Zoo Bank Talk Ms Ccourse09 Compressed Test

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  • solves a longstandding impediment to getting good taxonomic references, addresses a growing problem for science in the cyber-age, is proactive in bringing taxonomy to users
  • solves a longstandding impediment to getting good taxonomic references, addresses a growing problem for science in the cyber-age, is proactive in bringing taxonomy to users
  • solves a longstandding impediment to getting good taxonomic references, addresses a growing problem for science in the cyber-age, is proactive in bringing taxonomy to users
  • solves a longstandding impediment to getting good taxonomic references, addresses a growing problem for science in the cyber-age, is proactive in bringing taxonomy to users
  • An important human disease protist, listed on the Index to Organism Names (ION) (interfaced with ZooBank) with 7 different species names. No indication as to which are ‘good’names as in: valid, available,
  • type is the objective link between the name and taxonomic concept
  • Zoo Bank Talk Ms Ccourse09 Compressed Test

    1. 1. LINNAEUS – SHERBORN - ZOOBANK Ellinor Michel 1,2 , Richard Pyle 3 & Andrew Polaszek 2 1 Int’l Commission for Zoological Nomenclature 2 The Natural History Museum, London UK 3 The Bishop Museum, Honolulu, HI, USA
    2. 2. THE LINNAEAN ENTERPRISE (E.O. Wilson) ________ the task of identifying all of Earth’s biodiversity
    3. 3. “ 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?”
    4. 4. COMPLETING THE LINNAEAN ENTERPRISE ________________________ Systema Naturae   Zoological Record   Nomenclator Zoologicus / Nomenclator Animalium Index Animalium   Encyclopedia of Life / Catalogue of Life   ZooBank
    5. 5. COMPLETING THE LINNAEAN ENTERPRISE ________________________ Systema Naturae   Zoological Record   Nomenclator Zoologicus / Nomenclator Animalium Index Animalium   Encyclopedia of Life / Catalogue of Life   ZooBank
    6. 6. Carolus Linnaeus 1707-1778 The first attempt to develop a catalogue of the Earth’s species Laid the foundation for binomial nomenclature Provided intellectual structure for how we see the living world
    7. 7. COMPLETING THE LINNAEAN ENTERPRISE ________________________ Systema Naturae   Zoological Record   Nomenclator Zoologicus / Nomenclator Animalium Index Animalium   Encyclopedia of Life / Catalogue of Life   ZooBank
    8. 8. Albrecht Günther 1830-1914 Founder and Editor Zoological Record A catalogue of all publications on zoology Integrating disparate scientific practice
    9. 9. A catalogue of all publications on zoology Integrating disparate zoological knowledge Continues as pivotal reference resource online today
    10. 10. COMPLETING THE LINNAEAN ENTERPRISE ________________________ Systema Naturae   Zoological Record   Nomenclator Zoologicus / Nomenclator Animalium Index Animalium   Encyclopedia of Life / Catalogue of Life   ZooBank
    11. 11. Franz Eilhard von Schulze 1840-1921 Nomenclator Animalium 1926-1954 (1758-1940) Sheffield Airey Neave 1879-1961 Nomenclator Zoologicus 1939-2004 (1758-2004) Available as reference resource online today
    12. 13. COMPLETING THE LINNAEAN ENTERPRISE ________________________ Systema Naturae   Zoological Record   Nomenclator Zoologicus / Nomenclator Animalium Index Animalium   Encyclopedia of Life / Catalogue of Life   ZooBank
    13. 14. Charles Davies Sherborn 1861-1942 Index Animalium 1902 (1758-1800) 1922-1933 (1801-1850) 11 volumes, 9000 pages ‘ Father of Biodiversity Informatics’
    14. 16. COMPLETING THE LINNAEAN ENTERPRISE ________________________ Systema Naturae   Zoological Record   Nomenclator Zoologicus / Nomenclator Animalium Index Animalium   Encyclopedia of Life / Catalogue of Life   ZooBank
    15. 17. ‘ 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
