TDWG 2007 Bratislava SPM from an SDD perspective: Generality and extensibility Gregor Hagedorn Federal Biological Research Center, Berlin, Germany

SDD Purpose was (From SDD Charter:) Develop standard computer-based mechanisms for expressing and transferring descriptive information about biological organisms or taxa (as well as similar entities such as diseases), including terminologies, ontologies, descriptions, identification tools and associated resources.

SPM vs. SDD SpeciesProfileModelCodedDescription |NaturalLanguageDescription aboutTaxon: The taxon this information is about.Scope/TaxonName associatedTaxon: Another taxon associated with this taxon and this piece of information e.g. a parasite or prey Scope/TaxonName context: A string representation of when this information is valid. (Categorical|Quantitative|Text)/Notes contextOccurrence: An indication of when this information is valid according to a geospatial data. Scope/GeographicArea contextValue: An indication of when this information is valid according to a controlled vocabulary. (Categorical|Quantitative|Text) /Modifier hasContent: A information about a taxon in the form of a string. Should be interpreted in combination with the type of the InfoItem (Categorical|Quantitative|Text) /Content hasValue: A information about a taxon in the form of a controlled vocabulary term. (Categorical|Quantitative|Text)/State

Richness & Atomization InfoItem aboutTaxon … … … Character Data Scopes … … Representation SummaryData Scopes SPMSDD Labels, Definitions, MediaObjects (multilingual) RevisionData SampleData … Taxa, Speci- mens, Observ., Publications, Parts, Stage, Sex. etc.

Naming differences Perhaps consider whether SPM: “context” is a good paradigm: A measurement can be made in the context of a study, and perhaps in the context of a season But is “geographical location”, “frequently”, “sex”, “above 1000 m” a context? SDD distinguishes between Scope of a description = criteria by which data have been aggregated (taxon, specimen, geolocation, season, publication source, etc.) and Modifiers that modify/qualify a statement

Naming differences “Value” for categorical measurements is OK in principle, but may affect extensibility to quantitative data. Publication references would be needed for source of information being aggregated, or citations therein

Occurrence / Distribution Occurrence used in contextOccurrence, Distribution as content term around it. Is the order of information reversed? spm:contextValue =“An indication of when this information is valid according to a controlled vocabulary.” → perhaps: Perhaps use a special type here?

Cardinality?

SPM Concepts BiologyCytology Physiology Ecology MolecularBiologyEvolution Conservation Distribution Use Description Size

Biology Description Overlap! Size Cytology Physiology MolecularBiology Ecology Evolution Conservation Distribution Use Ecology Distribution Evolution Biology

Description Conclusive? Size Cytology Physiology MolecularBiology Ecology Evolution Conservation Distribution Use Ecology Distribution Evolution Biology Anatomy Biochemistry Morphology Secondary metabolites

Biology Description Size Cytology Physiology MolecularBiology Ecology Evolution Conservation Distribution Use Ecology Distribution Evolution Biology Anatomy Biochemistry Morphology Secondary metabolites LifeExpectancy LookAlikes Diagnostic Description LifeCycle PopulationBiology Behavior Associations SPM Version Earlier terms used in SPM example files Weight

Number of characters Size LIAS has 987 “characters”, incl. ca. 30 “pseudo- characters” GrassBase has 1090 characters LifeExpectancy SDD concluded to separate character standardization from structural separation Waiting for exchange of existing definitions and patterns to arise rather than round table

SPM content vocabulary A concise “major concept headings” vocabulary like SPM is certainly desirable But definitions are needed! Human-readable definitions should be developed OWL/RDF currently provides a single semantic information: Size is subclass of Description Provision of general abstract data structures (content, value, contextXXX) should perhaps be separated from definition of biological concepts

Ontologies 1 (Descriptive Terms) Leaf Green leafPetal Cladode (= stem looking like leaf) Leaflike structure Stem Coded Summary Descriptions Taxon 1: Green leaf: Length 7 cm Taxon 2: Green leaf: Length 5 cm Taxon 3: Cladode: Length 8 cm Taxon 4: Cladode: Length 2 cm Identification: Which species have leaf-like structures on the stem between 7 and 10 cm long? Flower

Ontologies 2 (Taxonomic Classes) ThisFamily Taxon concepts are a natural ontology with multiple inheritance from within taxon concept classes and Rank classes. Identification: Which family has species with leaf-like structures on the stem between 7 and 10 cm long? Genus Genus spec1Genus spec2 Genus Genus spec1Genus spec2 Taxonomic Rank Family Genus Species

Break down of communication? SDD was designed for the purpose SPM has been developed for SDD and SPM are strongly analogous SDD has invested much time in trying to find an application profile supporting rich editing applications in a way consistent with simple identification keys and taxon-page creation software. SDD structures and terms have not been evaluated for SPM

“Structured Descriptive Data” “Biological Descriptions” Interest Group: “Structured Descriptive Data” → Interest Group: “Biological Descriptions” →TG SDD-Schema →TG SPM →TG SDD/RDF???

Conveners?

Thank you: For volunteering your personal time in discussions, implementation and testing! Projects and companies for testing and implementing! GBIF, TDWG, and BMBF for traveling and workshop support! TDWG-IP for financing an SDD primer!