1. Vegetation Data Management:
VegBank
John Harris - NCEAS
January 9, 2002
Funding: National Science Foundation (DBI )

2. VegBank Project organized and conducted by:
Robert K. Peet, University of North Carolina
Marilyn Walker, USDA Forest Service & U. Alaska
Dennis Grossman, The Nature Conservancy / NatureServe
Michael Jennings, USGS-BRD
John Harris, NCEAS
Project supported by:
National Center for Ecological Analysis & Synthesis
U.S. National Science Foundation
USGS-BRD Gap Analysis Program
NatureServe / The Nature Conservancy

3. VegBank Design Goals Support the National Vegetation Classification.
Provide a comprehensive facility to store the most
commonly collected vegetation plot data attributes.
Provide the user with a large number of user-defined
attributes to store not-so-commonly collected data.
Integrate plots with the dynamic plant taxonomy
and vegetation community data.

4. Core elements of the National Plots Database
Project
Plot
Plot
Observation
Taxon
Observation
Taxon
Interpretation
Plot
Interpretation

10. Partial view of the VegBank
Entity-Relationship Diagram
Partial view of the VegBank
Entity-Relationship Diagram

11. VegBank Plots Database

12. Taxonomy Module Smithsonian meeting:
Peet-Taswell model vs Berendsohn model
FGDC Biological Nomenclature Working Group
Update on NatureServe & HDMS
Prospects for implementation

13. A usage represents a unique combination of a taxon and a name.
Usages can be used to track nomenclatural synonyms
Name
Usage
Taxon

16. ‘www.VegBank.org’ beta release March 2002
Bulk of work to date has been on the ‘back-end’ and that have been waiting for the meeting to discuss the ‘front-end’ or interface issues
Maybe this should only be the backend discussion?
Conceptual diagrams showing client server relationships
show the architectural/system diagrams - servlet
information
question the importance of a standalone system and
discuss the use of morpho and beans
pinpoint the integration of the chosen tools to the system
that already has been designed

18. Bulk of work to date has been on the ‘back-end’ and that have been waiting for the meeting to discuss the ‘front-end’ or interface issues
Maybe this should only be the backend discussion?
Conceptual diagrams showing client server relationships
show the architectural/system diagrams - servlet
information
question the importance of a standalone system and
discuss the use of morpho and beans
pinpoint the integration of the chosen tools to the system
that already has been designed

21. Publication
Analysis
Extraction
Archival
Integration
Collection

22. Development Cycle Preliminary design Build prototype #1 interface
User
evaluates
Evaluation
studied by
designer
Design
modification
are made
prototype #n
Supported by 3 other NCEAS Developers
Database Design: Aug – Jan. 2001
Interface Design: Nov – Feb. 2001
Backend Development: Jan
Interface Development: Mar –
Backend Version: Prototype 3
Interface Version: Prototype 1
Expected Beta Release: Late Sept. – Mid Oct.

24. Taxonomy Database Design Goals
Logical separation of a "taxonomic name" with the
"taxonomic concept", so that taxonomic data
can be stored at the most 'atomic' level without ambiguity
The ability to incorporate multiple organizations' 'views'
of how a taxonomic name is applied to a taxonomic concept
The ability to link a taxonomic name used in the Plots
database with a 'name - concept' pair in the taxonomic
database.
*Although one can store vegetation community data in the same database table-structure as the plant
taxonomy database, we have implemented two separate table structures and have created two separate data sets.

25. Development Choices
Representative tools reflect the desire to have the following features:
High performance
Robust
Open architecture
Platform neutral
Scaleable
Recognition that tools will have to be flexible/scaleable to act as central server and a desktop client
minimum hardware requirements
this is not locked because the interface design may impact the use of some of these tools

26. Features - JAVA
Java -- Write once, Cross platform – Linux, Windows, MacOS*
Java Servlet -- Dynamic, database-driven,
web content
JDBC -- Connect to any database - Oracle, PostgreSql, SQL Server backend
Swing -- Classy interface tools
Beans -- Reusable components
Servlets: dynamic html generation including media generated from:
database query results
logic
calculations etc..
* Not tested yet :-)

27. Features - XML XML: is the format for structured data on the Web.
Simple and flexible data conversions, using XSLT
Straightforward to write generic tools which export parts of a relational database as XML encoded data, or even to write generic code that serializes Java (or other) objects as XML
data structures.
Examples later…
Recognition that tools will have to be flexible/scaleable to act as central server and a desktop client

28. An Example Workflow Using Wisconsin Plots Data
What data integration means to us
Taxonomic / Semantic Integration
Data formatting for database ingestion
General Comments about Current Format
Data Parsing
Transformation to XML standard
Legacy Data Loader

29. Plots Data Integration & DB Ingestion
Reformat by Hand
Research
MS Access
MS Excel
Perl
Shell scripts ?
Plots DB
Integration
What is meant by data integration? …

30. (Ashe) Engler & Graebner
Taxonomic Integration
Carya ovata
(Miller)K. Koch
Carya carolinae-sept.
(Ashe) Engler & Graebner
sec. Gleason 1952
sec. Radford et al. 1968
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.
Integration

31. Semantic Integration of Plot Attributes
‘Basic yet Important’
Cover Scales
Strata Dimensions
Environmental Attributes
Integration

32. XML Parse Data from Forms into Table Structure to be Transformed into
XML Consistent with the Database Structure
Text
Forms
Columnar
Tables
XML
Integration

33. Parsed Data
Text
Forms
Columnar
Tables
Integration

34. Plots DB XML Data Definition (XML)
Transform Parsed Data to XML Consistent with the Plots Database
Columnar
Tables
Legacy
Data
Loader
Plots DB
XML
Data Definition (XML)
Integration

