EcoInformatics

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EcoInformatics Vegetation Science
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The symposium message Plant community ecology is
on the brink of a dramatic transformation that
will be made possible by the emergence of the new
field of ecoinformatics. An important role for
IAVS is to encourage, facilitate, and direct this
transformation.
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The challenge ecology is a science of
contingent generalizations, where future trends
depend (much more than in the physical sciences)
on past history and on the environmental and
biological setting. Robert May 1986.
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Traditional Community Ecology

• The questions
• How are communities structured?
• How do taxa interact?
• The solutions
• Simple observations.
• Simple experiments.
• The scale
• Stand or landscape.

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Major data types

• Site data climate, soils, topography, etc.
• Taxon attribute data identification, phylogeny,
  distribution, life-history, functional
  attributes, etc.
• Occurrence data attributes of individuals
  (e.g., size, age, growth rate) and taxa (e.g.,
  cover, biomass) that co-occur at a site.

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• EcoInformatics opportunities
• The availability of massive quantities of data
  (and co-occurrence data in particular) has the
  potential to create new directions and allow
  critical syntheses in ecology.
• Theoretical community ecology. Who occurs
  together, and where, and following what rules?
• Vegetation species modeling. Where should we
  expect species communities to occur after
  environmental changes?
• Remote sensing. What is really on the ground?
• Monitoring restoration. What changes are
  really taking place in the communities?

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How do we get there?

• Standard data structures.
• Public data archives (deposit, withdraw, cite,
  annotate).
• Standard exchange formats.
• Standard protocols.
• Tools for semantic mediation data discovery.

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• What next?
• International data exchange standard IAVS
• Requirement for data archiving JVS and other
  journals
• Requirement for documentation of taxonomic
  concepts
• Linked system of international databases

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• 2003 Charge to the Working Group
• Develop international data exchange standard
  including XML schema.
• Recommend standards and requirements for
  archiving plot data.
• Communicate with TDWG, IOPI, GBIF, ITIS and
  others regards our taxonomic database needs.
• Address issues related to requirements for
  extended queries, intellectual property rights,
  confidentiality.
• IAVS EcoInformatics Working Group website
  http//www.bio.unc.edu/faculty/peet/vegdata/

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An information infrastructure for vegetation
science in North America
Robert K. Peet University of North Carolina in
collaboration with Don Faber-Langendoen, Michael
Jennings, Dennis Grossman, Michael Lee, Mark
Anderson
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I am pleased to acknowledge the support and
cooperation of
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The North American Initiative

• Ecological Society of America Development of
  standards and implementation of peer review
  maintenance of VegBank archive.
• US Federal Geographic Data Committee
  Establishment of US government standards.
• NatureServe Maintenance and distribution of the
  International Classification of Ecological
  Communities.
• USDA PLANTS ITIS Maintenance of a standard
  taxonomic database for organisms.

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Physiognomic categories Category
Example Class . . . . . . . . . . Woodlands
Subclass . . . . . . .Mainly Evergreen Woodlands
Group . . . . . . . . .Evergreen
Needle-leaved Woodlands Subgroup . .
. . . Natural/Seminatural
Formation . . . . Evergreen Coniferous Woodland
with Rounded Crowns Floristic
categories Alliance . . . . .
. Juniperus occidentalis
Association . . . . Juniperus occidentalis
/ Artemesia tridentata
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Guidelines for Vegetation Classification The ESA
Vegetation Panel and its partners have
collaborated to develop guidelines for the
floristic levels of the classification covering

• Requirements for vegetation field plots.
• Documentation description of floristic types.
• Submission peer review of proposed types.
• Management, citation, archiving of vegetation
  data.

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• Guidelines for describing
• the associations and alliances of the
• U.S. National Vegetation Classification.
• Michael Jennings, Don Faber-Langendoen,
  Robert Peet, Orie Loucks, David Glenn-Lewin,
  Antoni Damman, Michael Barbour, Robert Pfister,
  Dennis Grossman, David Roberts, David Tart,
  Marilyn Walker, Stephen Talbot, Joan Walker, Gary
  Hartshorn, Gary Waggoner, Marc Abrams, Alison
  Hill, Marcel Rejmanek
• The Ecological Society of America Vegetation
  Classification Panel. Version 4.0. July, 2004
• http//www.esa.org/vegweb/
• Under review by FGDC as a U.S. federal standard

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Overview of online resources
Stores plots and makes them publicly accessible
Stores current communities in the NVC
Stores current plant taxonomy
Allows people to change and update NVC and plants
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US-NVC--- Proposed data flow
NatureServe Explorer
Extraction
NatureServe Biotics
Classification Mgt.
NVC Proceedings
US-NVC Panel
Peer Review
Revision Proposal
Legend
External Action
Analysis Synthesis
Internal Action
VegBank other plot archives
Entity
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• VegBank
• The ESA Vegetation Panel is developing a public
  archive for vegetation plots known as VegBank
  (http//vegbank.org).
• 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.
• The database architecture is generalizable to
  most types of species co-occurrence data.

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Challenges

• Distributed databases and data exchange formats
• Data ownership, intellectual property rights,
  confidentiality
• Multiple classifications of organsms and
  communities
• Multiple plot types (relevés Hubbell plots)
• Data entry submission tools
• Perfect archiving
• Plot and taxon interpretation

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Biodiversity data structure
SynTaxon
Community type databases
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Core elements of VegBank
Project
Plot
Plot Observation
Taxon / Individual Observation
Taxon Interpretation
Plot Interpretation
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http//www.vegbank.org
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• VegBank Interface Tools
• Desktop client (VegBranch) for data preparation
  and local use.
• Flexible XML data import supporting VegBranch
  TurboVeg formats.
• Flexible data export.
• Easy web access to central archive

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VegBranch can be used for converting legacy data,
entering data, and maintaining a local plot
database.
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The Taxonomic database challengeStandardizing
organisms and communities The problem
Integration of data potentially representing
different times, places, investigators and
taxonomic standards. The traditional solution
A standard list of organisms / communities.
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• Most standardized taxon lists fail to allow
  effective integration of datasets
• 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.
• The single largest impediment to large-scale
  synthesis in community ecology

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Three concepts of shagbark hickory Splitting one
species into two illustrates the ambiguity often
associated with scientific names. If you
encounter the name Carya ovata (Miller) K. Koch
in a database, you cannot be sure which of two
meanings applies.
Carya carolinae-sept. (Ashe) Engler Graebner
Carya ovata (Miller)K. Koch
Carya ovata (Miller)K. Koch
sec. Gleason 1952
sec. Radford et al. 1968
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A taxonon concept represents a unique combination
of a name and a reference taxon concept is
equivalent to Potential taxon taxonomic
assertion
Name
Reference
Concept
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Six shagbark hickory assertions Possible
taxonomic synonyms are listed together
Names Carya ovata Carya carolinae-septentrionalis
Carya ovata v. ovata Carya ovata v. australis
Taxon 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
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• Party Perspective
• The Party Perspective on an Assertion
  includes
• Status Standard, Nonstandard, Undetermined
• Correlation with other assertions Equal,
  Greater, Lesser, Overlap, Undetermined.
• Lineage Predecessor and Successor assertions.
• Start Stop dates.

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http//www.natureserve.org/explorer
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Coming soon direct links to views of typal and
occurrence plots in VegBank
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• Concluding remarks
• Much of what we are doing in the US is common to
  the vegetation classification enterprise
  worldwide, but much is also novel. We need and
  encourage greater international communication and
  collaboration.
• Public plot archives, initially driven by the
  classification enterprise, have the potential to
  radically change the development of vegetation
  science in general.