Open Access to Legacy Biodiversity Literature

NVC NSDL April, 25, 2006Arlington, Virginia

Martin R. KalfatovicSmithsonian Institution Libraries

Open Access to Legacy Taxonomic Literature

The Biodiversity Heritage Library

Martin R. Kalfatovic with edits by Tom GarnettSmithsonian Institution Libraries



Biodiversity Heritage LibraryIn any well-appointed Natural History Library there should be found every book and every edition of every book dealing in the remotest way with the subjects concerned. One never knows wherein one edition differs from or supplements the other and unless these are on the same table at the same time it is not possible to collate them properly. Moreover for accurate work it is necessary for the student to verify every reference he may find; it is not enough to copy from a previous author; he must verify each reference itself from the original.

Charles Davies Sherborn, Epilogue to Index Animalium, March 1922

Charles Davies Sherborn (1861-1942)



Biodiversity Heritage LibraryYet another physical difficulty is the task of assembling the library and indexes which will enable the student to work under proper conditions…. the beginner must now be prepared to spend liberally, or else must establish himself in an institution where a large library exists; if he work by himself with only a few books, he will have to confine himself to a very narrow specialty indeed.'The Limitations of Taxonomy' by J.M. Aldrich, Science, April 22,

1927, vol. LXV, no. 1686, p.381

Insecta. Diptera. Volume I (1886-1901)



Biodiversity Heritage LibraryThe cited half-life of publications in taxonomy is longer than in any other scientific discipline

-Macro-economic case for open access, Tom Moritz

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

Levinus Vincent

Elenchus tabularum, pinacothecarum, 1719



Biodiversity Heritage Library

The Taxonomic Impediment

“The taxonomic impediment is a term that describes the gaps of knowledge in our taxonomic system”

- Darwin Declaration, 1998

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




Thylacine from Philip Lutley Sclater, Guide to the Gardens of the Zoological Society of London, 1891

• that there is access to information held in national/regional/global collections

• that electronic data is efficiently captured and provided in useable form

• that existing information held in literature and by current experts is made available electronically

• that stability of scientific names of organisms, used to access this information, is promoted

- Darwin Declaration, 1998

The essential requirements for accessing and utilising this global information are:





Convention on Biological Diversity: Article 17… exchange of information shall include exchange of results of technical, scientific and socio-economic research … It shall also, where feasible, include repatriation of information.




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US & Canada Europe Mexico & C.America

SouthAmerica

Biologia Centrali-AmericanaEdited by Frederick Ducane Godman and Osbert SalvinLondon : Pub. for the editors by R. H. Porter, 1879-1915

Chart showing distribution in public collections of the complete 63 volume sets held worldwide.2 complete copies in Central America held at the Smithsonian Tropical Research Institute Library




Henry Walter BatesThe Naturalist on the River Amazons, 1863

Vishwas Chavan travels a lot. An informatician based at the National Chemical Laboratory in Pune, India, he collects data on what types of animal live where in India to enter into a biodiversity database … Much of the information Chavan seeks is in old, out-of-print tomes … To find them, Chavan has spent years trailing around libraries. He dreams of the day when books such as these are scanned and made available as digital files on the Internet.

“Science in the Web Age: The Real Death of Print”by Andreas von Bubnoff

Nature 438, 550-552 1 December 2005




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.




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

May 2005, the libraries represented at the London meeting gathered in Washington to lay out the ground work for the Biodiversity Heritage Library.

Representatives of a number of major natural history and botanical libraries met at the Smithsonian National Museum of Natural History in Washington, D.C., with the support of the Smithsonian Institution, to develop a strategy and operational plan to digitize the published literature of biodiversity held in their respective collections and to make that literature available for open access and responsible use as a part of a global “biodiversity commons.”




• Museums– American Museum

of Natural History (New York)

– Natural History Museum (London)

– Smithsonian Institution (Washington)




• Botanical Gardens– Missouri Botanical

Garden– New York Botanical

Garden– Royal Botanic

Garden, Kew




• University Libraries– Botany Libraries,

Harvard University– Ernst Meyer Library

of the Museum of Comparative Zoology, Harvard University




• Bioinformatics Member– Marine Biological

Laboratory / Woods Hole Oceanographic Institution Library (MBL/WHOI)




• Bioinformatics Member– Marine Biological

Laboratory / Woods Hole Oceanographic Institution Library (MBL/WHOI)

– uBio project of MBL/WHOI



Biodiversity Heritage LibraryCollaborators: Internet Archive



Biodiversity Heritage LibraryCollaborators: Online Computer Library Center

(OCLC)



Biodiversity Heritage LibraryCollaborators: Research Library Group (RLG)



Biodiversity Heritage LibraryCollaborators: Open Content Alliance




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

Mandates:

Open Access: all content can be reused, repurposed, reformatted, sliced, diced, scraped, and ???




