Zoo Bank Talk Ms Ccourse09 Compressed Test

LINNAEUS LINNAEUS

–– SHERBORNSHERBORN

-- ZOOBANKZOOBANKEllinor Michel1,2 ,Richard Pyle3 &

Andrew Polaszek2

1 1 Int’l Commission for Zoological NomenclatureInt’l Commission for Zoological Nomenclature 22The Natural History Museum, London UK The Natural History Museum, London UK 33The Bishop Museum, Honolulu, HI, USA The Bishop Museum, Honolulu, HI, USA

THE LINNAEAN ENTERPRISE

(E.O. Wilson) ________

the task of identifying all of

Earth’s biodiversity

“Setting all the reservations and biases aside, the total number of living organisms that have received Latin binomial names is currently around 1.5 million or so. Amazingly, there is as yet no centralized computer index of these recorded species. It says a

lot about intellectual fashions, and about our values, that we have a computerized catalogue entry, along with many details, for each of several million books in the Library of Congress but

no such catalogue for the living species we share our world with. Such a catalogue, with appropriately coded information about

the habitat, geographical distribution, and characteristic abundance of the species in question (no matter how rough or impressionistic), would cost orders of magnitude less money than sequencing the human genome; I do not believe such a project is orders of magnitude less important. Without such a

factual catalogue, it is hard to unravel the patterns and processes that determine the biotic diversity of our planet.”

Robert M. May,

1988, Science. “How many species are there on Earth?”

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COMPLETING THE LINNAEAN

ENTERPRISE________________________

Systema Naturae

Zoological Record

Nomenclator Zoologicus / Nomenclator Animalium

Index Animalium

Encyclopedia of Life / Catalogue of Life

ZooBank

Carolus Linnaeus 1707-1778

The first attempt to develop a catalogue of the Earth’s species

Laid the foundation for binomial nomenclatureProvided intellectual structure for how we see the living world


ENTERPRISE________________________

Systema Naturae

Zoological Record


Index Animalium


ZooBank

Albrecht Günther 1830-1914 Founder and Editor

Zoological Record

A catalogue of all publications on zoology

Integrating disparate scientific practice

A catalogue of all publications on zoology

Integrating disparate zoological knowledge

Continues as pivotal reference resource online today


ENTERPRISE________________________

Systema Naturae

Zoological Record


Index Animalium


ZooBank

Franz Eilhard von Schulze 1840-1921

Nomenclator Animalium 1926-1954 (1758-1940)

Sheffield Airey Neave 1879-1961

Nomenclator Zoologicus1939-2004 (1758-2004)

Available as reference resource online today


ENTERPRISE________________________

Systema Naturae

Zoological Record

Nomenclator Zoologicus / Nomenclator

Animalium

Index Animalium


ZooBank

Charles Davies Sherborn 1861-1942

Index Animalium

1902 (1758-1800)1922-1933 (1801-1850)

11 volumes, 9000 pages

‘Father of Biodiversity Informatics’


ENTERPRISE________________________

Systema Naturae

Zoological Record


Animalium

Index Animalium


ZooBank

‘Major Habitats’ in the Ecosystems of Websites

Encyclopedia of Life ….makes all key information about all life on Earth accessible to anyone, anywhere in the world.’ …….a constantly evolving encyclopedia that lives on the internet, aggregating virtually all known data about every living species.

Catalogue of Life….a validated checklist of all the world's species (plants, animals, fungi and microbes). …from an array of global species databases covering each of the major groups of organisms.….a "federation" of database organisations


ENTERPRISE________________________

Systema Naturae

Zoological Record


Animalium

Index Animalium


ZooBank

ZooBank – the concept•Names are the logical anchor for knowledge Names are the logical anchor for knowledge for most biologists and other stakeholdersfor most biologists and other stakeholders

•A web registry for all scientific names of animals

•An AUTHORITY for zoological nomenclature

• A HUB or backbone, providing a dynamic web nomenclature for all other web-bioinformatics systems

•The International Commission of Zoological Nomenclature (ICZN) is the voluntary, authoritative body that has taken responsibility for development of a registry for animal names (Protists-Chordates, extant and fossil)

www.zoobank.orgwww.iczn.org

http://www.zoobank.org/



http://www.iczn.org/



ZooBank – the users•Open access for scientific community use

OA = free, immediate, permanent, online access, for any user, web-wide, to digital scientific and scholarly material

