North American

Mammals, Swedish ArtDatabanken, Atlas of Living Australia, Netherlands species compendium …

• Specimen-based networks: HerpNet, MANIS, ORNIS, • Regional networks: IABIN, OBIS, …• Biogeomancer--2005• IdentifyLife--2005• JRS Biodiversity Foundation--2005• European Distributed Institute of Taxonomy (EDIT)--2006• BDI curricula

– University of Illinois Master of Science in Biological Informatics--2006

• Encyclopedia of Life (EOL)--2007



Crowdsourced Articles

• http://www.biodiversitylibrary.org/pdfgen/17298

Demo: http://youtube.com/watch?v=oidf3b26jVs




• 12,000 PDFs generated through September 2009– 4,900 submitted with article metadata – Analysis: http://bit.ly/4Jqu9



Great, but how to…

• display / manage?

• meet community demands for bibliography / citation management?

• build from more open source tools?



Development goals re: citations

• Create a repository for community-vetted taxonomic bibliographies.

• Ability to ingest, display, download, and index articles so that the BHL can operate as an article repository.

• Build from existing community of work around Drupal / Biblio.– In use by collaborators



“something like GenBank or NameBank for citations…”

So, CitationBank…or CiteBank (saves chars)

NEED…



http://citebank.biodiversitylibrary.org/




• PDFs from BHL pushed into Drupal/Biblio:



CiteBank boundaries

Book

Citation

Pageturning UIPDFOCR

eBook/Kindle

Stored *somewhere* & retrievable via HTTP URI

CitationCitationCitation

Bibliography

CiteBank


© 2011 Biodiversity Heritage Library www.biodiversitylibrary.orgBHL Data Flow – Sep 2009

CiteBank



Copyright

Bold statements that need some good legal counsel: Citations don’t have copyright

Unless you get them from OCLC, other services

Bibliographies have copyright They’re a scholarly work

Underlying content has copyright Except when it doesn’t





Reuse, don’t rebuild



“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



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




BHL Taxonomic Intelligence Tool

Georges Louis Leclerc, comte de BuffonHistoire naturelle : générale et particulière (Oiseaux), 1799-1808



uBio

• 10.7 Million+ Name Strings

• Reconciliation Groups

• http://www.ubio.org



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





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)



BEYOND

AND



EMF Biology of Aging

Ellison Medical Foundation (EMF)“Enable the Study of Aging Across

the Spectrum of Life”Officially Began January 2008



FEDORA Commons

EMF Biology of AgingConditions

Locations

Organisms

Genes



EMF/EOL Key Resources

• Medline, BHL (Literature)

• GenBank (Molecular)

• EOL (Habitat & Location)



• All organisms are affected by aging

• Not all aging is associated with disease

• The flip side: Understanding aging might give insights to regeneration

A constant



Biomedical Focus

• Expand the scope of organisms beyond the “classic” models:



Goals of EMF (years one & two)• What genes are associated with aging conditions?• What are the conditions associated with these

genes?• What organisms are associated with the aging genes

and conditions?• What other organisms might also have aging genes?• Where do the identified organisms live, and in what

types of habitats?• What are the demographic patterns associated with

organisms across the spectrum of life?• What are common phenotypes associated with

organisms that share common aging genes?



• Proven the concept of mass scanning of general collections• Proven concept of automated structured markup done in collaboration with

Penn Stat and the Internet Archive• Built proof of concept portal on proprietary ( .Net) environment.• High levels of OCR accuracy in late 19th and 20th century printing• Applied taxonomic intelligence ( species name finding) across million of pages

Across millions of pages against nearly 11 million names in Name Bank..• Data mining BHL for other bioinformatics projects.(EOL/BOA)• Obtained buy-in from a diverse group of learned societies for the BHL opt-in • Copyright model• Support and encouragement from our traditional bibliophile, and scientific • Audiences• Collaboration with an international group of competitive organizations

Status today



•Get equal cost efficiencies and speed for special collections• Nail down automated structural mark up to a high level of accuracy•Improve OCR for publications in other languages with little human intervention•Broaden the use of taxonomic intelligence algorithm Data mining BHL for other bioinformatics projects.• Work with commercial publishers for fair and equitable use of their publications•Expand audiences through social networking and repurposing content for• new audiences• Expand the consortium to bring in more partners, and more partners in Asia, South •and the developing world

Status Tomorrow











www.eol.org

www.ubio.org

www.biodiversitylibrary.org



Acknowledgments

Jewett FoundatonA.W. Mellon Foundation

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

Internet Archive

Documents

Biodiversity Heritage Library © 2011 Biodiversity Heritage Library Scientific Disciplines From Discovery to Delivery Cathy Norton