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The VegBank taxonomic datamodel Robert K. Peet

The VegBank taxonomic datamodel Robert K. Peet. Sponsored by: The Ecological Society of America US National Science Foundation Produced at: The National Center for Ecological Analysis and Synthesis. 1. The Intended User Groups. Specifically

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The VegBank taxonomic datamodel Robert K. Peet

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  1. The VegBank • taxonomic datamodel • Robert K. Peet • Sponsored by: • The Ecological Society of America US National Science Foundation • Produced at: • The National Center for Ecological Analysis and Synthesis

  2. 1. The Intended User Groups Specifically • “Ecologists” who record species composition of vegetation. • “Ecologists” who use records of vegetation composition. In general • Creators and distributors of data wherein organisms need to be labeled. • Users and consolidators of data wherein organisms are labeled.

  3. VegBank • The ESA Vegetation Panel is currently developingVegBank (www.vegbank.org) as a public vegetation plot archive • VegBank is expected to function for vegetation plot data in a manner analogous to GenBank. • Primary data will be deposited for reference, novel synthesis, and reanalysis, particularly for classification.

  4. 2. Intended Functionality • Ecologists, like most users of organism names, care about how to label organisms, and how to interpret labels others have placed on organisms. • We wish for ease in combining datasets. • We abhor name changes and ambiguity

  5. Plot Core elements of VegBank Plot Observation Taxon Observation Plot Interpretation Taxon Interpretation Plot Assignment Taxon Assignment

  6. Taxonomic database challenge:Standardizing organisms and communities The problem: Integration of data potentially representing differenttimes, places, investigators and taxonomic standards. The traditional solution: A standard checklists of organisms.

  7. Standard lists are available for Taxa Representative examples for higher plants in North America / US USDA Plants http://plants.usda.gov ITIS http://www.itis.usda.gov NatureServe http://www.natureserve.orgBONAP Flora North America These are intended to be checklists wherein the taxa recognized perfectly partition all plants. The lists can be dynamic.

  8. Most taxon checklists fail to allow effective dataset integration • The reasons include: • The user cannot reconstruct the database as viewed at an arbitrary time in the past, • Taxonomic concepts are not defined (just lists), • Multiple party perspectives on taxonomic concepts and names cannot be supported or reconciled.

  9. Intended functionality • Organisms are labeled by reference to concept (name-reference combination), • Party perspectives on concepts and names can be dynamic, • User can select which party perspective to follow, • Party perspectives are perfectly archived, • Different names systems are supported, • Enhanced stability in recognized concepts by separating name assignment and rank from concept,

  10. 3. Taxonomic theory A taxon concept represents a unique combination of a name and a reference “Taxon concept” roughly equivalent to “Potential taxon” & “assertion” Name Concept Reference

  11. A usage represents a unique association of a concept with a name. Name Usage Concept • Usage does not appear in the IOPI model, but instead is a special case of concept • Usage can be used to apply multiple name systems to a concept • Desirable for stability in recognized concepts

  12. Data relationshipsVegBank taxonomic data model Name Concept Start, Stop ConceptStatus Level, Parent Usage Start, Stop NameStatus Name system Reference Single party, dynamic perspective

  13. Party Perspective • The Party Perspective on a concept includes: • Status – Standard, Nonstandard, Undetermined • Correlation with other concepts – Equal, Greater, Lesser, Overlap, Undetermined. • Lineage – Predecessor and Successor concepts. • Start & Stop dates.

  14. Data relationshipsVegBank taxonomic data model Name Concept Usage Start, Stop NameStatus Name system Status Start, Stop ConceptStatus Level, Parent Party Reference Multiple parties, dynamic perspectives

  15. Data relationshipsVegBank taxonomic data model Name Concept Usage Start, Stop NameStatus Name system Correlation Party Status Start, Stop ConceptStatus Level, Parent Lineage Reference With party correlations and lineages

  16. Primary differences between the VegBank and IOPI models • The IOPI model is optimized for • describing taxonomic decisions represented in literature. • The VB model is optimized for • stability in accepted concepts (super concepts), • support of multiple dynamic party perspectives, • support of multiple name systems.

  17. 4. State of Development 1. VegBank 2. Collaborators • NatureServe Biotics4 • USDA PLANTS & ITIS

  18. Status of VegBank • Working Prototype; open for deposit Nov 1 • Production version July 2004 • Access version on VegBranch today • Efficient data exchange by July 2004 • Functionality mandated in draft FGDC standards • IAVS working group established for data exchange standards established 2003

  19. VegBank data content Prototype populated with USDA PLANTS lists and synonyms = weak concepts. Contract with NatureServe and John Kartesz • Develop reference-based concepts for 14000 by July 2004 of the ~32000 vascular plant taxa at species level and below • List of unambiguous taxa (~6000?) • Treatment of most ambiguous taxa • Demonstration mapping to FNA • A few demosntration groups in depth

  20. Concept workbench • Concept workbench for both plant concepts and community concepts is planned.

  21. NatureServe Biotics 4 • In production • Loading the same initial concepts • Already using concepts where strong differences between state programs • Routine data exchange with Vegbank under development.

  22. PLANTS & ITIS • Frequent communication during redesign. • Design documents for conversion to concept-based system complete • Collaboration to assure that the concepts we develop will be employed in the new system • Uncertainties about funding

  23. Six shagbark hickory concepts Possible synonyms are listed together Names Carya ovata Carya carolinae-septentrionalis Carya ovata v. ovata Carya ovata v. australis Concepts (One shagbark)C. ovata sec Gleason ’52 C. ovata sec FNA ‘97 (Southern shagbark)C. carolinae-s. sec Radford ‘68C. ovata v. australis sec FNA ‘97 (Northern shagbark) C. ovata sec Radford ‘68 C. ovata (v. ovata) sec FNA ‘97 References Gleason 1952. Britton & Brown Radford et al. 1968. Flora Carolinas Stone 1997. Flora North America

  24. Application of Party Perspective Party Concept ITIS FNA CommitteeNatureServe Carya ovatasec Gleason 1952 Carya ovata sec FNA 1997 Carya ovata sec Radford 1968 Carya carolinae sec Radford 1968 Carya ovata (ovata) sec FNA 1997 Carya ovata australissec FNA 1997 Status Party Concept Status Start Usage:SciName ITIS ovata –G52 NS 1996 ITIS ovata –R68 St 1996 C. ovata ITIS carolinae-s –R68 St 1996 C. carolinae-sept. ITIS carolinae-s –R68 NS 2000 ITIS ovata aust –FNA St 2000 C. carolinae-sept. ITIS ovata – R68 NS 2000 ITIS ovata ovata –FNA St 2000 C. ovata

  25. Data relationshipsVegBank taxonomic data model Name Concept Usage Start, Stop NameStatus Name system Correlation Party Status Start, Stop ConceptStatus Level, Parent Lineage Reference With party correlations and lineages

  26. Core elements of the IOPI model Name Concept Is author SourceType: Lit, Org Reference Correlation Assigns status Status

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