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

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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

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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….

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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

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Templates in Data DesignTemplates in Data Design

Green = entity Blue = observation

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MS Access DataBank DesignMS Access DataBank Design

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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.