Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Scientific Disciplines From Discovery to Delivery Cathy Norton.

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Scientific Disciplines From Discovery to Delivery Cathy Norton Deputy Director BHL Princeton January 18, 2011

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org “ 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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 Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Serine Molecule Biodiversity Heritage Library Synthesis Center Field Museum Informatics Marine Biological Laboratory & MOBOT Education & Outreach Smithsonian/Harvard Secretariat Smithsonian Missouri Botanical Garden

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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.

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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.

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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.www.fishbase.org 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.www.catalogueoflife.org 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.www.tolweb.org 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.www.gbif.org AmphibiaWeb (http://amphibiaweb.org), an online system enabling anyone with a Web browser to search and retrieve information relating to amphibian biology and conservation.http://amphibiaweb.org 2011 Now over 120 partners! See them at: http://www.eol.org/content/partners. Data Partners

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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 9 th May, 2007 –First 30,000 pages launched at TED Feb 27th, 2008

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

© 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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 Meeting 2005 London. Library and laboratory: the Marriage of Research, Data, and Taxonomic Literature. June 2006 Washington. Organization and Technical Meeting October 2006 St Louis/San Francisco Technical Meeting

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Reptilia and Batrachia. (1885-1902) by Albert C.L.G. Günther February 2007 MCZ Harvard Organizational Meeting May 2007 Encyclopedia of Life Launch. Washington DC From 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Collaborators Sanborn Tenney Natural History of Animals...1868. Internet Archive Set up scanning centers in London, New York, Washington, Boston, etc. High-quality, non-destructive Scanning. Image files and text derived from OCR. Internet Archive International Commission on Zoological Nomenclature Open Content Alliance European Distributed Institute of Taxonomy Global Biodiversity Information Facility (GBIF) Many more under negotiation Sanborn Tenney Natural History of Animals...1868.

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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 © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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 –

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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?

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org GLOBAL BHL –BHL Europe – 47 libraries –BHL China – National Academy of China –BHL Australia- Atlas of Living Australia –BHL South America – Brazil –BHL- Egypt

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Classes of texts Public Domain – pre-1923 US Pre 1955 Australia, all different Non-profit society journals Post-1923 monographs some with copyright renewals some without copyright renewals Commercial journals

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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.

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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.

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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. -Macro-economic case for open access Tom Moritz Current taxonomic literature often relies on texts and specimens >100 years old.

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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. –Interoperability is the key.. Repository islands will sink The Long NOW Strategy

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Biologia Centrali-American Physical Distribution… Now… you can Parse data, harvest out data, Wealth of information locked on the pages are now liberated!

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Henry Walter Bates The Naturalist on the River Amazons, 1863 Most literature is in the developed world the Northern Hemisphere Most Biodiversity is in the developing world the Southern Hemisphere

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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!

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Crowdsourced Articles http://www.biodiversitylibrary.org/pdfgen/17298 Demo: http://youtube.com/watch?v=oidf3b26jVshttp://youtube.com/watch?v=oidf3b26jVs

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Crowdsourced Articles 12,000 PDFs generated through September 2009 –4,900 submitted with article metadata –Analysis: http://bit.ly/4Jqu9http://bit.ly/4Jqu9

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Great, but how to… display / manage? meet community demands for bibliography / citation management? build from more open source tools?

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org CiteBank boundaries Book Citation Pageturning UI PDF OCR eBook/Kindle Stored *somewhere* & retrievable via HTTP URI Citation Bibliography CiteBank

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org “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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Biodiversity Heritage Library BHL Taxonomic Intelligence Tool Georges Louis Leclerc, comte de Buffon Histoire naturelle : générale et particulière (Oiseaux), 1799-1808

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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 Taxonomic intelligence works miracles

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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)

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org EMF Biology of Aging Ellison Medical Foundation (EMF) “Enable the Study of Aging Across the Spectrum of Life” Officially Began January 2008

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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?

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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 19 th and 20 th 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org 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

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Acknowledgments Jewett Foundaton A.W. Mellon Foundation Alfred P. Sloan Foundation John D. & Catherine T. MacArthur Foundation Internet Archive

Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Scientific Disciplines From Discovery to Delivery Cathy Norton.

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Biodiversity Heritage Library © 2011 Biodiversity Heritage Librarywww.biodiversitylibrary.org Scientific Disciplines From Discovery to Delivery Cathy Norton.

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