•Taxonomists as ZooBank builders, revisers and quality controllers

•Additional stakeholders run the range from ecologists, conservationists, medical and veterinary workers, planners, policy makers, lawyers, even to customs enforcers

•‘One world’ - access to nomenclature data for stakeholders in under-resourced situations (e.g. emerging economies, ‘non-professional’ taxonomists)

Formally proposed: Nature 437: 477 (22 September 2005)

Co-authurs:Donat Agosti Miguel Alonso-ZarazagaGeorge BeccaloniPer de Place BjørnPhilippe BouchetDenis BrothersNeal EvenhuisGathorne CranbrookCharles GodfrayNorm JohnsonFrank KrellDiana LipscombChris Lyal Georgina MaceShunsuke MawatariScott Miller Sandro Minelli Solene MorrisPeter Ng David PattersonRich PyleNigel RobinsonLucie Rogo Janice TaverneChris Thompson Jan van TolQuentin WheelerEd Wilson

ZooBank

Why do we need it?Why do we need it?•Accessibility of animal names & nomenclatural actsAccessibility of animal names & nomenclatural acts

ZooBank


• Descriptions and nomenclatural acts “hidden” in journals Descriptions and nomenclatural acts “hidden” in journals and other publications (1,100 different journals for and other publications (1,100 different journals for entomology alone; monographs, CDs; Bouchet reported 2/3 entomology alone; monographs, CDs; Bouchet reported 2/3 of newly described marine species published in unlisted of newly described marine species published in unlisted sources)sources)

ZooBank



• a web search alone is not enough to do robust taxonomic a web search alone is not enough to do robust taxonomic referencing, but increasingly ‘if its not on the web it doesn’t referencing, but increasingly ‘if its not on the web it doesn’t exist’exist’

ZooBank

Why do we need it?Why do we need it?


• a web search alone is not enough to do robust taxonomic a web search alone is not enough to do robust taxonomic referencing, but increasingly ‘if its not on the web it doesn’t referencing, but increasingly ‘if its not on the web it doesn’t exist’exist’

• Streamlining taxonomic work as taxonomists become rarerStreamlining taxonomic work as taxonomists become rarer

•Accessibility of animal names & nomenclatural actsAccessibility of animal names & nomenclatural acts

ZooBank


• Descriptions and nomenclatural acts “hidden” in journals and Descriptions and nomenclatural acts “hidden” in journals and other publications (1,100 different journals for entomology other publications (1,100 different journals for entomology alone; monographs, CDs; Bouchet reported 2/3 of newly alone; monographs, CDs; Bouchet reported 2/3 of newly described marine species published in unlisted sources)described marine species published in unlisted sources)

• A web search alone is not enough to do robust taxonomic A web search alone is not enough to do robust taxonomic referencing, but increasingly ‘if its not on the web it doesn’t referencing, but increasingly ‘if its not on the web it doesn’t exist’exist’

• Streamlining taxonomic work as taxonomists become rarerStreamlining taxonomic work as taxonomists become rarer

• Nomenclatural data will be freely available and provide the Nomenclatural data will be freely available and provide the signposts to published taxonomic works (hub)signposts to published taxonomic works (hub)

ZooBank

Why do we need it?Why do we need it?• Accessibility of animal names & nomenclatural Accessibility of animal names & nomenclatural actsacts • Completeness of the animal species Completeness of the animal species databasedatabase

Goal:Goal: Primary source of authoritative animal names & Primary source of authoritative animal names &

datadata

ZooBank

Why do we need it?Why do we need it?•Accessibility of animal names & nomenclatural Accessibility of animal names & nomenclatural actsacts• Completeness of the animal species Completeness of the animal species databasedatabase

• Need list of Need list of allall available names (whether in current available names (whether in current use or not) to provide stability despite taxonomic use or not) to provide stability despite taxonomic changeschanges

ZooBank

Why do we need it?Why do we need it?•Accessibility of animal names & nomenclatural Accessibility of animal names & nomenclatural actsacts• Completeness of the animal species Completeness of the animal species databasedatabase

• Need list of Need list of allall available names (whether in current available names (whether in current use or not) to provide stability despite taxonomic use or not) to provide stability despite taxonomic changeschanges

