Transition to taxon concepts from a world of legacy data

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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
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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.
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• 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.

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• A Case StudyFlora 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

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• 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 (gt2000)

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Andropogon virginicus complex in the Carolinas 9
elemental units 17 base concepts, 27 scientific
names
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Massive Import

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

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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/

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Concept mapper
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How have things changed? Concept relationships of
Southeastern US plants treated in different
floras.
Based on gt 50,000 concept relationshipshttp//her
barium.unc.edu/flora.htm
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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
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Add dynamic access to NCU collection
NCU RAB
Carya carolinae-septentrionalis
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Add USDA PLANTS records CVS vegetation plot
data
NCU RAB USDA CVS
Carya carolinae-septentrionalis
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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

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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.

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Nominal occurrences represent occurrences that
might or might not represent the taxon
Carya carolinae-septentrionalis
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All specimens of Carya ovata must be identified
to nominal concepts
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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.

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http//herbarium.unc.edu/seflora/firstviewer.htm
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Other data are linked by name and concept
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Specimens matching the name
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• ..\..\New Folder\Snap32.jpg

Images matching the name
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Community types with the concept
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Link to Vegetation plots with the taxon
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Types of Concepts
Category Explanation
Original Appears in the reference where the new name/type association was established. Example Andropogon virginicus L. sec. Linnaeus (1753).
Revisional Appears in a comprehensive revision of an existing Taxonomic name and lineage, e.g. a monograph. Example Andropogon virginicus L. sec. Campbell (1983).
Relational Appears in a comprehensive compilation without descriptions) meaning may be inferred from the list of mutually exclusive concepts. Example Andropogon virginicus L. sec. ITIS (2006).
Informal Appears in a taxonomic treatment yet is poorly specified, being outside of the focal names and taxa. Example Andropogon hallii Hackel sec. Weakley (2006). (a Midwestern species)
Nominal Appears outside of the context of a particular source indirectly links to all other concepts with the name. Example Andropogon virginicus L.
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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

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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