A gentle introduction to the Species Profile Model

Robert A. MorrisDepartment of Computer Science

UMASS-Boston

Doesn’t talk as fast as Greg Whitbread

Species Profile Model

• An extension of the TDWG LSID RDF Vocabularies (“lsid vocs”)

• Designed by Roger Hyams with input from a small GBIF workshop in 2007

• Adds named classes of objects representing 37 biological concepts

• Supports, but doesn’t specify, controlled vocabularies for use with those concepts

SPM Advantages

• Lightweight (with suitable tools) way to say stuff about a Taxon(Concept) in such a way that – producer and consumer software can “agree” about

the domain of discourse (e.g. Description, Cytology, Phenology, Ecology, LifeCycle, Reproduction, ...)

– can represent attributes either in plain text or with controlled vocabulary (or both)

– can extend TDWG LSID vocabularies to encompass existing controlled vocabularies (with care)

SPM Advantages

• Lightweight (with suitable tools) way to say stuff about a Taxon(Concept) in such a way that – supports data integration– supports machine reasoning (presently)– can express context of assertions about taxa, e.g. :

• Callithomia hezia has larval host plant Lycianthes sanctaeclarae throughout Central America

• More ubiquitous than you think:RSS Annotea

Adobe XMP

SPM Disadvantages

• RDF technology harder to master and support than XML Schema

RDF

• Triples – (Subject, Predicate, Object)

– Stack of sublanguages, progressively more expressive, but the last (“OWL Full”) is logically incomplete and computationally intractible (i.e. scales exponentially)

– Next to last (“OWL DL”) is quite good for machine reasoning

– Several expressions, including RDF/XML, not meant to be human readable, but mostly are.

(c)W3C

See also SPM lsid vocs

InfoItems

• Biology• Description

– Size• Cytology• Physiology• Molecular Biology• Ecology• Conservation• Distribution• Use

• Evolution• TaxonBiology• TrophicStrategy• Cyclicity• Dispersal• Migration• LifeCycle• Reproduction• Growth• Life Expectancy

InfoItems

• Genetics• Associations• Diseases• Habitat• Behaviour• PopulationBiology• GeneralDescription• DiagnosticDescription• LookAlikes

• Key• Morphology• Management• ConservationStatus• Legislation• Threats• Trends• Procedures

SPM Applications

Data integration

Quality assurance via machine reasoning

Hypothesis testing, assertion comparisons, ....

IPR

• Quercus ilex rotundifolia (c) Valter Jacinto http://farm1.static.flickr.com/125/344302650_3fc76697d0.jpg?v=0cc by-nc-sa licensed

• RDF stack (c)W3C used with permission

• Cartoon fruit from Microsoft PowerPoint images web library. Permission unknown.