the canopy database project observation model canopy . evergreen
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1Cushing; NCEAS 2007 – Observation Workshop
The Canopy Database Project Observation Model
http://canopy.evergreen.edu
The Canopy Database Project Observation Model
http://canopy.evergreen.edu
Judy Cushing, Nalini Nadkarni
Anne McIntosh, Lee Zeman and others
The Evergreen State College
Judy Cushing, Nalini Nadkarni
Anne McIntosh, Lee Zeman and others
The Evergreen State College
NSF CISE and BIO 04-0417311, 03-019309, 01-31952, 01-9309 99-75510, 9630316, 93-07771
Ecologists
Van Pelt, Bond, Dial, Ishii, Keim, Parker, Shaw, Sillett, Sumida, et al
LTER IMs & Network Folks
N. Kaplan SGS, K. Vanderbilt SEV, K. Ramsey JRN, E. Melendez LUQ, J.
Brunt NET, M. Servilla NET
Computer Scientists
Dave Maier
Lois Delcambre
(PSU)
Collaborators
2Cushing; NCEAS 2007 – Observation Workshop
Canopy DB ProjectCanopy DB ProjectStudying complex ecosystems across multiple scales requires data
integration & analysis and synthesis… different types of information – different formats & different sources….
To synthesize, data must be archived & documented, locatable & integrate-able• Who has time to document data… (need better tools)• What documentation is useful…(need synthesis case studies)
Database & Component Technology could help, BUT Ecology studies cannot afford programmers, and
Scientists want to do research, not be programmers.
We aim for Eco-Informatics tools that enable scientists to program• Increase individual (field ecologist) researcher productivity….• Facilitate later data integration and ecological synthesis
3Cushing; NCEAS 2007 – Observation Workshop
Canopy DB Project Scientific Vision
Thousand Year Chronosequence (1kcs)
Canopy DB Project Scientific Vision
Thousand Year Chronosequence (1kcs)
1. Categorize within-tree & -stand structure across age classes.
2. Conduct structure-function synthesis. Relate structure (stems, crowns, understory, branches, interstices, etc.) to functional characteristics (through-fall, light, sap-flow, water use).
Forest structure determines forest functions.
Image by Bob Van Pelt
4Cushing; NCEAS 2007 – Observation Workshop
Canopy DB Primary Use CasesCanopy DB Primary Use Cases1. Given a study design, create a research database using system-
supplied domain-specific Components• Empty MS Access database or Excel spreadsheet, metadata
profile, input forms, validation.2. Create-edit components (templates)
• End user (or user community) template library.3. Given a database in our format, generate standard
visualizations, e.g., impose observations on structural data.4. Upload to and download from a data repository (Study Center).
Dwarf Mistletoe (Arceuthobium) infection in a Pacific Northwest forest
Data: David Shaw
5Cushing; NCEAS 2007 – Observation Workshop
Canopy DBObservation Model Overview
Canopy DBObservation Model Overview
Domain Type Is of Obs. Type Has Units Has Modifier Nat Lang Equiv
length, height linear measure m, cm, ft, yd, … crown-, … Measure of distance
diameter, DBH, … stem-, …
isDead, Boolean A truth value
(true/false, yes/no, …)isAlive,
isSampled
species Enumerated-
type
{coded value} pnw-conifer-,… A set of
code-value pairs{user-defined, e.g., status, decay class}
count Count -- <species-cd>
Evergreen,
herbacious
A summary value of the number of some set of things
tally
total
6Cushing; NCEAS 2007 – Observation Workshop
Organization of the Implemented Model Objects and Observations translate to templates Organization of the Implemented Model
Objects and Observations translate to templates
DBH
Stem
Height
Branch
Length
Spread
ENTITIES
OBSERVATIONS
Species
7Cushing; NCEAS 2007 – Observation Workshop
Organization of the Implemented Model Templates “understand” observation structureOrganization of the Implemented Model Templates “understand” observation structure
DBH
Stem
Height
Branch
Length
Spread
1 Many
Species
Species
Name
Auth.