    16. 18. COMPLETING THE LINNAEAN ENTERPRISE ________________________ Systema Naturae   Zoological Record   Nomenclator Zoologicus / Nomenclator Animalium Index Animalium   Encyclopedia of Life / Catalogue of Life   ZooBank
    17. 19. ZooBank – the concept <ul><li>Names are the logical anchor for knowledge for most biologists and other stakeholders </li></ul><ul><li>A web registry for all scientific names of animals </li></ul><ul><li>An AUTHORITY for zoological nomenclature </li></ul><ul><li>A HUB or backbone, providing a dynamic web nomenclature for all other web-bioinformatics systems </li></ul><ul><li>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) </li></ul>www. zoobank .org www. iczn .org
    18. 20. ZooBank – the users <ul><li>Open access for scientific community use </li></ul><ul><ul><ul><li>OA = free, immediate, permanent, online access, for any user, web-wide, to digital scientific and scholarly material </li></ul></ul></ul><ul><li>Taxonomists as ZooBank builders, revisers and quality controllers </li></ul><ul><li>Additional stakeholders run the range from ecologists, conservationists, medical and veterinary workers, planners, policy makers, lawyers, even to customs enforcers </li></ul><ul><li>‘ One world’ - access to nomenclature data for stakeholders in under-resourced situations (e.g. emerging economies, ‘non-professional’ taxonomists) </li></ul>
    19. 21. F ormally proposed: Nature 437: 477 (22 September 2005) Co-authurs: Donat Agosti Miguel Alonso-Zarazaga George Beccaloni Per de Place Bjørn Philippe Bouchet Denis Brothers Neal Evenhuis Gathorne Cranbrook Charles Godfray Norm Johnson Frank Krell Diana Lipscomb Chris Lyal Georgina Mace Shunsuke Mawatari Scott Miller Sandro Minelli Solene Morris Peter Ng David Patterson Rich Pyle Nigel Robinson Lucie Rogo Janice Taverne Chris Thompson Jan van Tol Quentin Wheeler Ed Wilson
    20. 22. ZooBank Why do we need it?
    21. 23. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul>
    22. 24. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Descriptions and nomenclatural acts “hidden” in journals and other publications (1,100 different journals for entomology alone; monographs, CDs; Bouchet reported 2/3 of newly described marine species published in unlisted sources) </li></ul>
    23. 25. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Descriptions and nomenclatural acts “hidden” in journals and other publications (1,100 different journals for entomology alone; monographs, CDs; Bouchet reported 2/3 of newly described marine species published in unlisted sources) </li></ul><ul><li>a web search alone is not enough to do robust taxonomic referencing, but increasingly ‘if its not on the web it doesn’t exist’ </li></ul>
    24. 26. ZooBank Why do we need it? <ul><li>Descriptions and nomenclatural acts “hidden” in journals and other publications (1,100 different journals for entomology alone; monographs, CDs; Bouchet reported 2/3 of newly described marine species published in unlisted sources) </li></ul><ul><li>a web search alone is not enough to do robust taxonomic referencing, but increasingly ‘if its not on the web it doesn’t exist’ </li></ul><ul><li>Streamlining taxonomic work as taxonomists become rarer </li></ul><ul><li>Accessibility of animal names & nomenclatural acts </li></ul>
    25. 27. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Descriptions and nomenclatural acts “hidden” in journals and other publications (1,100 different journals for entomology alone; monographs, CDs; Bouchet reported 2/3 of newly described marine species published in unlisted sources) </li></ul><ul><li>A web search alone is not enough to do robust taxonomic referencing, but increasingly ‘if its not on the web it doesn’t exist’ </li></ul><ul><li>Streamlining taxonomic work as taxonomists become rarer </li></ul><ul><li>Nomenclatural data will be freely available and provide the signposts to published taxonomic works (hub) </li></ul>
