Patrick Leary23 October, 2008TDWG Fremantle

Experiences With Species Profile Model

Current EOL Content

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Sources of content– Content Partners– User Contributions

(LifeDesks, Flickr, …)

Data objects– Classification– Descriptions– Multimedia– Occurrence Maps– Outlinks

Content Partners

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Content Partners (e.g. FishBase, Tree of Life, LifeDesks, …)

XML Schema

Processing

Content Cache

EOL Databases

APIs, Excel, Export

Models and Classes

APIs

Content Trajectory

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And that is now

“to have 1 million high-quality pages within 5 years and a complete Encyclopedia of known species within 10 years” Submission to the MacArthur Foundation

‘A major challenge in 2008 will be to maintain, or even increase, this pace, in order to meet our milestones” MacArthur Foundation report, 2007

Description of Pilot Project

Literature in– Marked up with GoldenGATE Editor

Served in Species Profile Model via REST service

Indexed by EOL for display on species pages

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GoldenGATE Markup

Digital Form

REST Service

Search Request SPM Species Profiles

EOL Index

RDF Parsing

LSID resolution

Technical Details

REST service to return Species Profile Models

SPM represented as RDF XML

RDF parsing in PHP– RDF API for PHP (RAP)

Source code available at http://sourceforge.net/projects/rdfapi-php/

TDWG LSID Resolvere.g. http://lsid.tdwg.org/urn:lsid:biosci.ohio-state.edu:osuc_pubs:5959

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Species Profile Model

Class: Species Profile Model

Class: InfoItem

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Property Range

aboutTaxon TaxonConcept

hasInformation InfoItem

Property Range

associatedTaxon TaxonConcept

category string

contextOccurence OccurenceRecord

context string

contextValue DefinedTerm

hasContent string

hasValue DefinedTerm

SPM Examples

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In Context

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Associations

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Current Classes of InfoItem

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LegislationLifeCycleLifeExpectancyLookAlikesManagementMigrationMolecularBiologyMorphologyPhysiologyPopulationBiologyProceduresReproductionRiskStatementSizeTaxonBiologyThreatsTrendsTrophicStrategyUse

AssociationsBehaviourBiologyConservationConservationStatusCyclicityCytologyDescriptionDiagnosticDescriptionDiseasesDispersalDistributionEcologyEvolutionGeneralDescriptionGeneticsGrowthHabitatKey

Current Classes of InfoItem

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LegislationLifeCycle

LifeExpectancy

LookAlikes

ManagementMigration

MolecularBiologyMorphologyPhysiology

PopulationBiologyProcedures

Reproduction

RiskStatementSizeTaxonBiologyThreatsTrendsTrophicStrategy

Use

Associations

Behaviour

BiologyConservationConservationStatusCyclicity

Cytology

DescriptionDiagnosticDescriptionDiseases

Dispersal

Distribution

Ecology

Evolution

GeneralDescriptionGenetics

Growth

Habitat

Key

More Structure

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Biology MolecularBiology PopulationBiology TaxonBiology

Conservation ConservationStatus Legislation Management RiskStatement Threats Trends

Description DiagnosticDescription GeneralDescription Morphology Size

Mapping to InfoItems

Initial mapping for Cypriniformes Tree of Life

Time consuming manual process

Support needed

Tools are desired to assist with mapping

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Mapping to InfoItems

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Morphology MorphologyGross external form MorphologyInternal anatomy MorphologyOsteology MorphologyPigmentation MorphologyIntegument and squamation MorphologyLateralis system MorphologyArmature MorphologyNuptial tuberculation and other structures MorphologyGenetics MorphologyKaryology MorphologyPloidy MorphologyHeritability MorphologySex determination MorphologyEnvironmental tolerances MorphologyLife history MorphologyNo-choice breeding experiments and interspecific genetic compatibility MorphologyNon-anthropogenic hybridization in the wild MorphologyAnthropogenic hybridization in the wild MorphologyGenetic manipulations Morphology