• Taxonomy is a science of alternative hypotheses, Taxonomy is a science of alternative hypotheses, tested with various kinds of data (molecular, tested with various kinds of data (molecular, morphological, developmental, ecological) and morphological, developmental, ecological) and interpreted with various philosophies (e.g. interpreted with various philosophies (e.g. recognizing only monophyloletic taxa, or recognizing only monophyloletic taxa, or paraphyletic taxa)paraphyletic taxa)

Nomenclature & Taxonomy

A B C D E F G H I

species

genusEus

Taxonomist 3EusAus

Taxonomist 2 EusCusgenera

Taxonomist 1

Type species

‘A very good tree’

Taxonomist 4Cus CusEus

NOTNomenclature provides the available names for taxonomy


Nomenclature Taxonomy

Type specimen


Nomenclature Taxonomy

Type specimen

Available vs. Valid Names

Nomenclaturally ‘legal’ -may or may not Nomenclaturally ‘legal’ -may or may not be in current usebe in current use

In current use indicating a recognized taxon, ‘taxonomically valid’

Available vs. Valid Names

Nomenclaturally ‘legal’ -may or may not Nomenclaturally ‘legal’ -may or may not be in current usebe in current use

In current use indicating a recognized taxon, ‘taxonomically valid’

ZooBank

Why do we need it?Why do we need it?• Accessibility of animal names & Accessibility of animal names & nomenclatural actsnomenclatural acts• Completeness of the animal species Completeness of the animal species databasedatabase

• Need list of Need list of allall available names (whether in current available names (whether in current use or not) provided to provide stability despite use or not) provided to provide stability despite taxonomic changestaxonomic changes

• Remains current - Registration as a mandatory Remains current - Registration as a mandatory requirement for availability of new names requirement for availability of new names (proposed for revised Code), coupled with (proposed for revised Code), coupled with retrospective registration of existing names, retrospective registration of existing names, ensures completeness of the resultant ensures completeness of the resultant register/databaseregister/database

ZooBank

Why do we need it?Why do we need it?•Accessibility of animal names & nomenclatural Accessibility of animal names & nomenclatural acts acts • Completeness of the animal species databaseCompleteness of the animal species database•‘‘Clean Data’ - Accuracy Clean Data’ - Accuracy

•Indicating correct spellings, ensuring most Indicating correct spellings, ensuring most effective data retrievaleffective data retrieval

nomenclature of Giardia lamblia complex

Unverified names from Zoological Record Unverified names from Zoological Record (in prototype ZooBank)(in prototype ZooBank)

7 variants:lablialambialambilalamblalamblialambllialamlia

Unverified names from Zoological Record Unverified names from Zoological Record (in prototype ZooBank)(in prototype ZooBank)

ZooBank



•Code-compliance of all names and actsCode-compliance of all names and acts

Code-compliance of all names and actsCode-compliance of all names and acts

flowchart from ‘The Code’, v4, 1999, p.123

Automatic Automatic checkingchecking• Prevention of Prevention of homonymyhomonymy

• Stabilisation of Stabilisation of spellingspelling

• Fixing genders Fixing genders and stemsand stems

• Stability in Stability in gender gender agreementagreement

relieving the burden of pedantry

ZooBank



•Code-compliance of all names and actsCode-compliance of all names and acts

•ultimately self-correcting as community ultimately self-correcting as community participation increasesparticipation increases

ZooBank

Why do we need it?Why do we need it?•Accessibility of animal names & nomenclatural Accessibility of animal names & nomenclatural acts acts • Completeness of the animal species databaseCompleteness of the animal species database•‘‘Clean Data’ - AccuracyClean Data’ - Accuracy• Quality control - ensuring the ‘gold Quality control - ensuring the ‘gold standard’ of good science and type standard’ of good science and type specimens to back up namesspecimens to back up names

Quality control - type specimens

•For stability a name needs a reference standard (type)

• No absolute requirement for type specimens under current Code

• Surrogates (e.g. images, including DNA sequences or trace files) are permitted with justification, where type specimens are “illegal unethical or impossible” under Code Article 73.1.4

Does this affect nomenclatural stability?

