TDWG SDD Oct 1516, 2002

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IMLSILLINOIS / NORTH CAROLINA COLLABORATIVE
ENVIRONMENT FOR BOTANICAL RESOURCES

• TDWG-SDD Design Discussion
• P. Bryan Heidorn
• October 15-16, 2002

2
Participants

• University of Illinois
• Grad. School of Library and Information Science
• Herbarium
• Illinois Natural History Survey and Herbarium
• University of North Carolina
• School of Information and Library Science
• North Carolina Botanical Garden

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Participants

• University of Illinois
• Grad. School of Library and Information
  ScienceLesley Deem, Xiao Hu, Jing Wu,
• Herbarium, Dave Siegler
• Illinois Natural History Survey and Herbarium,
  Ken Robertson, Michael Jeffords
• University of North Carolina
• School of Information and Library ScienceJane
  Greenberg, Evaline Daniels
• North Carolina Botanical GardenBob White

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Project Objectives

• Develop a distributed Polyclave
• Character Lists, Taxonomic descriptions
• Develop Distributed Taxonomic Descriptions
• Text, in situ images, ID images, herbarium sheets
• Highlight Museum Holdings
• Audience Citizen Scientists, Schools, Scientists

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Addressed Issues Encountered with Collaboration

• Inability to produce a final character matrix
• Introduction of new characteristics
• Differing definitions of like terms.
• Need to be defined in context
• Can not proliferate (reuse)

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Character (Image) Sharing
OA Harvester
PV.XML
Federated Database
OA Server
OA Server
Polyclave Server
UNC Database
UI Database
The world
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Open Archive

• Server from NCSA (Joe Futrelle)
• Project Programmer - Mark Sullivan (on
  OpenKeyDev)
• Maybe SOAP connection

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Open Archive Properties

• Harvester accesses resource list.
• Ask servers for new records
• Metadata oriented (Dublin core)
• Does not transport content directly
• For now, OpenArchive not needed, using httpspider

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Character (Image) Sharing
Web Harvester
PV.XML
Federated Database
HTTP Server
HTTP Server
Polyclave Server
UNC Database
UI Database
The world
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Distributed Properties

• Image and / or Character States need not be
  harvested until access time
• No change or new log in http unlike Open
  Archive
• Property definitions but not references may
  change without notification
• New instances may be added without notification

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Schemata

• Taxon Description
• Characteristic
• Character Value
• Character Image
• Contributor

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Component of Description
RefKeyCharacteristicIDValue
RefKeyCharacteristicID
ValueID
Image ID
ContributorID
Contributor may be used for all objects
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Decomposition and Distribution

• The selection of characteristics and their values
  can be distributed
• No need to have definitive set
• Potential for reuse in new taxonomic descriptions
• Potential for differing definitions but in well
  defined space

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Taxonomic Description

• Project Definition (ala Australia 2002)
• Identification Taxon
• Collection of Characteristics values

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Taxonomic Description

• Project Definition (ala Autralia 2002)
• Identification Taxon
• ltTaxongt ltRankgtSpecieslt/Rankgt ltNamegtEchinacea
  pallidalt/Namegt ltAuthoritygt(Nutt.)
  Nuttlt/Authoritygt ltVernaculargtPale purple
  coneflowerlt/Vernaculargt lt/Taxongt

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Taxon (Australia, 2002)
ltcharacter keyref"stipules, color"
type"nominal"gt (type should be in Characteristic
definitions) ltstate keyref"brown"
autoordered"no"gt ltmodifier keyref"dark
reddish-"/gt lt/stategt ltstate keyref"yellow"
autoordered"no"gt ltmodifier keyref"extremely
rarely"/gt lt/stategt lt/charactergt
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Preamble.. ltxsdelement name
"CharacterState"gt ltxsdcomplexTypegtltxsdsequencegt
ltxsdelement ref "Character"/gt ltxsdelement
ref "Value"/gt (State) ltxsdelement ref
"Image" minOccurs "0"/gt ltxsdelement ref
"Definition" minOccurs "0"/gt ltxsdelement ref
"Synonym" minOccurs "0"/gt ltxsdelement ref
"BroaderTerms" minOccurs "0"/gt ltxsdelement
ref "NarrowerTerms" minOccurs
"0"/gt ltxsdelement ref "RelatedTerms"
minOccurs "0"/gt lt/xsdsequencegt
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Character State
ltCharacters xmlnsxsi " http//www.w3.org/2001/XM
LSchema-instance" xsinoNamespaceSchemaLocation
" file///C/lesley/Character4.xsd"gt
ltCharactergtLeaf Shapelt/Charactergt
ltStategtlanceolatelt/Stategt ltImagegthttp//www.isr
l.uiuc.edu/openkey/demo/lanceolate.xmllt/Imagegt
ltImagegthttp//www.isrl.uiuc.edu/openkey/demo/lan
ceolate2.xmllt/Imagegt ltDefinitiongtLance-shaped
much longer than wide, with the widest point
below the middle.lt/Definitiongt ltSynonym/gt
ltBroaderTermsgtovallt/BroaderTermsgt
ltNarrowerTerms/gt ltRelatedTermsgtelliptic-lanceo
latelt/RelatedTermsgt lt/Charactersgt
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Character State Notes