Physiology PhysiologyVisual pigments and structures PhysiologyAcousticolateralis system PhysiologySound production PhysiologyThermal biology and metabolism PhysiologyOxygen requirements PhysiologySalinity tolerance PhysiologyAcclimation to temperature and salinity PhysiologySalinity tolerances and osmoregulation PhysiologyTemperature PhysiologyOxygen PhysiologyInteraction effects of salinity and temperature on survivability PhysiologyEffects on reproduction and development PhysiologyHydrogen ion concentration PhysiologyEffects of age and interactions among environmental variables PhysiologyBehavioral responses to environmental extremes Physiology

Mapping to InfoItems

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ReproductionGeneral featuresFecundityAge at sexual maturityModes of spawningCourtship and spawningMate choiceParental careSpawning locationsLarval developmentSeasonalityEgg characteristics and developmentGrowth, sexual maturity, and life span

Reproduction

Mapping to InfoItems

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Reproduction

spmi:Reproductionctol_spmi:GeneralFeaturesctol_spmi:Fecundityctol_spmi:SexualMaturityctol_spmi:Spawningctol_spmi:Courtshipctol_spmi:MateChoicectol_spmi:ParentalCarectol_spmi:SpawningLocationsctol_spmi:LarvalDevelopmentctol_spmi:Seasonalityctol_spmi:EggCharacteristicsctol_spmi:SexualGrowth

Use Controlled Terms

Easier for consumers to interpret:

…is less ambiguous than

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Subject Predicate Object

urn:lsid:site.org:info_items:123 spm:hasValue status:Endemic

urn:lsid:site.org:info_items:123 spm:contextValue georegion:12

Subject Predicate Object

urn:lsid:site.org:info_items:123 spm:hasContent Endemic

hasInformation spm:context Southeastern Europe

Use Controlled Terms

TaxonName:

Specimen:

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Subject Predicate Object

urn:lsid:site.org:taxon_name:987 tn:rankString sp.

urn:lsid:site.org:taxon_name:987 tn:rankString especie

urn:lsid:site.org:taxon_name:987 tn:rank rank_terms:Species

Subject Predicate Object

urn:lsid:site.org:specimen:345 tsp:kindOfSpecimenString Picture

urn:lsid:site.org:specimen:345 tsp:kindOfSpecimenString Photograph

urn:lsid:site.org:specimen:345 tsp:kindOfSpecimenString Image

urn:lsid:site.org:specimen:345 tsp:kindOfSpecimen spec_type:StillImage

Attribution and Licensing

Is data different from content?

Much of TDWG ontology covers data

Species profiles can be data or content

Text descriptions have authors and can be creative works

Attribution is necessary for reuse and display

IPR varies by country

Explicit declarations needed for machine processing

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Attribution and Licensing

Dublin Core

Creative Commons

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Subject Predicate Object

urn:lsid:site.org:info_items:5 dc:creator John Smith

urn:lsid:site.org:info_items:5 dcterms:rights Available under CC-BY-NC 3.0

urn:lsid:site.org:info_items:5 dcterms:rightsHolder Marine Biological Laboratory

Subject Predicate Object

urn:lsid:site.org:info_items:5 dcterms:license http://creativecommons.org/licenses/by/3.0/

urn:lsid:site.org:info_items:5 dcterms:license http://creativecommons.org/licenses/by-nc/3.0/

urn:lsid:site.org:info_items:5 dcterms:license http://creativecommons.org/licenses/by-sa/3.0/

urn:lsid:site.org:info_items:5 dcterms:license Unknown

urn:lsid:site.org:info_items:5 dcterms:license Not Applicable

Final Thoughts

InfoItems need more structure / group-specific

Tools for mapping local DBs to InfoItems

More (diverse) SPM instance examples

Don’t forget about attribution and licensing

Would be nice to have easy local LSID resolvers

SPM Could use more attention from TDWG

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Thank You

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