ZooBank

Why do we need it?Why do we need it?•Accessibility of animal names & nomenclatural Accessibility of animal names & nomenclatural actsacts• Completeness of the animal species databaseCompleteness of the animal species database• ‘ ‘Clean data’- AccuracyClean data’- Accuracy• Quality controlQuality control• Facilitation of “true” web taxonomyFacilitation of “true” web taxonomy•An alerting service can be provided for nomenclatural An alerting service can be provided for nomenclatural changes for taxa of interest to the userchanges for taxa of interest to the user

Web-based taxonomy

Relational databasing capacity

DNA taxonomy & barcodes(GenBank)

Web-based taxonomy

Relational databasing capacity

Imaging & quantitative morphometrics(MorphBank)

Web-based taxonomy

Wheeler, Q. 2008

ZooBank



ZooBank

Why do we need it?Why do we need it?•Accessibility of animal names & nomenclatural Accessibility of animal names & nomenclatural actsacts• Completeness of the animal species databaseCompleteness of the animal species database• ‘ ‘Clean data’- AccuracyClean data’- Accuracy• Quality controlQuality control• Facilitation of “true” web taxonomyFacilitation of “true” web taxonomy

• ZooBank/ICZN is NOMENCLATURAL registration only, but should ZooBank/ICZN is NOMENCLATURAL registration only, but should become integral to taxonomic practicebecome integral to taxonomic practice

• Web(-only) taxonomy in the absence of a registration system is Web(-only) taxonomy in the absence of a registration system is a recipe for increased chaosa recipe for increased chaos

ZooBank

Why do we need it?Why do we need it?•““Visibility” of animal names and Visibility” of animal names and nomenclatural acts nomenclatural acts • Completeness of the animal species Completeness of the animal species databasedatabase• Code-compliance of all names and actsCode-compliance of all names and acts• Quality controlQuality control• Facilitation of “true” web taxonomyFacilitation of “true” web taxonomy• Signposting to available descriptions Signposting to available descriptions (references and links to online (references and links to online publications)publications)

ZooBank: Scope of RegistryZooBank: Scope of Registry

Nomenclatural Acts- Acts establishing new species-, genus- and

family-group names in Zoology- Lectotypifications/Neotypifications, Emendations,

First reviser, etc.- Higher-rank names? Published misspellings?

New combinations?

Nomenclatural Acts- Acts establishing new species-, genus- and

family-group names in Zoology- Lectotypifications/Neotypifications, Emendations,

First reviser, etc.- Higher-rank names? Published misspellings?

New combinations?

Publications- As defined in Article 8 of the ICZN Code.

Publications- As defined in Article 8 of the ICZN Code.

Authors- As authors of registered publications- ZooBank content providers

Authors- As authors of registered publications- ZooBank content providers

Type Specimens- Integral to nomenclature; cross-linked to Museums

Type Specimens- Integral to nomenclature; cross-linked to Museums

ZooBank: Registry IdentifiersZooBank: Registry Identifiers

Globally Unique Identifiers (GUIDs)- Names alone are not unique (i.e., homonymy)- Author names inconsistently formatted

Globally Unique Identifiers (GUIDs)- Names alone are not unique (i.e., homonymy)- Author names inconsistently formatted

LinnaeusLinnéLinn.L.

LinnaeusLinnéLinn.L.

- Identifiers need to be permanent and unambiguous- Identifiers need to be permanent and unambiguous

Life Science Identifiers (LSIDs)- Originally developed by IBM- Adopted and recommended by TDWG, GBIF, others- Non-centralized issuance, no cost to issue- Open-source software in development & available

Life Science Identifiers (LSIDs)- Originally developed by IBM- Adopted and recommended by TDWG, GBIF, others- Non-centralized issuance, no cost to issue- Open-source software in development & available

Cuvier and ValenciennesCuvier & ValenciennesC. & V.C&V

Cuvier and ValenciennesCuvier & ValenciennesC. & V.C&V

Nomenclatural Act: Chromis abyssusurn:lsid:zoobank.org:act:8BDC0735-FEA4-4298-83FA-D04F67C3FBEC



Publication: Pyle et al., 2008urn:lsid:zoobank.org:pub:68376390-7809-46FF-9EC4-1371B4AAD0FF


Author: Richard L. Pyleurn:lsid:zoobank.org:author:8C466CBE-3F7D-4DC9-8CBD-26DD3F57E212


Type Specimen: BPBM 40861urn:lsid:zoobank.org:specimen:FDE70A5C-59C3-407B-B9A6-5A9A2DA14BD1





Parts of an LSID- URN and LSID identification

Parts of an LSID- URN and LSID identification
















Parts of an LSID- URN and LSID identification- Authority identification

Parts of an LSID- URN and LSID identification- Authority identification










Parts of an LSID- URN and LSID identification- Authority identification- Namespace identification

Parts of an LSID- URN and LSID identification- Authority identification- Namespace identification










Parts of an LSID- URN and LSID identification- Authority identification- Namespace identification- Object identification

Parts of an LSID- URN and LSID identification- Authority identification- Namespace identification- Object identification




Why UUIDs?- ISO standard, widely adopted (Windows, Mac, Linux)- GUIDs unto themselves, generated locally- Not self-resolving, but can be “wrapped” within a

resolution protocol (LSID, Handle, DOI, etc.)- INTENDED FOR COMPUTERS, NOT HUMANS!

