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Transition to taxon concepts from a world of legacy data ---

Transition to taxon concepts from a world of legacy data ---. R.K. Peet 1 , A.S. Weakley 1,2 , X. Liu 1,3 , & N. Franz 4,5 1 The University of North Carolina at Chapel Hill 2 The North Carolina Botanical Garden 3 National Evolutionary Synthesis Center

december
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Transition to taxon concepts from a world of legacy data ---

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  1. Transition to taxon concepts from a world of legacy data --- • R.K. Peet1, A.S. Weakley1,2, X. Liu1,3, & N. Franz4,5 • 1The University of North Carolina at Chapel Hill • 2The North Carolina Botanical Garden • 3National Evolutionary Synthesis Center • 4National Center for Ecological Anal. & Synthesis • 5University of Puerto Rico, Mayagüez

  2. Taxonomic database challenge • The well-known problem: • Integration of data from different times & places, by multiple investigators using varied taxonomic standards. • The well-known solution: • Identifications to taxon concepts that have mapped relationships to related concepts.

  3. The good news: • TDWG has embraced taxonomic concepts and adopted TCS. • Multiple organizations are developing tools for concept use and integration. • The challenge: • Few large-scale compilations of concepts and their relationships are available. • Legacy data lacking concept annotation will be around forever.

  4. A Case Study:Flora of the Southeastern US • Regional floras were badly obsolete and incomplete • No flora covered the Atlantic SE • Ecological datasets with multiple taxonomic authorities and inconsistent taxonomic concepts defied integration • Need for an updated atlas of the flora of the Southeast • Good candidate for a demonstration

  5. Critical SE floristic works • Weakley 2005. Flora of the Carolinas, Virginia, Georgia, and Surrounding Areas • Small 1933. Manual of the southeastern flora • Fernald 1950. Gray's manual of botany • Gleason 1952. Britton and Brown illustrated flora • Radford, Ahles & Bell 1968. Manual of the vascular flora of the Carolinas • Gleason & Cronquist 1991. Manual of vascular plants of northeastern United States and adjacent Canada • 1993-2005. Flora of North America north of Mexico • Kartesz 1999. A synonymized checklist for the vascular flora of the United States, Canada, and Greenland • Wofford 1989. Vascular Plants of the Blue Ridge • Godfrey & Wooton 1979. Aquatic and Wetland Plants of Southeastern United States • 1980-1990. Vascular Flora of the Southeastern United States • Recent monographs and revisions (>2000)

  6. Andropogon virginicus complex in the Carolinas 9 elemental units; 17 base concepts, 27 scientific names

  7. Massive Import • Scanned indices -- OCR • Spreadsheets for preliminary concept documentation • Import into software tool for managing concepts and relationships

  8. ConceptMapper • Document and manage taxon concepts from multiple sources • Document and manage concept relationships from multiple sources • Input data files as txt, xls, mdb, or TCS-XML • Export data as txt, mdb, or TCS-XML http://152.2.14.231/conceptmapper/

  9. Concept mapper

  10. 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

  11. 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

  12. Add dynamic access to NCU collection NCU RAB Carya carolinae-septentrionalis

  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. Nominal occurrences represent occurrences that might or might not represent the taxon Carya carolinae-septentrionalis

  17. All specimens of Carya ovata must be identified to nominal concepts

  18. Consider Cleistes • Cleistes bifaria was split off C. divaricata after Radford et al. was published. • Radford et al. records must be mapped as ambiguous. • Kartesz incorrectly maps all Cleistes in the Carolinas as C. divaricata owing to uncritical import of records from Radford.

  19. http://herbarium.unc.edu/seflora/firstviewer.htm

  20. Other data are linked by name and concept

  21. Specimens matching the name

  22. ..\..\New Folder\Snap32.jpg Images matching the name

  23. Community types with the concept

  24. Link to Vegetation plots with the taxon

  25. Types of Concepts

  26. Next step? Multiple party perspectives Objectives: • Allow user to select date-specific version of Weakley. • Allow user to select a Weakley, PLANTS, or FNA perspective. Data needs: • Map relationships to PLANTS v 4.0 • Map relationships between PLANTS and FNA • Date-stamp changes in Weakley

  27. Links ConceptMapper http://152.2.14.231/conceptmapper/ Weakley flora http://herbarium.unc.edu/flora.htm NCU Atlas of the SE flora http://herbarium.unc.edu/seflora/firstviewer.htm Thanks NSF (SEEK, VegBank) & the NC Botanical Garden

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