Backdoor Broadcasting Company

Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Richard Pyle
Towards a Global Names Architecture: The future of indexing scientific names 

Bishop Museum, Honolulu, HI, USA & ICZN
Email: deepreef@bishopmuseum.org

For more than 250 years, the taxonomic enterprise has remained almost unchanged. Certainly the tools of the trade have improved: months-long journeys aboard sailing ships have been reduced to hours aboard jet airplanes; advanced technology allows humans to access environments that were once utterly inaccessible; GPS has replaced crude maps; digital hi-resolution imagery provides far more accurate renderings of organisms that even the best commissioned artists of a century ago; and primitive candle-lit microscopes have been replaced by an array of technologies ranging from scanning electron microscopy to DNA sequencing. But the basic paradigm remains the same. Perhaps the most revolutionary change of all ñ which we are still in the midst of, and which has not yet been fully realized ñ is the means by which taxonomists manage and communicate the information of their trade. The rapid evolution in recent decades of computer database management software, and of information dissemination via the internet, have both dramatically improved the potential for streamlining the entire taxonomic process.  Unfortunately, the ìpotentialî still largely exceeds the reality.  The vast majority of taxonomic information is either not-yet digitized, or digitized in a form that does not allow direct and easy access.  Moreover, the information that is easily accessed in digital form is not yet seamlessly interconnected.  In an effort to bring ìrealityî closer to ìpotentialî, a loose affiliation of major taxonomic resources, including GBIF, the Encyclopedia of Life, NBII, Catalog of Life, ITIS, IPNI, ICZN, Index Fungorum, and many others have been crafting a ìGlobal Names Architectureî (GNA).  The intention of the GNA is not to replace any of the existing taxonomic data initiatives, but rather to serve as a dynamic index to interconnect them in a way that streamlines the entire taxonomic enterprise: from gathering specimens in the field, to publication of new taxa and related data.

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Rod Page
Towards an open taxonomy

Professor of Taxonomy, Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences, University of Glasgow
Email: r.page@bio.gla.ac.uk

Taxonomy is in many ways still pre-digital. Most taxonomic databases are little more than digitised index cards linking names to often-cryptic bibliographic citations, oblivious to the growing volume of scientific literature that is now online. A growing fraction of taxonomic literature is becoming freely available, either through adoption of Open Access publishing models, or through digitising efforts such as the Biodiversity Heritage Library. Yet much of the most basic information about biodiversity, namely taxonomic description, remains either behind a pay wall, or only available in paper form. This talk sketches the goal of an “Open Taxonomy.” The first step towards this goal is digitally linking scientific names to the primary literature using standard identifiers such as DOIs. I argue that until we make serious inroads into this task, taxonomic knowledge will remain in a ghetto largely ignored by the wider scientific community. will explore the context of CD Sherbornís Index Animalium and those looming problems and issues which a laborious and comprehensive ìindex of natureî was meant to solve.

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Lyubomir Penev
ZooKeys: Streamlining the registration – to – publication pipeline

Pensoft Publishers, Sofia, Bulgaria
Email: info@pensoft.net

Electronic registration of nomenclatural acts is a dynamic process which still needs to be elaborated in accordance with the Biological Codes. The main questions to resolve are: (1) When a registration should take place, before or after publication? (2) Who is doing the registration? (3) Who approves the registration record? (4) Who confirms the validity of the registration record at the moment of publication? (5) At which point a registration record should be validated (e.g., a new name available), on the day of electronic or printed publication? At the International Botanical Congress in Melbourne in July 2011 it became clear that the registration process will be organized in different ways for the different organismsí kingdoms (Fungi, Plants, Protista and Animals).

ZooKeys was the first journal to provide a mandatory registration in ZooBank for all newly described taxa and to include the ZooBankís LSIDs in the original publication. In our view, the registration of nomenclatural acts and the quality control of the bibliographic metadata in ZooBank should be a responsibility of taxonomy publishers. Besides, we are convinced that registration of nomenclatural acts should be mandatory, independently of that will these be published on paper or online-only.

Within the framework of the EU FP7 project ViBRANT, and in a close collaboration with Zoological Record, ZooBank, the International Plant Name Index (IPNI), MycoBank and Index Fungorum, we are elaborating a workflow and associated software tools to streamline the registration within the editorial, publication and dissemination process. The talk will present Pensoftís vision on how to make the registration process secure and cost-efficient, through the currently developed Pensoft Writing Tool (PWT).

