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Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
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Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2

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  • In 1758 it was feasible to create a catalog of life using ink on paper. <click> Today, it would require the equivalent of nearly 264 volumes of Systema Naturae to achieve the same thing. Or, you could fit the whole thing on a tiny memory card.
  • It’s no surprise that the biodiversity community is going digital. <click> Many Natural History Museums are databasing their collections. <click> Historical literature is being digitized by the Biodiversity Heritage Library and others… <click> … and many modern scientific journals are embracing the digital age directly. <click> Authoritative Nomenclators have been built, <click> and a variety of groups are working to distill the taxonomic concepts from the sea of names. <click> Databases of observation records are growing at a fast rate, <click> as are genomic databases. <click> The internet has made feasible the cheap and easy dissemination of multimedia files related to biodiversity. <click> And, of course there is biodiversity content spread across the billions of web pages indexed by Google. <click> To make sense of it all, several organizations serve as aggregators of all this diverse content. And this is just a small sample of icons that could fit on a slide. This massive effort to digitize biodiversity information is a great step in the right direction. But it is only one step. We must now focus our energies on integrating all of this information in a coordinated, cohesive way. <click> The critical informatic piece to this puzzle is Taxonomy, because almost all of these data providers link their content to taxon names one way or another.
  • It’s no surprise that the biodiversity community is going digital. <click> Many Natural History Museums are databasing their collections. <click> Historical literature is being digitized by the Biodiversity Heritage Library and others… <click> … and many modern scientific journals are embracing the digital age directly. <click> Authoritative Nomenclators have been built, <click> and a variety of groups are working to distill the taxonomic concepts from the sea of names. <click> Databases of observation records are growing at a fast rate, <click> as are genomic databases. <click> The internet has made feasible the cheap and easy dissemination of multimedia files related to biodiversity. <click> And, of course there is biodiversity content spread across the billions of web pages indexed by Google. <click> To make sense of it all, several organizations serve as aggregators of all this diverse content. And this is just a small sample of icons that could fit on a slide. This massive effort to digitize biodiversity information is a great step in the right direction. But it is only one step. We must now focus our energies on integrating all of this information in a coordinated, cohesive way. <click> The critical informatic piece to this puzzle is Taxonomy, because almost all of these data providers link their content to taxon names one way or another.
  • To overcome these and other problems, we need to build a Global Names Architecture. The first and perhaps most critical component to integrating all of this biodiversity information is the broader adoption of Globally Unique Identifiers, or GUIDs. <click> If you already know about GUIDs, then the question of whether we should use LSIDs or DOIs or Handles, or PURLs or UUIDs is of secondary importance to their more general implementation. If you don’t already know about GUIDs, then learn about them, or trust your IT staff when they say then need support to implement them. Also, always keep in mind that they are intended for use by computers, not humans, so don’t worry about how ugly they may appear. But while GUIDs make things a lot easier, they do not, by themselves, solve the problem of linking the world’s biodiversity information.
  • GUIDs are globally unidque identifiers, readable only to computers The two major components of the Global Names Architecture currently under development are the Global Names Index, or “GNI”… <click> And the Global Names Usage Bank, or “GNUB”. <click> The GNI is optimized to manage information from content providers that treat names as text-string attributes of other data objects. For example, it provides a species-level index of content within data bases and facilitates linking of disparate data sources through species names. <click> The GNUB is designed to manage taxon names and their usages as curated data objects in and of themselves. These components will not only help build links among their own contributing data providers, but also to bridge the gap between them. <click> Services will allow the GNI to serve as a “gateway” into the GNUB. And, of course, the GNUB will serve as a source of validated taxon name strings back to GNI. The Global Names Architecture is currently in development with support from GBIF, the Encyclopedia of Life, and National Biological Information Infrastructure. A prototype of GNI is already available at globalnames.org, and the GNUB is currently being populated with content from Index Fungorum and ZooBank, the latter of which will include content from many of these taxon-specific nomenclators. <click> Ultimately, all of these content providers will be plugged into the Global Names Architecture, and the biodiversity data content will start to flow.
  • The good news is that Taxonomic names represent one of the greatest and long-lasting examples of true international cooperation in all of science, if not all of human history. <click> This is a result of the various Codes of Scientific Nomenclature; two of which have been in place for more than a century, and apply to all names going back to Linnaeus. In a sense, the Codes of Nomenclature represent our saving grace for organizing biodiversity information. Without their existence, longevity, and near-universal adoption, the prospects for integrating biodiversity information would be orders of magnitude more difficult today. Unfortunately, as important as these Codes of nomenclature have been and continue to be, there are still some issues to overcome.
  • Transcript

