ecoinformatics & vegetation science

EcoInformatics &

Vegetation Science

The symposium messagePlant 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.

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.

Traditional Community Ecology

The questions:• How are communities structured?• How do taxa interact?

The solutions :• Simple observations.• Simple experiments.

The scale:• Stand or landscape.

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.

EcoInformatics opportunitiesThe 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?

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.

What next? 1. International data exchange standard –

IAVS 2. Requirement for data archiving – JVS and

other journals3. Requirement for documentation of

taxonomic concepts4. Linked system of international databases

2003 Charge to the Working Group

1. Develop international data exchange standard including XML schema.

2. Recommend standards and requirements for archiving plot data.

3. Communicate with TDWG, IOPI, GBIF, ITIS and others regards our taxonomic database needs.

4. 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/

An information infrastructure for

vegetation science in North America

Robert K. PeetUniversity of North Carolina

in collaboration with Don Faber-Langendoen, Michael Jennings, Dennis Grossman, Michael Lee, & Mark Anderson

I am pleased to acknowledge the support and cooperation

of:

Ecological Society of America

Gap Analysis Program

National Center for Ecological Analysis and Synthesis

National Biological Information Infrastructure

Federal Geographic Data Committee

National Science Foundation

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.

Physiognomic categoriesCategory ExampleClass . . . . . . . . . . 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

• Requirements for vegetation field plots.• Documentation & description of floristic

types.• Submission & peer review of proposed

types.• Management, citation, & archiving of

vegetation data.

Guidelines for Vegetation Classification

The ESA Vegetation Panel and its partners have collaborated to develop guidelines for the floristic levels of the classification covering:

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

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

vegbank.org natureserve.org

plants.usda.govTBA

NatureServe Biotics

Classification Mgt.

US-NVC Panel

Revision Proposal

Analysis & Synthesis

VegBank & other plot archives

US-NVC---

Proposed data flowExtraction

NatureServe Explorer

Peer Review

NVC Proceedings

Legend

External Action

Internal Action

Entity

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.

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

Biodiversity data structure

Taxonomic databases

Plot/Inventory databases

Specimen databases

Observation/CollectionEvent

Object or specimen

BioTaxon

Locality

SynTaxon

Community type databases

Project

Plot PlotObservation

Taxon / Individual Observation

Taxon Interpretation

PlotInterpretation

Core elements of VegBank

http://www.vegbank.org

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

VegBranch can be used for converting legacy data, entering data, and

maintaining a local plot database.

The Taxonomic database challenge:

Standardizing 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.

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

Carya ovata(Miller)K. Koch

Carya carolinae-sept.(Ashe) Engler & Graebner

Carya ovata(Miller)K. Kochsec. Gleason

1952sec. Radford et al. 1968

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.

Name ReferenceConcept

A taxonon concept represents a unique combination of a name and

a reference

“taxon concept” is equivalent to “Potential taxon” & “taxonomic assertion”

NamesCarya ovata Carya carolinae-septentrionalisCarya ovata v. ovataCarya ovata v. australis

Taxon concepts(One shagbark)C. ovata sec Gleason ’52C. ovata sec FNA ‘97

(Southern shagbark)C. carolinae-s. sec Radford ‘68C. ovata v. australis sec FNA ‘97

(Northern shagbark)C. ovata sec Radford ‘68C. ovata (v. ovata) sec FNA ‘97

ReferencesGleason 1952 Britton & BrownRadford et al. 1968 Flora CarolinasStone 1997 Flora North America

Six shagbark hickory assertionsPossible taxonomic synonyms are listed

together

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.

http://www.natureserve.org/explorer

Coming soon – direct links to views of

typal and occurrence plots in VegBank

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.