    26. 28. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><li>Goal: </li></ul><ul><li>Primary source of authoritative animal names & data </li></ul>
    27. 29. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><ul><li>Need list of all available names (whether in current use or not) to provide stability despite taxonomic changes </li></ul></ul>
    28. 30. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><ul><li>Need list of all available names (whether in current use or not) to provide stability despite taxonomic changes </li></ul></ul><ul><ul><li>Taxonomy is a science of alternative hypotheses, tested with various kinds of data (molecular, morphological, developmental, ecological) and interpreted with various philosophies (e.g. recognizing only monophyloletic taxa, or paraphyletic taxa) </li></ul></ul>
    29. 31. Nomenclature & Taxonomy A B C D E F G H I species ‘ A very good tree’ Nomenclature provides the available names for taxonomy genus Eus Taxonomist 3 Eus Aus Taxonomist 2 Eus Cus genera Taxonomist 1 Type species Taxonomist 4 Cus Cus Eus NOT
    30. 32. Nomenclature & Taxonomy Nomenclature Taxonomy Type specimen
    31. 33. Nomenclature & Taxonomy Available vs. Valid Names Nomenclaturally ‘legal’ -may or may not be in current use In current use indicating a recognized taxon, ‘taxonomically valid’ Nomenclature Taxonomy Type specimen
    32. 34. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><ul><li>Need list of all available names (whether in current use or not) provided to provide stability despite taxonomic changes </li></ul></ul><ul><ul><li>Remains current - Registration as a mandatory requirement for availability of new names (proposed for revised Code), coupled with retrospective registration of existing names, ensures completeness of the resultant register/database </li></ul></ul>
    33. 35. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><li>‘ Clean Data’ - Accuracy </li></ul><ul><ul><li>Indicating correct spellings, ensuring most effective data retrieval </li></ul></ul>
    34. 36. nomenclature of Giardia lamblia complex
    35. 37. Unverified names from Zoological Record (in prototype ZooBank)
    36. 38. 7 variants: lablia lambia lambila lambla lamblia lambllia lamlia Unverified names from Zoological Record (in prototype ZooBank)
    37. 39. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><li>‘ Clean Data’ - Accuracy </li></ul><ul><ul><li>Indicating correct spellings, ensuring most effective data retrieval </li></ul></ul><ul><ul><li>Code-compliance of all names and acts </li></ul></ul>
    38. 40. Code-compliance of all names and acts <ul><li>Automatic checking </li></ul><ul><ul><li>Prevention of homonymy </li></ul></ul><ul><ul><li>Stabilisation of spelling </li></ul></ul><ul><ul><li>Fixing genders and stems </li></ul></ul><ul><ul><li>Stability in gender agreement </li></ul></ul>relieving the burden of pedantry flowchart from ‘The Code’, v4, 1999, p.123
    39. 41. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><li>‘ Clean Data’ - Accuracy </li></ul><ul><ul><li>Indicating correct spellings, ensuring most effective data retrieval </li></ul></ul><ul><ul><li>Code-compliance of all names and acts </li></ul></ul><ul><ul><li>ultimately self-correcting as community participation increases </li></ul></ul>
    40. 42. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><li>‘ Clean Data’ - Accuracy </li></ul><ul><li>Quality control - ensuring the ‘gold standard’ of good science and type specimens to back up names </li></ul>
    41. 43. Quality control - type specimens <ul><li>For stability a name needs a reference standard (type) </li></ul><ul><li>No absolute requirement for type specimens under current Code </li></ul><ul><li>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 </li></ul>Does this affect nomenclatural stability?