• OpenKey needs to add ltwordinggt
• Inclusion of thesaurus fields

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Character Schema Element
ltxsdelement name "Value" type
"xsdstring"gt ltxsdannotationgt ltxsddocumentatio
ngtThis is the values of a "character" or
"characteristic" of an item, the value of a
property. For example the legal values for
/leaves/leaf_arrangement are alternate,
opposite, basal,whorled and cauline lt/xsddocumen
tationgt lt/xsdannotationgt
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Image Schema
ltxsdelement ref "Identifier"/gt ltxsdelement
ref "Description" minOccurs "0"/gt
ltxsdelement ref "CopyrightPermission"/gt
ltxsdelement ref "ImageLocation" minOccurs
"0"/gt ltxsdelement ref "CopyrightHolder"
minOccurs "0"/gt ltxsdelement ref "Source"
minOccurs "0"/gt ltxsdelement ref
"DerivedFrom" minOccurs "0"/gt ltxsdelement ref
"DateCreated" minOccurs "0"/gt ltxsdelement
ref "Species" minOccurs "0"/gt ltxsdelement
ref "ContributorID" minOccurs "0"/gt
ltxsdelement ref "SpecimenID" minOccurs "0"/gt
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Image Schema

• ltxsdelement ref "Identifier"/gt
• ltxsdelement ref "Description" minOccurs
  "0"/gt
• ltxsdelement ref "CopyrightPermission"/gt
• ltxsdelement ref "ImageLocation" gt
• ltxsdelement ref "CopyrightHolder" gt
• ltxsdelement ref "Source" minOccurs "0"/gt
• ltxsdelement ref "DerivedFrom" gt
• ltxsdelement ref "DateCreated" gt
• ltxsdelement ref "Species" minOccurs "0"/gt
• ltxsdelement ref "ContributorID gt
• ltxsdelement ref "SpecimenID" gt

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Abstract Structure
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Partial Candidate Structure
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Part wise Decomposition
Part
Connection
Leaf
Stem
Lobe
Blade
Sinus
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Part wise Decomposition
Part
Length
Connection
Width
Shape
Leaf
Length
Cardinality
Shape
Petiole
Lobe
Blade
Shape?
Length
Sinus
Cross section
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Part Relation

• (defclass Acorn-to-Cup (Connection)((Dominant
  initform 'Acorn) Reference object
  (Subservient initform 'AcornCup) Object being
  dominated (Dominant-Locus initform 'base)
  (Subservient-Locus initform 'InnerTop) (X-Angle
  initform 0) (Y-Angle initform 0) (Z-Angle
  initform 0) (RelLength initform .3)
  relative length of Subservient to Dominant
  (RelWidth initform 1.2) relative width to
  account for rim (RelDepth initform 1.2)
  relative depth of Subservient to Dominant))

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Design Objectives

• Support Distributed Image-based Polyclave Keys
• Distribution (OAI)
• Feature Lists w/ images
• Similarity Space
• Taxonomic Images and Description

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PlantCharacteristic

• lt?xml version"1.0"?gt
• lt!DOCTYPE PlantCharacteristic SYSTEM
  "http//soldev.isrl.uiuc.edu/webvibe/PlantCharact
  ers/PlantImageCharacteristic.dtd"gt
• ltImageElementsgt
• ltPartgtLeaf-Stemlt/Partgt
• ltValueNamegtAlternatelt/ValueNamegt
• ltDescriptiongtLeaf Arrangements -
  Alternatelt/Descriptiongt
• ltImageLocationgthttp//soldev.isrl.uiuc.edu/webvib
  e/PlantCharacters/images/AlternateLeaf.jpglt/ImageL
  ocationgt
• ltCopyrightHoldergtIllinois Natural History
  Surveylt/CopyrightHoldergt

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PlantCharacteristic

• ltSourcegtObserving, Photographing, and Collecting
  Plants. Illinois Natural History Survey Circular
  55, 1980lt/Sourcegt
• ltDateCreatedgtJanuary 29, 2002lt/DateCreatedgt
• ltSpeciesgtlt/Speciesgt
• ltDerivedFromgtAnother Imagelt/DerivedFromgt
• ltContributorgt
• ltContributorIDgtpbheidornlt/ContributorIDgt
• ltContributorNamegtP. Bryan
  Heidornlt/ContributorNamegt
• ltContributorDetailsgtUniversity of
  Illinois, GSLISlt/ContributorDetailsgt
• lt/ImageElementsgt

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Kevin Thiele's working document for SDD

• http//www.tdwg.org/tdwg2001/SDD_TDWG_2001.htm