35. Data Definition (XML) – Single file
<plotDataPackage>
<plotDataFile>
<fileName>siteData.csv</fileName>
<attributeDelimeter>’,’</attributeDelimeter>
<fileTheme> site data </fileTheme>
<attribute>
<attributeName>plotCode</attributeName>
<plotDBAttribute>authorPlotCode</plotDBAttribute>
<attributePosition>1</attributePosition>
</attribute>
<attributeName>communityName</attributeName>
<plotDBAttribute>communityName</plotDBAttribute>
<attributePosition>2</attributePosition>
… <state>
</plotDataFile>
</plotDataPackage>
Integration

36. Data Definition (XML) – Multiple files
<plotDataFile>
<fileName>vegData.csv</fileName>
<constraint>
<fileName>siteData.csv</fileName>
<themeName> site data </themeName>
<attributeName>authorPlotCode</attributeName>
<cardnality>'+'</cardnality>
</constraint>
<attributeDelimeter>‘,’</attributeDelimeter>
<fileTheme>species</fileTheme>
<attribute>
<attributeName>plotName</attributeName>
<plotDBAttribute>authorPlotCode</plotDBAttribute>
<attributePosition>1</attributePosition>
</attribute>
<attributeName>scientificName</attributeName>
<plotDBAttribute>taxonName</plotDBAttribute>
<attributePosition>2</attributePosition>
Integration

37. Plots Database XML Integration <strata> <plot>
<authorPlotCode> </authorPlotCode>
<plotType> </plotType>
<samplingMethod> </samplingMethod>
<plotOriginLat> </plotOriginLat>
<plotOriginLong> </plotOriginLong>
<plotShape> </plotShape>
<plotSize> </plotSize>
<plotSizeAcc> </plotSizeAcc>
<altValue> </altValue>
<altPosAcc> </altPosAcc>
<slopeAspect> </slopeAspect>
<slopeGradient> </slopeGradient>
<slopePosition> </slopePosition>
<hydrologicRegime> </hydrologicRegime>
<soilDrainage> </soilDrainage>
<surfGeo> </surfGeo>
<plotObservation>
<previousPlot> </previousPlot>
<plotStartDate> </plotStartDate>
<plotStopDate> </plotStopDate>
<dateAccuracy> </dateAccuracy>
<effortLevel> </effortLevel>
<strata>
<stratumCover> </stratumCover>
<stratumHeight> </stratumHeight>
</strata>
<taxonObservations>
<authNameId> </authNameId>
<originalAuthority> </originalAuthority>
<strataComposition>
<strataType> </strataType>
<percentCover> </percentCover>
</strataComposition>
</taxonObservations>
<communityType>
<classAssociation> </classAssociation>
<classQuality> </classQuality>
<startDate> </startDate>
<stopDate> </stopDate>
</communityType>
</plotObservation>
<plotContributor>
<role> </role>
<party> </party>
</plotContributor>
</plot>
Integration

38. Existing Prototype Functionality
Bulk of work to date has been on the ‘back-end’ and that have been waiting for the meeting to discuss the ‘front-end’ or interface issues
Maybe this should only be the backend discussion?
Conceptual diagrams showing client server relationships
show the architectural/system diagrams - servlet
information
question the importance of a standalone system and
discuss the use of morpho and beans
pinpoint the integration of the chosen tools to the system
that already has been designed

39. Vegetation Database Client
Bulk of work to date has been on the ‘back-end’ and that have been waiting for the meeting to discuss the ‘front-end’ or interface issues
Maybe this should only be the backend discussion?
Conceptual diagrams showing client server relationships
show the architectural/system diagrams - servlet
information
question the importance of a standalone system and
discuss the use of morpho and beans
pinpoint the integration of the chosen tools to the system
that already has been designed

40. Agenda:
Over-Arching Concepts
Project Overview
· Impact
· Database Design
· System Architecture
· Challenges
Use-Case Example: Wisconsin Data
Data Management Recommendations
Future Directions

41. Bulk of work to date has been on the ‘back-end’ and that have been waiting for the meeting to discuss the ‘front-end’ or interface issues
Maybe this should only be the backend discussion?
Conceptual diagrams showing client server relationships
show the architectural/system diagrams - servlet
information
question the importance of a standalone system and
discuss the use of morpho and beans
pinpoint the integration of the chosen tools to the system
that already has been designed

42. Bulk of work to date has been on the ‘back-end’ and that have been waiting for the meeting to discuss the ‘front-end’ or interface issues
Maybe this should only be the backend discussion?
Conceptual diagrams showing client server relationships
show the architectural/system diagrams - servlet
information
question the importance of a standalone system and
discuss the use of morpho and beans
pinpoint the integration of the chosen tools to the system
that already has been designed

43. Bulk of work to date has been on the ‘back-end’ and that have been waiting for the meeting to discuss the ‘front-end’ or interface issues
Maybe this should only be the backend discussion?
Conceptual diagrams showing client server relationships
show the architectural/system diagrams - servlet
information
question the importance of a standalone system and
discuss the use of morpho and beans
pinpoint the integration of the chosen tools to the system
that already has been designed

44. Vegetation Desktop Database Client

49. Extra slides to follow:

52. General Data Management Practices
general formats
weird formats
unusable formats
modeled the software after the way that people
collect plots data -- at least that is what I thought
At times tortuous path to the database in terms of
reformating
class indicies (these are rectified at the
plots loading software step)

53. Management Case: Example from Wisconsin
Baraboo Hills -- Collected Yesterday
PEL -- Legacy Data

54. Data Transformation of Forms