1 1
8Cushing; NCEAS 2007 – Observation Workshop
Canopy DBAssociated tools, features, framework
Canopy DBAssociated tools, features, framework
1. Canopy DataBank – generates research field database and EML metadata file.
2. Component (template) Library Editor – creates an end user (or user community) template library.
3. CanopyView – performs data visualization on DataBank DBs.
4. Canopy Study Center – Online Warehouse for Canopy DBs.
9Cushing; NCEAS 2007 – Observation Workshop
MS Access Database
Forms
Ecological Metadata Language document *_eml.xml
Ecological Metadata Language document *_eml.xml
DocumentationDocument
DataBank ProductsDataBank Products.HTMLFile.HTMLFile
Other Metadata Software
.mdb file.mdb file
.xls file.xls fileMS Excel SpreadsheetMicrosoft Excel.lnk
10Cushing; NCEAS 2007 – Observation Workshop
MS Access Database
Forms
*_eml.xml*_eml.xml
.CVState File.CVState File
_workspace.xml_workspace.xml
DocumentationDocument
DataBank ProductsDataBank Products.HTMLFile.HTMLFile
Other Metadata Software
.mdb file.mdb file
.xls file.xls file MS Excel Spreadsheet
CanopyViewCanopyView
11Cushing; NCEAS 2007 – Observation Workshop
How the ‘Observation’ became Central First Cut Templates were structure-based
How the ‘Observation’ became Central First Cut Templates were structure-based
Branch Foliage Model
FoliageStart, stop
Foliageinner, mid,outer
Foliagelength andwidth
Upright linear,Height only
Upright cylinder,Height, DBH
Upright stepped cylinder,Multiple girth measures
Upright cone,Height, DBH
Stem Model
Branch lengthperpendicularto stem
Branch lengthalong branch
Branch Length Measurement
Validate generated databases with rulese.g., Stem:
• depends on study area, plot• includes species table
Capitalize on core components for toolsVisualization, Metadata Provision,Data Acquisition & Validation, research protocol, statistical analysis….
12Cushing; NCEAS 2007 – Observation Workshop
Current DataBank TemplatesObservation-Based
Current DataBank TemplatesObservation-Based
1. Entities = structural components of the
forest canopy
2. Observations = measurements taken
on an entityBranch length along branch
Branch length perpendicular to
stem
13Cushing; NCEAS 2007 – Observation Workshop
Templates in Data DesignTemplates in Data Design
Green = entity Blue = observation
14Cushing; NCEAS 2007 – Observation Workshop
MS Access DataBank DesignMS Access DataBank Design
15Cushing; NCEAS 2007 – Observation Workshop
CanopyView CanopyView
Dwarf Mistletoe (Arceuthobium) infection in a PacificNorthwest forest
Data: David Shaw
Foliage coverage on two Douglas Firs (Pseudotsugamenziesii).
Data: Robert Van Pelt
16Cushing; NCEAS 2007 – Observation Workshop
Model Extensibility(what we do)
Model Extensibility(what we do)
1. How do we extend … if new domain terms• the model has been static• the tool (DataBank) – use the Template Editor• the tool (CanopyView) – designate color-coding
2. Restrictions on allowed extensions – none for now
3. How extensions are supported• Template Library Editor
17Cushing; NCEAS 2007 – Observation Workshop
Model Extensibility(what we’d like to do)Model Extensibility
(what we’d like to do)
1. How do we extend … if new domain terms• Better connections between the model and the tool(s) • Template library naming • Identification by CanopyView of ‘observations’ and codes• Connect templates to higher level abstractions
• structure, conceptual framework
2. Add some restrictions on allowed extensions
3. How extensions are supported• Add theoretical restrictions to Template Editor• Use better naming conventions• StudyCenter query capabilities, linked to observations
18Cushing; NCEAS 2007 – Observation Workshop
Collection, Network, Continuous ComponentCollection, Network, Continuous Component
0-, 1-, 2-, 3-dimensionalA.
. . … … … . . .. . . ..
0 1 2 3
Reactive or non-reactive B.
Spatially referenced or spatially independentC.
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