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Vegetation databases

Vegetation databases. Lessons from VegBank, SEEK, TDWG, IAVS, & NCEAS. Robert Peet University of North Carolina. Locality. Observation/Collection Event. Plot/Inventory databases. Object or specimen. Object databases. BioTaxon. Taxonomic databases. Biodiversity data structure.

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Vegetation databases

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  1. Vegetation databases Lessons from VegBank, SEEK, TDWG, IAVS, & NCEAS Robert Peet University of North Carolina

  2. Locality Observation/Collection Event Plot/Inventory databases Object or specimen Object databases BioTaxon Taxonomic databases Biodiversity data structure SynTaxon Community type databases

  3. Topics • Introduction • Taxonomic data • Observation data • Identification • Vegetation data standards • VegBank • Data archiving and sharing

  4. 1. Taxonomic database challenge:Standardizing taxa The problem: Integration of data potentially representing different times, places, investigators and taxonomic standards. The traditional solution: A standard list of organisms / communities.

  5. One concept ofAbieslasiocarpa USDA Plants & ITIS Abies lasiocarpa var. lasiocarpa var. arizonica

  6. A narrow concept of Abies lasiocarpa Flora North America Abies lasiocarpa Abies bifolia Partnership with USDA plants to provide plant concepts for data integration

  7. Taxonomic theory A taxon concept represents a unique combination of a name and a reference. Report -- name sec reference. . Name Concept Reference

  8. Relationships among conceptsallow comparisons and conversions • Congruent, equal (=) • Includes (>) • Included in (<) • Overlaps (><) • Disjunct (|) • and others …

  9. High-elevation firtrees of western US AZ NM CO WY MT AB eBC wBC WA OR Distribution Abies lasiocarpa var. arizonica var. lasiocarpa USDA & ITIS Abies bifolia Abies lasiocarpa Flora North America A. lasiocarpasec USDA > A. lasiocarpasecFNA A. lasiocarpasecUSDA > A. bifoliasecFNA A. lasiocarpa v. lasiocarpasecUSDA > A. lasiocarpasecFNA A. lasiocarpa v. lasiocarpasecUSDA|A. bifoliasecFNA A. lasiocarpa v. arizonicasecUSDA < A. bifoliasecFNA

  10. Andropogon virginicus complex in the Carolinas 9 elemental units; 17 base concepts

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

  12. Toward a new Atlas http://herbarium.unc.edu/seflora/firstviewer.htm How to integrate new sources of data?? Carya carolinae-septentrionalis, Radford et al. 1968

  13. Add USDA PLANTS records & CVS vegetation plot data NCU RAB USDA CVS Carya carolinae-septentrionalis

  14. But wait !There is a concept issue • According to Radford 1968, USDA PLANTS v 4.0, & Weakley 2005 • Carya carolinae-septentrionalis • Carya ovata • According to Stone 1997 in FNA • Carya ovata var australis • Carya ovata var. ovata

  15. How to merge records that may be based on different concepts?? • Weakley 2005 – Reference concepts • Radford 1968 – Concepts mapped • NC Heritage Program – Weakley concepts • CVS – Weakley concepts (mostly) • USDA – Kartesz 1999 concepts (mostly) • NCU & NCSC – Nominal concepts only Most museum collection identifications must be interpreted as nominal concepts!! To do otherwise would be to introduce false positives.

  16. How have things changed? Concept relationships of Southeastern US plants treated in different floras. Based on > 50,000 concept relationshipshttp://herbarium.unc.edu/flora.htm

  17. Taxonomic standards • TDWG, TCS • SEEK, TOS • GUIDs, DOIs, LSISs • IPNI

  18. 2. Observation data • TDWG proposal • NatureServe EOs & Cornell bird data • Basics • Place, time, protocol, taxa, attributes • Plots constitute a subset • Museum collections constitute a subset

  19. 3. Identifications • A name in a publication could be either a concept or an identification. • Identifications should include linkage to at least one concept, but need not be limited to a single concept. Eg. -- < Potentilla sec. Cronquist 1991 + ~ Potentilla simplex sec Cronquist 1991 + ~ Potentilla canadensis sec Cronquist 1991

  20. Uncertainty • Absolutely wrong • Understandable but wrong • Acceptable but not typical • Good fit • Ideal, typical

  21. 4. Vegetation data standards • FGDC, ESA, IAVS • VegBank XML • VegetWeb • IAVS: 24-27 April @ NESCent • EML • Supports blocks of data • No concepts, no identification uncertainty

  22. 5 .VegBank • The ESA Vegetation Panel has developed VegBank-- a public archive for vegetation plots (http://vegbank.org). • VegBank is expected to function for vegetation plot data in a manner analogous to GenBank. • Primary data will be archived for future reference, novel synthesis, and reanalysis. • The database architecture is compatable with most types of species co-occurrence data.

  23. VegBank data are open access All data placed in VegBank are available to the public at no charge (unless the plot contributor places restrictions to protect location information for rare and endangered species or private lands). Key data can be viewed by a simple web link. The following link shows information for two VegBank plots: http://vegbank.org/get/std/observation/5153,5906

  24. Core elements of VegBank Project Plot Plot Observation Taxon / Individual Observation Taxon Interpretation Plot Interpretation

  25. http://www.vegbank.org http://www.vegbank.org

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  27. http://vegbank.org/get/std/observation/'VB.Ob.26013.027020404http://vegbank.org/get/std/observation/'VB.Ob.26013.027020404

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  32. VegBank design issues • Idiosyncratic ecologists • Soils and environment • Intellectual property & confidentiality • Notes • Input and output • Stems • Change tracking • Multiple name records • Stem databases?

  33. New directions Data archiving & sharing • ESA data sharing and ease of discovery • Data sharing trends ESA, NSF, NIH • Institutional repositories Taxon attributes • BiolFlor, LEDA, USDA • TraitNet RCN

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