    42. 44. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><li>‘ Clean data’- Accuracy </li></ul><ul><li>Quality control </li></ul><ul><li>Facilitation of “true” web taxonomy </li></ul><ul><li>An alerting service can be provided for nomenclatural changes for taxa of interest to the user </li></ul>
    43. 45. Web-based taxonomy Relational databasing capacity DNA taxonomy & barcodes (GenBank)
    44. 46. Web-based taxonomy Relational databasing capacity Imaging & quantitative morphometrics (MorphBank)
    45. 47. Web-based taxonomy Wheeler, Q. 2008 ZooBank
    46. 48. ZooBank Why do we need it? <ul><li>Accessibility of animal names & nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><li>‘ Clean data’- Accuracy </li></ul><ul><li>Quality control </li></ul><ul><li>Facilitation of “true” web taxonomy </li></ul><ul><ul><li>ZooBank/ICZN is NOMENCLATURAL registration only, but should become integral to taxonomic practice </li></ul></ul><ul><ul><li>Web(-only) taxonomy in the absence of a registration system is a recipe for increased chaos </li></ul></ul>
    47. 49. ZooBank Why do we need it? <ul><li>“ Visibility” of animal names and nomenclatural acts </li></ul><ul><li>Completeness of the animal species database </li></ul><ul><li>Code-compliance of all names and acts </li></ul><ul><li>Quality control </li></ul><ul><li>Facilitation of “true” web taxonomy </li></ul><ul><li>Signposting to available descriptions (references and links to online publications) </li></ul>
    48. 50. ZooBank: 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? Publications - As defined in Article 8 of the ICZN Code. Authors - As authors of registered publications - ZooBank content providers Type Specimens - Integral to nomenclature; cross-linked to Museums
    49. 51. ZooBank: Registry Identifiers Globally Unique Identifiers (GUIDs) - Names alone are not unique (i.e., homonymy) - Author names inconsistently formatted Linnaeus Linn é Linn. L. - 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 Cuvier and Valenciennes Cuvier & Valenciennes C. & V. C&V
    50. 52. Nomenclatural Act: Chromis abyssus urn:lsid:zoobank.org:act:8BDC0735-FEA4-4298-83FA-D04F67C3FBEC ZooBank: Registry Identifiers Publication: Pyle et al. , 2008 urn:lsid:zoobank.org:pub:68376390-7809-46FF-9EC4-1371B4AAD0FF Author: Richard L. Pyle urn:lsid:zoobank.org:author:8C466CBE-3F7D-4DC9-8CBD-26DD3F57E212 Type Specimen: BPBM 40861 urn:lsid:zoobank.org:specimen:FDE70A5C-59C3-407B-B9A6-5A9A2DA14BD1
    51. 53. Nomenclatural Act: Chromis abyssus urn:lsid :zoobank.org:act:8BDC0735-FEA4-4298-83FA-D04F67C3FBEC ZooBank: Registry Identifiers Parts of an LSID - URN and LSID identification Publication: Pyle et al. , 2008 urn:lsid :zoobank.org:pub:68376390-7809-46FF-9EC4-1371B4AAD0FF Author: Richard L. Pyle urn:lsid :zoobank.org:author:8C466CBE-3F7D-4DC9-8CBD-26DD3F57E212 Type Specimen: BPBM 40861 urn:lsid :zoobank.org:specimen:FDE70A5C-59C3-407B-B9A6-5A9A2DA14BD1
    52. 54. Nomenclatural Act: Chromis abyssus urn:lsid: zoobank.org :act:8BDC0735-FEA4-4298-83FA-D04F67C3FBEC ZooBank: Registry Identifiers Publication: Pyle et al. , 2008 urn:lsid: zoobank.org :pub:68376390-7809-46FF-9EC4-1371B4AAD0FF Author: Richard L. Pyle urn:lsid: zoobank.org :author:8C466CBE-3F7D-4DC9-8CBD-26DD3F57E212 Type Specimen: BPBM 40861 urn:lsid: zoobank.org :specimen:FDE70A5C-59C3-407B-B9A6-5A9A2DA14BD1 Parts of an LSID - URN and LSID identification - Authority identification
    53. 55. Nomenclatural Act: Chromis abyssus urn:lsid:zoobank.org: act :8BDC0735-FEA4-4298-83FA-D04F67C3FBEC ZooBank: Registry Identifiers Publication: Pyle et al. , 2008 urn:lsid:zoobank.org: pub :68376390-7809-46FF-9EC4-1371B4AAD0FF Author: Richard L. Pyle urn:lsid:zoobank.org: author :8C466CBE-3F7D-4DC9-8CBD-26DD3F57E212 Type Specimen: BPBM 40861 urn:lsid:zoobank.org: specimen :FDE70A5C-59C3-407B-B9A6-5A9A2DA14BD1 Parts of an LSID - URN and LSID identification - Authority identification - Namespace identification
