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LSIDs for Taxon Names: The ZooBank Experience

LSIDs for Taxon Names: The ZooBank Experience. Richard L. Pyle. Bishop Museum, Honolulu International Commission for Zoological Nomenclature Pacifc Basin Information Node, NBII. ZooBank: Background. Official “Registry” for scientific names and nomenclatural acts as governed by the ICZN

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LSIDs for Taxon Names: The ZooBank Experience

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  1. LSIDs for Taxon Names: The ZooBank Experience Richard L. Pyle Bishop Museum, Honolulu International Commission for Zoological Nomenclature Pacifc Basin Information Node, NBII

  2. ZooBank: Background • Official “Registry” for scientific names and nomenclatural acts as governed by the ICZN • Commentary published in Nature (2005 437:477) • Technical Article in BZN (2005: 62:210-220) describing alternate implementation scenarios • Draft “ZooBank Principles and Policies”http://www2.bishopmuseum.org/iczn/ZooBank-GPP.pdf • Bishop Museum to develop initial prototype • TDWG support for LSID & TAPIR services • Initial test data content from Bill Eschmeyer’s “Catalog of Fishes” (and HNS)

  3. TaxonNameUsage TaxonNameUsageID ProtonymID ReferenceID TaxonRankID ValidUsageID ParentUsageID ReliabilityID NameString Prefix Suffix Pages Illustration IsNothoTaxon IsQuestioned IsNewCombination IsFirstRevision tsn CheatNameComplete CheatIsAutonym CheatStatus • Data Structure modeled after Taxonomer • Unit of ZooBank is a Taxon Name Usage Instance (=“Assertion” of Taxonomer) • Scope of ZooBank Includes: • ICZN-governed Nomenclatural Acts • “Original Descriptions” of new names • Lectotypifications/Neotypifications • Emendations • First Reviser • Etc. • Non-governed Usage Instances • Unavailable Names • Higher-rank names • First usage instance of a new combination? • Misspellings?

  4. TaxonNameUsage TaxonNameUsageID Protonym ProtonymID ProtonymID ReferenceID TypeProtonymID TaxonRankID WordTypeID ValidUsageID NomenCodeID ParentUsageID GenderID ReliabilityID IsFossil NameString Grade Prefix CheatAvailable Suffix CheatHomonym Pages CheatFullProtonym Illustration CheatAcceptedUsageID IsNothoTaxon CheatHierarchy IsQuestioned IsNewCombination IsFirstRevision tsn CheatNameComplete CheatIsAutonym CheatStatus PROTONYM = Code-compliant Creation Event for a Scientific Name • E.g. Protologue of Basionyms • All Usage Instances of scientific names are referable to a Protonym • Represents a recursive link back to Taxon Name Usage Protonyms are the “Anchorpoints” through which ALL Taxon Name Usage Instances can be Cross-Linked

  5. TaxonNameUsage TaxonNameUsageID Protonym ProtonymID ProtonymID ReferenceID TypeProtonymID TaxonRankID WordTypeID ValidUsageID NomenCodeID ParentUsageID GenderID ReliabilityID IsFossil NameString Grade Prefix CheatAvailable Suffix CheatHomonym Pages CheatFullProtonym Illustration CheatAcceptedUsageID IsNothoTaxon CheatHierarchy IsQuestioned IsNewCombination IsFirstRevision tsn Reference CheatNameComplete ReferenceID CheatIsAutonym ParentReferenceID CheatStatus ReferenceTypeID LanguageID Year Title SecondaryTitle Publisher PlacePublished Volume NumberVolumes Number Pages InPages Section Edition DatePublished TypeWork ShortTitle Figures StartDate EndDate URL CheatCitation CheatAuthors CheatFullAuthors CheatCitationDetails REFERENCE = Documentation Instance in which Taxon Name Usage appeared • In the context of ZooBank, always a publication (much broader scope in Taxonomer)