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

Mandates:Opt in Copyright Model: The BHL will actively work with professional societies and associations to integrate their publications into the BHL in a way that serves the societies’ missions and goals




Jacob Christian SchäfferElementa entomologica . . . 1766.

Metadata RepositoryStore all bibliographic metadata for the member libraries; create volume, part, piece metadata; ingest page level metadata at scanning level for the creation of page level Globally Unique Identifiers (GUIDs) for linking to other taxonomic services



BHL Metadata Repository

Member Catalog A Member Catalog B

Item Records

Bib. Records

Item RecordsItem Records

Bib. Records

Item RecordsItem RecordsItem Records

BHL MR Bib Records




Member Catalog A Member Catalog B

Item Records

Bib. Records

Item RecordsItem Records

Bib. Records

Item RecordsItem RecordsItem Records

BHL MR Bib Records

BHL MR Item Records BHL MR Repository




Internet Archive

Z39.50 Fetch: Internet Archive from BHL (Current Practice)Could be some other way to depending on metadata scheme (e.g. OAI-PHM?)

BHL MR Bib Records

BHL MR Item Records



BHL Metadata RepositoryFirst Ingest

Internet Archive

Bib # Barcode Sub-element

45632 390888343

45632 390888344

45632 390888345

45632 390888346

45632 390888347



BHL Metadata RepositorySub-Element Map

Internet Archive


45632 390888343 1

45632 390888343 2

45632 390888343 3

45632 390888343 4

45632 390888343 5





45632 390888343 1

Page Structure Map

Internet Archive

Image Number

0001

0002

0003

0004

0005If possible, auto create explicit automated page numbering at this point



BHL Metadata Repository II

Internet Archive

Z39.50 Fetch: BHL from Internet Archive or some other way to upload matching description with the scanned images.

BHL MR Bib Records

BHL MR Item Records

Sub-element & page /image structure

map





45632 390888343 1

Bib/Sub-element/Page Structure MapImage

Number

0001

0002

0003

0004

0005BHL MR

BHL MR




Internet ArchiveBHL MR

BHL Public Interface

BHL MR

BHL MR




Internet ArchiveBHL MR

BHL Public Interface

Taxonomic Web Servicese.g. CBOL, GBIF, ITIS,

GenBank, INOTAXA documents, etc.

BHL MRBHL MR



Biodiversity Heritage Library“Guano diggers among the

albatrosses. Laysan Island”

At this stage, we would have page pictures, “dirty OCR”, some metadata, but what good is it? Will researchers be left like these guano diggers in Hawaii?

Lionel Walter RothschildThe avifauna of Laysan and the neighboring islands, 1893-1900




Agatea violarisType specimen from the U.S. National Herbarium (Smithsonian Institution) collected by the United States Exploring Expedition, 1838-1842




- Specimen- Plate or other visual image- Taxonomic description




Eleazar AlbinA natural history of English song-birds…, 1741

Massachusetts. Zoological and Botanical Survey

Reports on the fishes, reptiles and birds of Mass., 1839



Biodiversity Heritage LibraryBHL Taxonomic Intelligence Tool

- Developed by David Remsen and staff MBL/WHOI Library




Biodiversity Heritage LibraryCo-evolving bioinformatics resources

produce a rich information ecology:Consortium for the Barcoding of Life

(CBOL) with gene sequences deposited in GenBank.

GBIF’s Electronic Catalog of Taxonomic Names

Hebaria and museum specimen databasesElectronic Gazetteers and GPS.Additional services – you’re invited to help



Open Access to Legacy Taxonomic Literature

The Biodiversity Heritage Library

Martin R. Kalfatovic with edits by Tom GarnettSmithsonian Institution Libraries

Open Access to Legacy Biodiversity Literature

Technology

Transcript of Open Access to Legacy Biodiversity Literature