    54. 56. Nomenclatural Act: Chromis abyssus urn:lsid:zoobank.org:act: 8BDC0735-FEA4-4298-83FA-D04F67C3FBEC ZooBank: Registry Identifiers Publication: Pyle et al. , 2008 urn:lsid:zoobank.org:pub: 68376390-7809-46FF-9EC4-1371B4AAD0FF Author: Richard L. Pyle urn:lsid:zoobank.org:author: 8C466CBE-3F7D-4DC9-8CBD-26DD3F57E212 Type Specimen: BPBM 40861 urn:lsid:zoobank.org:specimen: FDE70A5C-59C3-407B-B9A6-5A9A2DA14BD1 Parts of an LSID - URN and LSID identification - Authority identification - Namespace identification - Object identification
    55. 57. Nomenclatural Act: Chromis abyssus urn:lsid:zoobank.org:act: 8BDC0735-FEA4-4298-83FA-D04F67C3FBEC ZooBank: Registry Identifiers 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! Publication: Pyle et al. , 2008 urn:lsid:zoobank.org:pub: 68376390-7809-46FF-9EC4-1371B4AAD0FF Author: Richard L. Pyle urn:lsid:zoobank.org:author: 8C466CBE-3F7D-4DC9-8CBD-26DD3F57E212 Type Specimen: BPBM 40861 urn:lsid:zoobank.org:specimen: FDE70A5C-59C3-407B-B9A6-5A9A2DA14BD1
    56. 58. Nomenclatural Act: Chromis abyssus urn:lsid:zoobank.org:act: 8BDC0735-FEA4-4298-83FA-D04F67C3FBEC ZooBank: Registry Identifiers Why UUIDs? “ ONE TRILLION UUIDs would have to be created EVERY NANOSECOND for TEN BILLION years to exhaust the number of UUIDs” Publication: Pyle et al. , 2008 urn:lsid:zoobank.org:pub: 68376390-7809-46FF-9EC4-1371B4AAD0FF Author: Richard L. Pyle urn:lsid:zoobank.org:author: 8C466CBE-3F7D-4DC9-8CBD-26DD3F57E212 Type Specimen: BPBM 40861 urn:lsid:zoobank.org:specimen: FDE70A5C-59C3-407B-B9A6-5A9A2DA14BD1
    57. 59. ZooBank: Content Launch - 1 January 2008, 00:00:00GMT - 250 th Anniversary of Systema Naturae 10 th Edition (per ICZN Code Art. 3) 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)
    58. 62. Pacific Abyss - 3 part series on BBC in August ‘08
    59. 67. January 1, 1758 January 1, 2008
    60. 69. ZooBank
    61. 70. ZooBank
    62. 71. ZooBank
    63. 72. ZooBank
    64. 73. ZooBank
    65. 74. Logistics of populating ZooBank <ul><li>16,000-20,000 new animal species described each year </li></ul><ul><li>1.7 million described extant species </li></ul><ul><li>5-50 million estimated total extant species (R. May, E.O. Wilson, T. Erwin) </li></ul><ul><li>Fossil species multiply this by orders of magnitude </li></ul>
    66. 75. Logistics of populating ZooBank <ul><li>16,000-20,000 new animal species described each year </li></ul><ul><li>1.7 million described extant species </li></ul><ul><li>5-50 million estimated total extant species (R. May, E.O. Wilson, T. Erwin) </li></ul><ul><li>Fossil species multiply this by orders of magnitude </li></ul><ul><li>Strategic approaches required </li></ul>
    67. 76. ZooBank <ul><li>Enables true web taxonomy </li></ul><ul><li>Works synergistically with other cybertaxonomic resources </li></ul><ul><li>Streamlines and democratises taxonomic process </li></ul><ul><li>An enabling tool for Code-compliance in nomenclature </li></ul><ul><li>ZooBank will be both HUB and AUTHORITY on animal names </li></ul>
    68. 77. <ul><li>Natural History Museum, London </li></ul><ul><li>Bishop Museum, Hawaii </li></ul><ul><li>Wellcome Trust </li></ul><ul><li>Taylor & Francis </li></ul><ul><li>Thomson Scientific / Zoological Record </li></ul><ul><li>GBIF & TDWG </li></ul><ul><li>The Commissioners & Trustees of ICZN / ITZN </li></ul>THANKS TO
    69. 78. Top 10 Species of the Year Quentin Wheeler - Int’l Institute for Species Exploration http://www.species.asu.edu/Top10
    70. 79. Holotype of Homo sapiens ?

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