  6. TaxonNameUsage TaxonNameUsageID Protonym ProtonymID ProtonymID ReferenceID TypeProtonymID TaxonRankID WordTypeID ValidUsageID NomenCodeID ParentUsageID GenderID ReliabilityID IsFossil NameString Grade Prefix CheatAvailable Suffix CheatHomonym Pages CheatFullProtonym Illustration CheatAcceptedUsageID IsNothoTaxon CheatHierarchy IsQuestioned IsNewCombination IsFirstRevision tsn Reference CheatNameComplete ReferenceID CheatIsAutonym ParentReferenceID CheatStatus ReferenceTypeID LanguageID Year Title SecondaryTitle Publisher PlacePublished Volume NumberVolumes tnuID Reference NameString Rank Number Pages 123 123 Baldwin & Smith, 1998 Baldwin & Smith, 1998 pylei pylei species species 234 InPages 234 234 Baldwin & Smith, 1998 Baldwin & Smith, 1998 Belonoperca Belonoperca genus genus Section 345 Edition 345 345 Baldwin & Smith, 1998 Baldwin & Smith, 1998 Diploprionini Diploprionini tribe tribe DatePublished 456 TypeWork 456 456 Baldwin & Smith, 1998 Baldwin & Smith, 1998 Epinephelinae Epinephelinae subfamily subfamily ShortTitle 567 567 567 Baldwin & Smith, 1998 Baldwin & Smith, 1998 Serranidae Serranidae family family Figures StartDate 678 678 678 ... ... ... Baldwin & Smith, 1998 ... Baldwin & Smith, 1998 ... Teleostei ... Teleostei ... order ... order EndDate URL CheatCitation CheatAuthors CheatFullAuthors CheatCitationDetails PtnuID 234 345 456 567 678

  7. TaxonNameUsage PK Protonym TaxonNameUsageID PKID ProtonymID ProtonymID CorrectID TypeProtonymID ReferenceID TableID WordTypeID TaxonRankID LegacyID NomenCodeID ValidUsageID LegacyID2 GenderID ParentUsageID UUID IsFossil ReliabilityID Grade Epithet CheatAvailable EpithetPrefix CheatHomonym EpithetSuffix CheatFullProtonym Pages CheatAcceptedUsageID Illustration CheatHierarchy IsNothoTaxon IsQuestioned IsNewCombination IsFirstRevision Reference tsn ReferenceID CheatNameComplete ParentReferenceID CheatIsAutonym ReferenceTypeID CheatStatus LanguageID Year Title SecondaryTitle Publisher PlacePublished Volume NumberVolumes Number Pages InPages Section Edition DatePublished TypeWork ShortTitle Figures StartDate EndDate URL CheatCitation CheatAuthors CheatFullAuthors CheatCitationDetails • All data tables derive integer primary key from central “PK” table • Centralized management of duplicate records, edit logging, etc. • All records get a UUID, used as externally-visible GUID (integer Primary Key for internal use only)

  8. TaxonNameUsage PK Protonym TaxonNameUsageID PKID ProtonymID ProtonymID CorrectID TypeProtonymID ReferenceID TableID WordTypeID TaxonRankID LegacyID NomenCodeID ValidUsageID LegacyID2 GenderID ParentUsageID UUID IsFossil ReliabilityID Grade Epithet CheatAvailable EpithetPrefix CheatHomonym EpithetSuffix CheatFullProtonym Pages CheatAcceptedUsageID Illustration CheatHierarchy IsNothoTaxon IsQuestioned • Authority Identification IsNewCombination IsFirstRevision Reference tsn zoobank.org ReferenceID CheatNameComplete ParentReferenceID CheatIsAutonym ReferenceTypeID CheatStatus • Namespace Identification • Object Identification LanguageID Year Title “act” (Taxon Name Usages) “pub” (References) UUID SecondaryTitle Publisher PlacePublished Volume NumberVolumes Number Pages InPages Section Edition DatePublished TypeWork ShortTitle Figures StartDate EndDate URL CheatCitation CheatAuthors CheatFullAuthors CheatCitationDetails LSID Assignment urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3-D1D97704A609 urn:lsid:zoobank.org:pub:F8ECE6CE-E77F-4768-A563-62E416592874

  9. GBIF BPBM Specimens Catalogof Fishes HymenopteraName Server Zoological Record Catalogueof Life FishBase Universal Biodiversity Data Bus UBDB (“yoo-bee doo-bee”) ZooBank Registry Workbench urn:lsid:zoobank.org:act:208...Rank: speciesEpithet: pyleiOrigGen: BelonopercaAuth: Baldwin & SmithYear: 1998Page: 325Source: urn:lsid:cof.org:sp:123... Links:urn:lsid:fb.org:sp:123...

