open access bhl ia

Science and Technology Research ForumALA June 25, 2006 New Orleans, LA

Martin R. Kalfatovic and Suzanne C. PilskSmithsonian Institution Libraries

Open Access to Legacy Taxonomic Literature

The Biodiversity Heritage Library&

Index Animalium

Martin R. KalfatovicSuzanne C. Pilsk

Smithsonian Institution Libraries



Taxonomic LiteratureIn 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)



Taxonomic Literature

Nomina si pereunt, perit et cognitio rerum

If the names are lost the knowledge also disappears

- J.C. Fabricius, 1778, Philosophia Entomologica VII,1




Nomina si nescis, perit et cognitio rerum

Who knoweth not the name, knoweth not the subject

-- Linnaeus, 1737, Critica Botanica n. 210



Taxonomic Literature• Binomial Nomenclature

– Genus name and Species - Epithet or descriptor– Latin or Latin-ized

Bill Gates' Flower FlyEristalis gatesi Thompson



Botany

• “The nomenclature of a taxonomic group is based upon priority of publication.” – Principle III of the St. Louis Code of International Code of Botanical Nomenclature

– Publication is effected, under this Code, only by distribution of printed matter (through sale, exchange, or gift) to the general public or at least to botanical institutions with libraries accessible to botanists generally.



Animals• “Priority of publication is a basic principle

of zoological nomenclature …” -- Preamble International Code of Zoological Nomenclature

– Must be issued for the purpose of providing a public and permanent scientific record ; it must be obtainable, when first issued, free of charge or by purchase ; it must have been produced in an edition containing simultaneously obtainable copies by a method that assures numerous identical and durable copies



Animals

– Works produced before 1986. To be published, a work produced before 1986 must have been produced on paper, by a printing method then conventional (such as letterpress, offset printing) or by hectographing or mimeographing.



Phylogenetic• Publication, under this code, is defined as

distribution of text (but not sound), with or without images, in a peer-reviewed book or periodical.

• To qualify as published, works must consist of numerous (at least 50 copies), simultaneously obtainable, identical, durable, and unalterable copies, some of which are distributed to major institutional libraries in the field so that the work is generally accessible as a permanent public record to the scientific community, be it through sale or exchange or gift, and subject to the restrictions and qualifications in the present article.



Phylogenetic

• Precedence, a clear order of preference, to determine the correct name of a taxon when synonyms or homonyms exist.

• Use the date of publication (chronological priority) as the primary criterion for establishing precedence. -- International Code of

Phylogenetic Nomenclature



…Names…

• In articles concerning the detailed listing or taxonomy of a species, the date and place of publication associated with the authorship– Coast Redwood first described by David Don

as Taxodium sempervirens D. Don but then S. L. Endlicher said it was too different from Taxodium and made it just Sequoia



…Names…

Full Citation Example:

Sequoia sempervirens (D. Don) Endl., Syn. Conif. 198 (1847)

Referring to page 198 of Endlicher's Synopsis Coniferarum, published in 1847.



…Names…

There must be a correction of terminology. If terminology is not corrected, then what is said cannot be followed. If what is said cannot be followed, then work cannot be accomplished.

The Analects of Confucius, Book 13, verse 3 (Muller translation, 1995)



…Names…Rectification of Names (Cheng Ming)What is necessary is to rectify names …

If names be not correct, language is not in accordance with the truth of things. If language be not in accordance with the truth of things, affairs cannot be carried on to success.

The Analects of Confucius, Book 13, verse 3 (Legge translation, 1980)



Taxonomic LiteratureThe cited half-life of publications in taxonomy is longer than in any other scientific discipline

* * * The decay rate is longer than in any scientific discipline

- Macro-economic case for open access, Tom Moritz

Levinus Vincent

Elenchus tabularum, pinacothecarum, 1719




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



Our Man Sherborn – the Squire

• Cataloger at heart• Slowly went through

every relevant text looking for names

• Created an index that was useful as soon as he started

• Index AND Bibliography of relevant texts from 1758 through 1850



Index Animalium



Index Animalium

• Re-keying of data

• Parsing data

• Using tools to harvest out data

• Manually matching data

• Wealth of information locked on the page is being liberated!



Index Animalium



Biodiversity Heritage Library



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)




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.




0

1

2

3

4

5

6

7

8

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



Biodiversity Heritage LibraryMy deepest gratitude for allowing me access to the digital version of the very rare "Bulletin des Séances de la Société Entomologique de France". It has been very important for my work on the database of the names of the butterflies of the world to be able to consult at leisure this series, which is held by extremely few libraries in the world.

I cannot stress enough the importance of having access to electronic versions of the literature, especially to us researchers who cannot benefit from well-endowed institutional libraries.



Biodiversity Heritage LibraryFebruary 2005: Library and Laboratory: the Marriage of Research, Data and Taxonomic Literature met in London.

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

June 2006: the members of the Biodiversity Heritage Library met in Washington to work on technical details of the project.

Ernest Ingersoll Hand-book to the National Museum … Smithsonian

Institution, 1886




• Museums– American Museum

of Natural History (New York)

– Natural History Museum (London)

– Smithsonian Institution (Washington, D.C.)




• 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)

– uBio project of MBL/WHOI



Biodiversity Heritage LibraryAffiliated Partner: Internet Archive




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



Biodiversity Heritage Library“Guano diggers among the

albatrosses. Laysan Island”

So, we have page pictures, we have some metadata, but what good is it? I fear that with millions of books, our users will just be left like these guano diggers in Hawaii.

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



Biodiversity Heritage LibraryBHL Taxonomic Intelligence Tool

- Developed by David Remsen and staff MBL/WHOI Library




BHL Metadata Repository II

Internet ArchiveBHL MR

BHL Public Interface

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

GenBank, INOTAXA documents, etc.

BHL MRBHL MR



Open Access to Legacy Taxonomic Literature

The Biodiversity Heritage Library&

Index Animalium

Martin R. KalfatovicSuzanne C. Pilsk

Smithsonian Institution Libraries

open access bhl ia

Technology

taxonomic impediment

legacy taxonomic literature

taxonomic group

phylogenetic publication

place of publication

obtainable copies

durable copies

permanent scientific