Name Registration: One Less Impediment to Taxonomy

Jim Woolley

Texas A&M UniversityRevolutionising taxonomy through an open-access web-register for

animal names and descriptions

ESA Program Symposium

December, 2005

• Collecting

• Preparation of specimens

• Study of specimens

• Revisions, monographs

• Access to literature

• New Technologies

A Renaissance in Systematics

• Digital technologies have changed all the rules

• Taxonomic collections, literature, expertise, digital libraries, virtual monographs should become a distributed, virtual research tool and education resource.

New Technologies for Taxonomists

• Web-based - Web provides a single, global point of access

• Distributed - eg > 350 web sites for Lepidoptera

• Authoritative - need Electronic Catalog of Life

• Accessible to multiple audiences

• Relevant to societal concerns - natural resource management, invasive species, agriculture, medicine etc.

• Taxonomic publications should not be end points, but “version control” devices

The New Taxonomy

(thanks to Malcolm Scoble, Natural History Museum)

• Lack of funding• Funding for taxonomy is insufficient• Most funding for systematics is devoted to constructing molecular phylogenies, not taxonomy

• Not enough taxonomists• Taxonomy is too difficult to learn and to practice

•Requires years to accumulate literature, specimens etc.• Critical resources are scattered and available to only a few

workers•Literature•Museum specimens

• There are few centralized sources of information

Impediments to The New Taxonomy

•Planetary Biodiversity Inventory (PBI)

• Global assaults on taxonomy of major groups

•RevSys - Revisionary Syntheses in Systematics

• Species-level treatments

• Develop new methodologies for revisionary work

•PEET - Partnerships for Enhanced expertise in Taxonomy

• Long-term monographic research

• Major training component

NSF has recognized the funding issues

ZOOBANK

• ZOOBANK will go a long way towards providing centralized sources of information

• We may quibble about the details and plan for implementation

• But this is really essential for progress

“The Atkins Report”

• Daniel Atkins, University of Michigan

• 8 other authors from academia and industry

Atkins Report

• “The Panel’s overarching finding is that a new age has dawned in scientific and engineering research,

• pushed by continuing progress in computing, information, and communication technology,

• and pulled by expanding complexity, scope and scale of today’s challenges”

Atkins Report

• The capacity of this technology has crossed thresholds that now make possible a comprehensive “cyberinfrastructure”

• on which to build new types of scientific and engineering knowledge environments and organizations,

• and to pursue research in new ways and with increased efficiency

Atkins Report

• use cyberinfrastructure to build more ubiquitous, comprehensive digital environments

• interactive and functionally complete for research communities in terms of people, data, information, tools, and instruments

• operate at unprecedented levels of computational, storage, and data transfer capacity

Cyberinfrastructure will include

• grids of computational centers, some with computing power second to none

• comprehensive libraries of digital objects including programs and literature

• multidisciplinary, well-curated, federated collections of scientific data

• thousands of on-line instruments and sensor arrays,• convenient software toolkits for resource, discovery,

modeling and interactive visualization• ability to collaborate with physically distributed teams of

people using all of these capabilities

Atkins Report

• many contemporary projects require effective federations

• distributed resources (data and facilities)

• distributed, multidisciplinary expertise

• (harvest of legacy data)

Virtual Science Communities

• National Ecological Observatory Network (NEON)

• National Virtual Observatory (NVO)• Space Physics and Aeronomy Research

Collaboratory (SPARC)• Grid Physics Network (GriPhyN)• Biomedical Informatics Research Network

(BIRN)• National Science Digital Library (NDSL)

• Workshop to Produce Decadal Vision for Taxonomy and Natural History Collections, Gainesville, November 2003

• Development of a National Systematics Infrastructure: A Virtual Instrument for the 21st Century, New York Botanical Garden, December 2003

• Workshop to Establish a Comprehensive Database for Plant Systematics, Gainesville, December 2003

• Biological Image Database Workshop, Tallahassee, Florida, September 2004

Recent Workshops Sponsored by NSF

A BIODIVERSITY OBSERVATORY

LINNÉ

LEGACY INFRASTRUCTURE NETWORK FOR NATURAL ENVIRONMENTS

Each collection or taxonomic research facility is potentially a node of a NATIONAL CYBERLABORATORY

•Each node will contribute its own particular strengths to the network

•(e.g., taxonomic or geographic uniqueness, unique instrumentation)

•The resources of each node will be available to all nodes

•(e.g., specimens, images, literature, DNA data)

Implementation of LINNE will

• Modernize the national infrastructure for taxonomic research– high resolution 2D and 3D surface and internal scanning using computer

tomography– Remote-controlled, digital microscopy– Comprehensive digital libraries

• Modernize collection facilities• Provide comprehensive access to taxonomic and

collections information, worldwide• Provide new tools for education and outreach

Virtual Research Platform

• Remove the ‘taxonomic impediment’

• See across historical and geological time, continents and seas, species and clades, ontogenetic paths & ecosystems.

