Transcript A gentle introduction to the Species Profile Model

A gentle introduction to the
Species Profile Model
Doesn’t talk as fast as Greg Whitbread
Robert A. Morris
Department of Computer Science
UMASS-Boston
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
Adobe XMP
Annotea
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
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Evolution
TaxonBiology
TrophicStrategy
Cyclicity
Dispersal
Migration
LifeCycle
Reproduction
Growth
Life Expectancy
InfoItems
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Genetics
Associations
Diseases
Habitat
Behaviour
PopulationBiology
GeneralDescription
DiagnosticDescription
LookAlikes
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Key
Morphology
Management
ConservationStatus
Legislation
Threats
Trends
Procedures
SPM Applications
Hypothesis testing,
assertion comparisons, ....
Quality assurance via machine reasoning
Data integration
IPR
• Quercus ilex rotundifolia
(c) Valter Jacinto
http://farm1.static.flickr.com/125/34430265
0_3fc76697d0.jpg?v=0
cc by-nc-sa licensed
• RDF stack (c)W3C used with permission
• Cartoon fruit from Microsoft PowerPoint
images web library. Permission unknown.