Why UUIDs?- ISO standard, widely adopted (Windows, Mac, Linux)- GUIDs unto themselves, generated locally- Not self-resolving, but can be “wrapped” within a

resolution protocol (LSID, Handle, DOI, etc.)- INTENDED FOR COMPUTERS, NOT HUMANS!










Why UUIDs?

“ONE TRILLION UUIDs would have to be createdEVERY NANOSECOND for TEN BILLION years to exhaust the number of UUIDs”

Why UUIDs?

“ONE TRILLION UUIDs would have to be createdEVERY NANOSECOND for TEN BILLION years to exhaust the number of UUIDs”







ZooBank: ContentZooBank: Content

Launch- 1 January 2008, 00:00:00GMT- 250th Anniversary of Systema Naturae 10th Edition

(per ICZN Code Art. 3)

Launch- 1 January 2008, 00:00:00GMT- 250th Anniversary of Systema Naturae 10th Edition

(per ICZN Code Art. 3)

Retrospective Content- 4,819 Names established in Linnaeus, 1758.

Retrospective Content- 4,819 Names established in Linnaeus, 1758.

Prospective Content- 5 New species of Chromis (Zootaxa)- Johnson et al.; Deans & Kawada (Zootaxa)- Fisher & Smith (PLoS ONE)- Assmann et al.; Aken'Ova et al.;

Hinojosa-Díaz (ZooKeys)

Prospective Content- 5 New species of Chromis (Zootaxa)- Johnson et al.; Deans & Kawada (Zootaxa)- Fisher & Smith (PLoS ONE)- Assmann et al.; Aken'Ova et al.;

Hinojosa-Díaz (ZooKeys)

Pacific Abyss - 3 part series on BBC in August ‘08





January 1, 2008January 1, 2008January 1, 1758January 1, 1758

ZooBank

Logistics of populating ZooBank•16,000-20,000 new animal species 16,000-20,000 new animal species described each yeardescribed each year•1.7 million described extant species1.7 million described extant species•5-50 million estimated total extant species 5-50 million estimated total extant species (R. May, E.O. Wilson, T. Erwin)(R. May, E.O. Wilson, T. Erwin)•Fossil species multiply this by orders of Fossil species multiply this by orders of magnitudemagnitude

Logistics of populating ZooBank•16,000-20,000 new animal species 16,000-20,000 new animal species described each yeardescribed each year•1.7 million described extant species1.7 million described extant species•5-50 million estimated total extant species 5-50 million estimated total extant species (R. May, E.O. Wilson, T. Erwin)(R. May, E.O. Wilson, T. Erwin)•Fossil species multiply this by orders of Fossil species multiply this by orders of magnitudemagnitude

•Strategic approaches requiredStrategic approaches required

ZooBank•Enables true web taxonomyEnables true web taxonomy

•Works synergistically with other Works synergistically with other cybertaxonomic resourcescybertaxonomic resources

•Streamlines and democratises taxonomic Streamlines and democratises taxonomic processprocess

•An enabling tool for Code-compliance in An enabling tool for Code-compliance in nomenclaturenomenclature

•ZooBank will be both HUB and AUTHORITY on ZooBank will be both HUB and AUTHORITY on animal namesanimal names

• Natural History Museum,

London

• Bishop Museum, Hawaii

• Wellcome Trust

• Taylor & Francis

• Thomson Scientific /

Zoological Record

• GBIF & TDWG

• The Commissioners &

Trustees of ICZN / ITZN

THANKS TO

Quentin Wheeler - Int’l Institute for Species ExplorationQuentin Wheeler - Int’l Institute for Species Exploration

Top 10 Species of the YearTop 10 Species of the Year

http://www.species.asu.edu/Top10

Holotype of Holotype of Homo sapiensHomo sapiens??

Zoo Bank Talk Ms Ccourse09 Compressed Test

Technology

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