The Big Questions

• What are earth’s species, and how do they vary?

• How are species distributed in geographical and ecological space?

• What is the history of life on Earth, and how are species interrelated?

• How has biological diversity changed through space and time?

• What is the history of character transformations?

• What factors lead to speciation, dispersal and extinction?

Is the vision impossibly grand?

• Virtually all of the necessary technology is is already in place or will be in the next few years

• Many national and international activities are already underway

Key Activities Related to Collections and Bioinformatics

• SEEK •NESCent•CIPRES•Species Analyst•MaNIS•HerpNET•FishNetII•ORNIS•ENHSIN•BioCASE•BioCISE•MaPSTEDI

•DiGIR•Specify•BioGeoMancer•Species2000

•ITIS•TDWG•OBIS•uBIO•IPNI

•DRSC•Index Herbariorum

•PBI•ERIN•CONABIO•CBIN•CHM•WDC•IABIN•PBIF•CBOL•MorphBank•MorphoBank•Digimorph•and ???

•Zoobank•NBII •GBIF•Synthesys•EBNI•CHRONOS•NEON•NSCA

• Linking databases, informatics products and analytical tools for data sharing among governmental agencies, NGO’s, academic institutions and industry

• At intersection of science, policy and applications• 47 member countries• Access - move data not people• Diversity - access to all types of data• Taxonomic Standards - need Electronic Catalog of Life• Data Quality - data cleaning tools• Interoperability - global identifiers for specimens, collections, etc.• Working Together - campaign approach to setting priorities

• GBIF can provide critical components of cyber-framework for LINNE

• In exchange, LINNE will provide data to GBIF

• 20 European Natural History Museums and Botanic Gardens

• FPVI European-funded Integrated Infrastructure Initiative Grant

• Create integrated European infrastructure for researchers in the natural sciences

• Started 2004 - five year project• 20 institutions• 11 national Taxonomic Facilities• Part 1 - Access - enables European researchers to access

earth and life science collections, facilities and taxonomic expertise

• Part 2 - Networking Activities• Complementarity - bring together information on collections and

expertise• Standards - long term preservation of collections• Databases - coordinate development of collection databases• New Collections - e.g. tissue samples• New Methodologies - e.g. computerized tomography

• European contribution to GBIF• Network for digitization and sharing of biodiversity data• Enhance communication and cooperation among GBIF nodes,

biodiversity institutes and related initiatives• 69 Partners• 26 Countries• Including all major natural history collections and systematics institutes

European Network for Biodiversity Information

• CHRONOS • Earth Science Community• Dynamic, interactive and time-calibrated network of

databases and visualization and analytical methodologies for sedimentary geology and paleobiology

• NEON - National Ecological Observatory Network– LINNE will provide critical baseline information for ecological

research

– NEON will provide resources for acquiring data and voucher specimens and improving collections infrastructure at selected locations

• Provides ideal communications forum and network to collections nationwide

• Provides presence in Washington D.C.

• Provides mechanism for tactical response if collections are threatened

The Foundations are Already in Place

• The challenge is not to invent all of the necessary components de novo

• But rather, to identify what is already there • Identify and implement the new cyberinfrastructure• And integrate these components into an operational

system• To do this will require that we establish a common

vision and research agenda• And that we work as a community, worldwide to

achieve it

This will require a change in our scientific culture

• Integrated, “big-science” approach• Need to identify common goals and work together• Other communities have done this, but there were

some tough transitions• For example, particle physicists had terrible

problems with career recognition and rewards with

the switch to a big science paradigm

Challenges

• It will cost billions of dollars• It will require Congressional action• It will require state action• It will require a unified user community• It will take many years• It will not be easy

LINNE Steering Committee

• Hank Bart, Jr., Tulane University• Reed Beaman, Yale University• Lynn Bohs, University of Utah• Brandi Coyner, Oklahoma State University (student)• Linda Deck, Idaho State Museum• Vicki Funk, Smithsonian Institution • Diana Lipscomb, George Washington University• Mike Mares, University of Oklahoma (co-chair)• Larry Page, Florida Museum of Natural History• Alan Prather, Michigan State University• Jan and Dennis Stevenson, New York Botanical

Garden• Quentin Wheeler, Natural History Museum• Jim Woolley, Texas A&M University (co-chair)

LINNE WILL PRESERVE OUR HERITAGE AND REVITALIZE

TAXONOMY

LINNE WILL BE THE MOST IMPORTANT NEW TOOL

AVAILABLE TO BIOLOGISTS IN THE 21ST CENTURY

Thank you