    • 1. Nomenclature forthe Future:The power andchallenges forstable andsensible scientificnames foranimalsEllinor Michel1,2,3Richard Pyle1,3,4Daphne Fautin1,3,5David Patterson1,3,6Jon Todd2,311Int’l Commission on Zoological NomenclatureInt’l Commission on Zoological Nomenclature22The Natural History Museum, London UKThe Natural History Museum, London UK33Int’l Committee on BionomenclatureInt’l Committee on Bionomenclature44Bishop Museum, HI, USABishop Museum, HI, USA55University of Kansas, USAUniversity of Kansas, USA66Arizona State Univ, AZ, USAArizona State Univ, AZ, USA
    • 2. All accumulated information ofa species is tied to a scientificname, a name that serves as alink between what has beenlearned in the past and what wetoday add to the body ofknowledge.- Grimaldi & Engel, 2005Names and the information revolutionNote: they don’t say THE scientific name (i.e., singular)
    • 3. Equivalent of 318 volumes of Systema NaturaeEstimated 2-6 names for every valid (=currentlyconsidered definable and ‘real’) species4,398 Species
    • 4. Nomenclature TaxonomyType specimenIs the objective physical standard for a namethat anchors the name.
    • 5. ✔ICZN types for the Future✔?✗?
    • 6. ✔ICZN types for the Future✔?✗?
    • 7. ✔Types for the Future?✗
    • 8. Scientific concept of biodiversityName(Scientific, common,provisional or open)Type specimen(objective standard)Data &Bibliography
    • 9. Stability, transparency and testabilityName(Scientific, common,provisional or open)Type specimen(objective standard)Data &Bibliography
    • 10. Archives forScientific concepts of biodiversityName(Scientific, common,provisional or open)Type specimen(objective standard)Data &BibliographyStable archivesneededNatural HistoryCollectionsLibrariesPublicationsData sources
    • 11. Registration in ZooBank• Now required for e-only publications• Has general community support
    • 12. E-only publication amendmentto ICZN Code published 4 SeptZooBank improved versionreleased, meetingrequirements of theAmendmentFrom zoobank.org/statistics
    • 13. • Now required for e-only publications• Has general community support• Registration of all names and nomenclaturalacts is strongly encouraged and being rapidlyimplemented• Next Step: ALL names (historical and future)registered and cross-linked!Registration in ZooBank
    • 14. A name = ‘computer’ readablecode that links information
    • 15. A5B835CF-BB3A-4CC9-BCBD-38BA253C8374Easy for a computer;Hard for a humanEasy for a human;Hard for a computer“Archaeopteryx”
    • 16. GenBankHymenopteraNameServerBDWBCalPhotosNamesconnecting informationToL
    • 17. GenBankHymenopteraNameServerBDWBCalPhotos“Archaeopteryx”ToL
    • 18. GenBankHymenopteraNameServerBDWBCalPhotosToLA5B835CF-BB3A-4CC9-BCBD-38BA253C8374(= Archaeopteryx)
    • 19. ToLGenBankHymenopteraNameServerBDWBCalPhotosA Global Names ArchitectureA Global Names ArchitectureA5B835CF-BB3A-4CC9-BCBD-38BA253C8374
    • 20. Big Data InfrastructureData re-useData generationDatapoolPatterson,BioSyst.EUKeynote
    • 21. Zoological Names in the Future• Global mandatory registration for all newnames – next edition of the Code?• Ultimate Goal: Registered = Available(Pyle & Michel, 2008; Minelli, 2013)
    • 22. Logistics of populating ZooBank• 16,000-20,000 new animal species described16,000-20,000 new animal species describedeach yeareach year• 1.9 million described extant species1.9 million described extant species• 5-50 million estimated total extant species (R.5-50 million estimated total extant species (R.May, E.O. Wilson, T. Erwin)May, E.O. Wilson, T. Erwin)• Fossil species multiply this by some factorFossil species multiply this by some factorStrategic approaches requiredStrategic approaches requiredPublishers highly supportive and beginningPublishers highly supportive and beginningto require ZooBank registrationto require ZooBank registrationAuthors & databases contributing nowAuthors & databases contributing now
    • 23. Logistics of populating ZooBankBuilding tools to streamline the capture of prospectivecontent•Publishers pipelines with XML tools•Requested and required ZooBank registration by authors ofnew papers•(all e-only publications must be registered to be available)Populating with retrospective content•Major sources – Sherborn, Hymenoptera Names Server,Hexacorallians of the World, etc.•Committed individuals – Rod Bray, Takafumi Nakano•Lists of Available Names (LANs)
    • 24. ZooBank links with the Biodiversity Heritage Library
    • 25. LANs – Lists of Available Names• Critical assembly of largenumbers of names• Community debate• Commission authoritativerulingArticle 79 - An international body ofzoologists… in consultation with theCommission may propose that the Commissionadopt for a major taxonomic field (or relatedfields) a Part of the List of Available Names inZoology. The Commission will consider theproposal and may adopt the Part subject to theproposing body and the Commission meetingthe requirements of this Article.
    • 26. 1)Ensures a candidate Part of the LAN isthoroughly vetted2)Pares away dubious names• like the Approved Lists of Bacterial Names that took effect on1 January 1980 – taxonomically recognizable as well asnomenclaturally available3) Prevents “nomenclatural archeology”• long-forgotten names displacing accepted names Creates a definitive nomenclatural inventory (anew zero point) for a portion of the taxonomicspectrum Source of names for ZooBankLANs – Lists of Available Names
    • 27. Two Possibilitiesto document everyavailable namewithin the scopeof the Partto pare the inventoryof names within thescope of the PartSTRICTLY NOMENCLATURALTAXONOMIC COMPONENT
    • 28. www.bionomenclature.net/Harmonising the Codes
    • 29. • Names are the anchor and link for biodiversity informationexchange• Types provide stability and meaning for taxon names• An stable archive of names is a critical taxonomicinfrastructure• ZooBank aims to be the authoritative source for scientificnames of animals and is growing rapidly• The future of nomenclature includes a harmonization ofbiological codes, especially through technical tools such asZooBank and the Global Names ArchitectureConclusions
    • 30. Natural History Museum, LondonBishop Museum, HawaiiITCN/ITZN supporting institutions(MNHN (France), Senckenberg(Germany), Naturalis, RBINS(Belgium), AAZN (USA))The Commissioners & Trustees ofICZN / ITZNICB – International Committee onBionomenclatureEveryone pitching in on buildingZooBank contentTHANKS
    • 31. Let’sdiscuss!

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