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

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

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

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.

USDA Plants & ITIS Abies lasiocarpa var. lasiocarpa var. arizonica One concept ofAbies lasiocarpa

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

NameReferenceConcept Taxonomic theory A taxon concept represents a unique combination of a name and a reference. Report -- name sec reference..

Relationships among concepts allow comparisons and conversions Congruent, equal (=) Includes (>) Included in (<) Overlaps (><) Disjunct (|) and others …

High-elevation fir trees of western US AZ NM CO WY MT AB eBC wBC WA OR var. arizonica Abies lasiocarpa Distribution USDA & ITIS Flora North America Abies bifoliaAbies lasiocarpa A. lasiocarpa sec USDA > A. lasiocarpa sec FNA A. lasiocarpa sec USDA >A. bifolia sec FNA A. lasiocarpa v. lasiocarpa sec USDA >A. lasiocarpa sec FNA A. lasiocarpa v. lasiocarpa sec USDA | A. bifolia sec FNA A. lasiocarpa v. arizonica sec USDA <A. bifolia sec FNA var. lasiocarpa

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

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

Toward a new Atlas Carya carolinae-septentrionalis, Radford et al How to integrate new sources of data??

Carya carolinae-septentrionalis NCURABUSDACVS Add USDA PLANTS records & CVS vegetation plot data

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

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

How have things changed? Concept relationships of Southeastern US plants treated in different floras. Based on > 50,000 concept relationships Based on > 50,000 concept relationships

Taxonomic standards TDWG, TCS SEEK, TOS GUIDs, DOIs, LSISs IPNI

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

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 ~ Potentilla simplex sec Cronquist ~ Potentilla canadensis sec Cronquist Identifications

1.Absolutely wrong 2.Understandable but wrong 3.Acceptable but not typical 4.Good fit 5.Ideal, typical Uncertainty

FGDC, ESA, IAVS VegBank XML VegetWeb IAVS: NESCent EML –Supports blocks of data –No concepts, no identification uncertainty 4. Vegetation data standards

5.VegBank The ESA Vegetation Panel has developed VegBank-- a public archive for vegetation plots ( 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.

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:

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

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

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