  10. GBIF BPBM Specimens Catalogof Fishes HymenopteraName Server Zoological Record Catalogueof Life FishBase Universal Biodiversity Data Bus UBDB (“yoo-bee doo-bee”) ZooBank ZooBank Offers: Registry Workbench • Authoritative (verified) Nomenclatural details urn:lsid:zoobank.org:act:208...Rank: speciesEpithet: pyleiOrigGen: BelonopercaAuth: Baldwin & SmithYear: 1998Page: 325Source: urn:lsid:cof.org:sp:123... urn:lsid:gbif.org:ident:987...Belonoperca pylei urn:lsid:gbif.org:ident:789...Belonoperca pyli urn:lsid:zr.org:usage:654...Belonoperca pylei urn:lsid:zr.org:usage:456... Belonoperca chabanaudi urn:lsid:col.org:species:345...Belonoperca pylei urn:lsid:col.org:ident:543... Belonoperca chabanaudi urn:lsid:bpbm.org:spec:321...Belonoperca pylei TYPE • Protonyms serve as “hub” for cross-linking taxonomic records (“building bridges”) Links:urn:lsid:fb.org:sp:812... urn:lsid:gbif.org:ident:987... urn:lsid:gbif.org:ident:789... urn:lsid:zr.org:usage:654... urn:lsid:col.org:species:345... urn:lsid:bpbm.org:spec:321...

  11. ZooBank: Questions • Issue ZooBank LSIDs for Literature Citations? Yes! • Issue ZooBank LSIDs for Author Names? Probably... • Issue ZooBank LSIDs for Workbench Records? Probably not... • Enumerated List of “Link Types”? • Distributed, Mirrored, or Centralized? • Finalize Principles and Policies? • Scratchpads?

  12. TaxonNameUsage PK Identifier Protonym TaxonNameUsageID PKID IdentifierID IdentifierDomain ProtonymID ProtonymID CorrectID IdentifierDomainID IdentifierDomainID TypeProtonymID ReferenceID TableID PKID AgentID WordTypeID TaxonRankID LegacyID Identifier Abbreviation NomenCodeID ValidUsageID LegacyID2 IdentifierDomain GenderID ParentUsageID UUID ObjectType IsFossil ReliabilityID Description Grade Epithet CheatAvailable EpithetPrefix CheatHomonym EpithetSuffix CheatFullProtonym Pages CheatAcceptedUsageID Illustration CheatHierarchy IsNothoTaxon IsQuestioned IsNewCombination IsFirstRevision Reference tsn ReferenceID ReferenceAuthor Agent CheatNameComplete ParentReferenceID CheatIsAutonym ReferenceAuthorID AgentID ReferenceTypeID CheatStatus AgentID ValidAgentID LanguageID ReferenceID DefaultAgentAssociationID Year IsAmbiguous AuthorTypeID Title BirthDate Sequence SecondaryTitle DeathDate Publisher CheatFullAgentName PlacePublished Volume NumberVolumes Number Pages InPages Section Edition DatePublished TypeWork ShortTitle Figures StartDate EndDate URL CheatCitation CheatAuthors CheatFullAuthors CheatCitationDetails

  13. TaxonNameUsage PK Identifier Protonym TaxonNameUsageID PKID IdentifierID IdentifierDomain ProtonymID ProtonymID CorrectID IdentifierDomainID IdentifierDomainID TypeProtonymID ReferenceID TableID PKID AgentID WordTypeID TaxonRankID LegacyID Identifier Abbreviation NomenCodeID ValidUsageID LegacyID2 IdentifierDomain GenderID ParentUsageID UUID ObjectType IsFossil ReliabilityID Description Grade Epithet CheatAvailable EpithetPrefix CheatHomonym EpithetSuffix CheatFullProtonym Pages CheatAcceptedUsageID Illustration CheatHierarchy IsNothoTaxon IsQuestioned IsNewCombination IsFirstRevision Reference tsn ReferenceID ReferenceAuthor Agent CheatNameComplete ParentReferenceID CheatIsAutonym ReferenceAuthorID AgentID ReferenceTypeID CheatStatus AgentID ValidAgentID LanguageID ReferenceID DefaultAgentAssociationID Year IsAmbiguous AuthorTypeID Title BirthDate Sequence SecondaryTitle DeathDate Publisher CheatFullAgentName PlacePublished Volume NumberVolumes Number Pages InPages Section Edition DatePublished TypeWork ShortTitle Figures StartDate EndDate URL CheatCitation CheatAuthors CheatFullAuthors CheatCitationDetails • List of Author Names in Zoology

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