1. Patrick Leary 23 October, 2008 TDWG Fremantle Experiences With Species Profile Model

2. Current EOL Content 2 Sources of content –Content Partners –User Contributions (LifeDesks, Flickr, …) Data objects –Classification –Descriptions –Multimedia –Occurrence Maps –Outlinks

3. Content Partners 3

4. Content Partners (e.g. FishBase, Tree of Life, LifeDesks, …) XML Schema Processing Content Cache EOL Databases APIs, Excel, Export Models and Classes APIs

5. Content Trajectory 5 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

6. 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 6

7. 7 GoldenGATE Markup Digital Form REST Service Search Request SPM Species Profiles EOL Index RDF Parsing LSID resolution

8. 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 Resolver e.g. http://lsid.tdwg.org/urn:lsid:biosci.ohio-state.edu:osuc_pubs:5959 8

9. Species Profile Model Class: Species Profile Model Class: InfoItem 9 PropertyRange aboutTaxonTaxonConcept hasInformationInfoItem PropertyRange associatedTaxonTaxonConcept categorystring contextOccurenceOccurenceRecord contextstring contextValueDefinedTerm hasContentstring hasValueDefinedTerm

10. SPM Examples 10

11. In Context 11

12. Associations 12

13. Current Classes of InfoItem 13 Legislation LifeCycle LifeExpectancy LookAlikes Management Migration MolecularBiology Morphology Physiology PopulationBiology Procedures Reproduction RiskStatement Size TaxonBiology Threats Trends TrophicStrategy Use Associations Behaviour Biology Conservation ConservationStatus Cyclicity Cytology Description DiagnosticDescription Diseases Dispersal Distribution Ecology Evolution GeneralDescription Genetics Growth Habitat Key

14. Current Classes of InfoItem 14 Legislation LifeCycle LifeExpectancy LookAlikes Management Migration MolecularBiology Morphology Physiology PopulationBiology Procedures Reproduction RiskStatement Size TaxonBiology Threats Trends TrophicStrategy Use Associations Behaviour Biology Conservation ConservationStatus Cyclicity Cytology Description DiagnosticDescription Diseases Dispersal Distribution Ecology Evolution GeneralDescription Genetics Growth Habitat Key

15. More Structure 15 Biology MolecularBiology PopulationBiology TaxonBiology Conservation ConservationStatus Legislation Management RiskStatement Threats Trends Description DiagnosticDescription GeneralDescription Morphology Size

16. Mapping to InfoItems Initial mapping for Cypriniformes Tree of Life Time consuming manual process Support needed Tools are desired to assist with mapping 16

17. Mapping to InfoItems 17 Morphology Gross external formMorphology Internal anatomyMorphology OsteologyMorphology PigmentationMorphology Integument and squamationMorphology Lateralis systemMorphology ArmatureMorphology Nuptial tuberculation and other structuresMorphology GeneticsMorphology KaryologyMorphology PloidyMorphology HeritabilityMorphology Sex determinationMorphology Environmental tolerancesMorphology Life historyMorphology No-choice breeding experiments and interspecific genetic compatibilityMorphology Non-anthropogenic hybridization in the wildMorphology Anthropogenic hybridization in the wildMorphology Genetic manipulationsMorphology Physiology Visual pigments and structuresPhysiology Acousticolateralis systemPhysiology Sound productionPhysiology Thermal biology and metabolismPhysiology Oxygen requirementsPhysiology Salinity tolerancePhysiology Acclimation to temperature and salinityPhysiology Salinity tolerances and osmoregulationPhysiology TemperaturePhysiology OxygenPhysiology Interaction effects of salinity and temperature on survivabilityPhysiology Effects on reproduction and developmentPhysiology Hydrogen ion concentrationPhysiology Effects of age and interactions among environmental variablesPhysiology Behavioral responses to environmental extremesPhysiology

18. Mapping to InfoItems 18 Reproduction General features Fecundity Age at sexual maturity Modes of spawning Courtship and spawning Mate choice Parental care Spawning locations Larval development Seasonality Egg characteristics and development Growth, sexual maturity, and life span Reproduction

19. Mapping to InfoItems 19 Reproduction spmi:Reproduction ctol_spmi:GeneralFeatures ctol_spmi:Fecundity ctol_spmi:SexualMaturity ctol_spmi:Spawning ctol_spmi:Courtship ctol_spmi:MateChoice ctol_spmi:ParentalCare ctol_spmi:SpawningLocations ctol_spmi:LarvalDevelopment ctol_spmi:Seasonality ctol_spmi:EggCharacteristics ctol_spmi:SexualGrowth

20. Use Controlled Terms Easier for consumers to interpret: …is less ambiguous than 20 SubjectPredicateObject urn:lsid:site.org:info_items:123spm:hasValuestatus:Endemic urn:lsid:site.org:info_items:123spm:contextValuegeoregion:12 SubjectPredicateObject urn:lsid:site.org:info_items:123spm:hasContentEndemic hasInformationspm:contextSoutheastern Europe

21. Use Controlled Terms TaxonName: Specimen: 21 SubjectPredicateObject urn:lsid:site.org:taxon_name:987tn:rankStringsp. urn:lsid:site.org:taxon_name:987tn:rankStringespecie urn:lsid:site.org:taxon_name:987tn:rankrank_terms:Species SubjectPredicateObject urn:lsid:site.org:specimen:345tsp:kindOfSpecimenStringPicture urn:lsid:site.org:specimen:345tsp:kindOfSpecimenStringPhotograph urn:lsid:site.org:specimen:345tsp:kindOfSpecimenStringImage urn:lsid:site.org:specimen:345tsp:kindOfSpecimenspec_type:StillImage

22. 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 22

23. Attribution and Licensing Dublin Core Creative Commons 23 SubjectPredicateObject urn:lsid:site.org:info_items:5dc:creatorJohn Smith urn:lsid:site.org:info_items:5dcterms:rightsAvailable under CC-BY-NC 3.0 urn:lsid:site.org:info_items:5dcterms:rightsHolderMarine Biological Laboratory SubjectPredicateObject urn:lsid:site.org:info_items:5dcterms:licensehttp://creativecommons.org/licenses/by/3.0/ urn:lsid:site.org:info_items:5dcterms:licensehttp://creativecommons.org/licenses/by-nc/3.0/ urn:lsid:site.org:info_items:5dcterms:licensehttp://creativecommons.org/licenses/by-sa/3.0/ urn:lsid:site.org:info_items:5dcterms:licenseUnknown urn:lsid:site.org:info_items:5dcterms:licenseNot Applicable

24. 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 24

25. Thank You 25

26. 26 All information currently in the public domain will remain in the public domain. Content providers are required to adopt a Creative Commons license for the information that they serve through the EOL. Except for public- domain content, the default and preferred license is CC-BY Content providers who request some restrictions on re- use of their information may select: CC-BY-SA CC-BY-NC CC-BY-NC-SA Licensing Policy for Content Partners To the greatest extent possible, the Encyclopedia of Life promotes an open-source, open-access approach. The EOL will provide attribution information for all content that it serves. EOL will also indicate the Creative Commons license attached to each object (text, structured data, graphics, multimedia, etc.). V5.0 5 April 2008