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Sandra Knapp
New workflows for describing and naming organisms 

International Association for Plant Taxonomy (IAPT); Intíl Trust for Zoological Nomenclature (ITZN);
Dept. Of Botany, The Natural History Museum;
Email: s.knapp@nhm.ac.uk

Monographs have long been considered the îgold-standardî of taxonomic treatments. These comprehensive compilations of all knowledge about particular taxa or groups of taxa traditionally culminated a taxonomistís career and often took a lifetime to produce. Descriptive taxonomy has been likened to a cottage industry, the antithesis of the big science approach to tackling global problems. Taxonomy itself is currently in a state of flux; opinions differ as to whether revolution or evolution is necessary, and even then, what should actually happen when we do decide. Do we still need ìgold-standardî, life-consuming single-author taxonomic works? Are traditional monographs doomed to go the way to dinosaurs? I will explore the elements of monographic, ìgold-standardî taxonomic work and examine the workflow we traditionally use to produce them. I will suggest that taxonomists are important for only some parts of this workflow, and with that explore what modern taxonomists are really for and by extension what a modern monographic/taxonomic workflow might look like.

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Chris Freeland
Preserving digitized taxonomic data: problems and solutions for print, manuscript and specimen data

Director, Center for Biodiversity Informatics,
Missouri Botanical Garden, St Louis, MO, USA
Email: chris.freeland@mobot.org

The availability of digitized taxonomic data has increased dramatically over the past twenty years as national funding agencies have strengthened their support of digitization activities and as scanning devices have become less expensive and easier to operate.  As such, natural history museums and libraries have taken on new responsibilities for managing electronic information as ways of providing enhanced opportunities for educational outreach and scholarly dissemination.  Museums and libraries have to consider how best to create and care for electronic resources given a volatile technology landscape with rapidly changing file formats and display devices.  This session will address methodologies for responsible curation of digitized prints, manuscripts, and specimens, and will outline best practices for safeguarding digitized taxonomic data to ensure longevity of resources.

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Daphne Fautin and Miguel Alonso-Zarazaga

LANs: Lists of Available Names – a new generation for stable taxonomic names in zoology? 

Professor, Ecology and Evolutionary Biology Curator, Natural History Museum (Biodiversity Institute) University of Kansas, USA & ICZN

Email: fautin@ku.edu

Depto. de Biodiversidad y BiologÌa Evolutiva Museo Nacional de Ciencias

Naturales Jose Gutierrez Abasca, Madrid, Spain (MNCN-CSIC) & ICZN

Email: zarazaga@mncn.csic.es

Article 79 of the ICZN Code, which appeared first in the Fourth Edition, outlines a procedure for adding large numbers of names to the List of Available Names simultaneously, as a Part of the List. This feature has gained importance with the development of Zoobank, because the LAN can be an important adjunct to or component of Zoobank. Article 79 describes a deliberative process, detailing steps for submission and for consideration by the public and Commission, and their chronology: submission must be by ìan international body of zoologists,î and the proposed Part must be available for ìcomments by zoologistsî for 12 months, followed by another 12-month period for comments on the proposed Part as revised in light of comments received. However, Article 79 it is mute about the contents of the submission. It is clear that adding a Part to the List will prevent long-forgotten names from displacing accepted ones ñ thus, for taxa on the List under the provisions of Article 79, nomenclatural archeology will not be worthwhile. Beyond that, Commissioners who participated in writing the Fourth Edition are divided about the intent of Article 79: some aver it is intended to document every available name within the scope of the Part, others it is to pare the inventory of names within the scope of the Part. The comprehensiveness of the names in the Part is critical because, according to Article 79.4.3, ìNo unlisted name within the scope (taxonomic field, ranks, and time period covered) of an adopted Part of the List of Available Names in Zoology has any status in zoological nomenclature despite any previous availabilityî (names may subsequently be added only ìin exceptional circumstances,î according to Article 79.6). Under the first interpretation, the Part functions as a strictly nomenclatural archive. Under the second interpretation, the Part pares away nomina dubia, so Parts of the List resulting from actions under Article 79 are like the Approved Lists of Bacterial Names that took effect on 1 January 1980 ñ taxonomically recognizable as well as nomenclaturally available. It is critical that a consistent basis for implementing Article 79 be adopted; it is unrealistic to expect unanimity, given the diversity of opinion among those who helped craft Article 79.

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

David Remsen
Biodiversity Informatics: GBIF’s role in linking information through scientific names

Senior Programme Officer. Electronic Catalog of Names of Known Organisms
Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark
Email: dremsen@gbif.org

The Global Biodiversity Information Facility provides access to primary biodiversity data.   It currently provides access to over 300 million data records from over 8000 different databases.    Data customers expect to be able to retrieve data records organised around taxa.   The challenges in integrating these data, originating in different sources, is considerable and requires access to both taxonomic and nomenclatural authority files.   These challenges and the subsequent capabilities these resources enables are presented.

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Henning Scholz
BHL-Europe: Tools and Services for Legacy Taxonomic Literature 

History of Science and Technology Programme,
University of Kingís College, Halifax, NS, CANADA
Email: gmcouat@dal.ca

Literature research is the base for the scientific work of taxonomists. Therefore, large and well-curated natural history libraries are a very important prerequisite to carry out scientific projects efficiently. The library work, however, has several serious limitations that slow down the work significantly. The natural history library corpus is highly fragmented and scattered. In particular much of the early published literature is rare or is only available in a very few libraries. A lot of time and effort is involved to find and collect all scientific works that are necessary for a specific project.

Today, quick and easy access to digital literature is more and more important to facilitate scientific work. Over the last few years a large number of library resources for taxonomists have been made available online. Since 2007, the Biodiversity Heritage Library (BHL) project is digitising the biodiversity literature holdings of numerous libraries in the UK and USA and making them available on the internet.

Since 2009, the eContentplus project Biodiversity Heritage Library for Europe (BHL-Europe) is developing four different access routes to the biodiversity literature digitised by many European and global partners over the last years. With the Global References Index to Biodiversity (GRIB, http://grib.gbv.de/), BHL-Europe provides in collaboration with the EDIT project a union catalogue of library holdings of many European and US libraries. This will facilitate the search for literature, either digitised or not. This tool will also facilitate the management of digitisation projects all over the world and collect scan request from the scientific community. For an effective access to already digitised literature, BHL-Europe is building a multilingual portal for the scientific community. This portal will also have functionalities currently not available in the BHL portal. The BHL-Europe Portal will, for example, facilitate the search for common and scientific names of biological organisms as well as person names through the implementation of various webservices (e.g. Catalogue of Life, VIAF). The backbone of the portal is a preservation and archive system built on a customised storage infrastructure housed by the Natural History Museum in London. We are currently collecting digitised literature from 27 different content providers on our servers, including all the content that is currently available through the BHL portal (http://www.biodiversitylibrary.org). In order to serve also a broader audience, the digitised literature available by BHL-Europe is also accessible by Europeana, Europe’s digital library, archive and museum (http://www.europeana.eu/).

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Chris Lyal
Digitising legacy taxonomic literature: processes, products and using the output 

Department of Entomology, Natural History Museum. London
Email: c.lyal@nhm.ac.uk

To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original ñ the output has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, for many scientific papers the means of indexing and locating them is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising names is still relatively poor, peopleís ability to use search engines effectively is mixed, and many papers cannot be directly searched. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original paper and extract target content manually. This opens the door to dynamic linking of new content with extant systems ñ automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children instantly accessible with a single search, comparison of classifications used in different publications, and so on. The means to do this is currently marking up content into XML, the more atomised the mark-up the greater the possibilities for data retrieval and integration. Mark-up requires XML that accommodates the required content elements and is interoperable with other XML schemas, and there are now several written to do this, particularly TaxPub, taxonX and taXMLit, the last of these being the most atomised. Building on earlier systems for mark-up of legacy literature ViBRANT is developing a new workflow and seeking to increase the automated component of the process. Manual and automatic data and information retrieval is demonstrated by projects such as INOTAXA and Plazi. As we move to creating and using taxonomic products through the power of the internet, we need to ensure the output, while satisfying the requirements of the Code, is fit for purpose in the future.

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Event Date: 28 October 2011
Flett Lecture Theatre
Natural History Museum

Anchoring Biodiversity Information:

From Sherborn to the 21st century and beyond

Nigel Robinson
Sherborn’s Index Animalium integration into ION: access to all 

Zoological Record Director, York Operations Thomson Reuters
Email: nigel.robinson@thomsonreuters.com

As a list of zoological taxonomic names used in the scientific literature, the Index to Organism Names (ION) has provided a reference service to researchers for a number of years, based on the content of international publications analysed for inclusion in Zoological RecordÆ.  However, this content is limited to names included in Zoological Record (1864-present). This project extends the names database and brings new opportunities through collaboration between the Smithsonian Institute, Thomson Reuters, and the Biodiversity Heritage Library to provide a more complete resource to compliment other taxonomic names services.

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