SLIDE 1 TDWG Annual Meeting; 2011-10-18
Darwin-SW: Darwin Core data for the Semantic Web Campbell Webb & Steven Baskauf
Arnold Arboretum of Harvard University /
- Dept. of Biological Sciences, Vanderbilt University
Version 0.2-2-ge7575a4
SLIDE 2 The Semantic Web
- Persistent, de-referenceable identifiers (GUIDs)
- A universal format for transmission (RDF)
- Semantically-rich descriptions (self-documenting)
- Opportunity for machine reasoning
SLIDE 3 TDWG’s Darwin Core (DwC)
- Biodiversity Information Standards (TDWG)
standard
- Stable, ‘Technology-independent’ vocabulary of
terms
- ‘Classes’ are categories, no formal domain
declarations for terms: – Direct use in RDF is unclear
- Foundation for building RDF Classes and properties
(TDWG RDF Task Group)
SLIDE 4 Darwin-SW
- We needed GUID/RDF solution now
- NOT officially associated with DwC or TDWG,
– but much effort to understand and apply TDWG community consensus
- Uses 5 existing DwC classes and adds 2 new ones
- Relationships among classes defined by pairs of
inverse object properties (new)
- Most existing DwC data properties can be used
SLIDE 5
Five core DwC classes
SLIDE 6
dsw:IndividualOrganism (new)
Needed for linkage to population data, observations (see Baskauf, 2010). Issue of clonal organisms, heterogeneous collection units.
SLIDE 7 Definition of Occurrence class
- DwC (‘class of data’) “The category of information
pertaining to evidence of an occurrence in nature, in a collection, or in a dataset” General; including specimens, observations, even species-place ‘checklist’ records
- DSW: “the instance of an individual organism at a
place and time”
- Much biodiversity data ‘hangs’ on an individual’s
- ccurrence
- Tidily incorporates location and time for other data
- bjects
SLIDE 8
dsw:Token (new)
‘Tokens’—Specimens, photos, even plant cuttings, that provide evidence of the Occurrence
SLIDE 9
Darwin-SW
Full set of new object properties
SLIDE 10 Modeling
- Using OWL DL (Web Ontology Language; adds
some necessary concepts to basic RDF Schema, RDFS)
eg´ e 4
- Took care about assigning domains and ranges to
properties (Morris, pers. comm.; Horridge, 2009)
- All classes other than Token are disjoint
- Validation of data statements using eyeball
SLIDE 11 Treatment of Taxon class
- DSW treats dwc:Taxon ≡ tc:TaxonConcept
(from the TDWG RDF ontology)
- A TaxonConcept combines both a TaxonName and a
statement of name usage, but usage seldom given
- Taxonomic names (genus, specific epithet) can hang
- n dwc:Taxon directly, or on tn:TaxonName
- Awaiting GNUB URIs for Taxon Names eagerly
SLIDE 12
Linking to other ontologies
Ontology at http://xmalesia.info/sw/onto/bot.rdf. Links to OBOE, PO, PATO, CDAO
SLIDE 13
E.g., Observation of an organism
SLIDE 14 Darwin-SW use examples
- Steve’s Bioimages database
– http://bioimages.vanderbilt.edu – A still image:
<http://bioimages.vanderbilt.edu/kirchoff/em2072>
- New collections (physical, images, DNA) in
Indonesia (Xmalesia NSF project) – http://xmalesia.info – A tree in an ecological plot, with specimen:
<http://xmalesia.info/sw/indiv/360>
SLIDE 15 Moving Forward
- Darwin-SW can contribute to discussion on TDWG
RDF recommendations
- Task Group meeting tomorrow PM
- Discussion items:
– Need for dsw:IndividualOrganism – A dsw:Token class? – Eliminate dwc:Event? – Linkage to other ontologies – Reasoning use cases – Timeline and plan for a TDWG-RDF BIS
SLIDE 16 Acknowledgments
- Important discussions Pete DeVries, Paul Murray,
Hilmar Lapp, Bob Morris, Matt Jones, Jim Balhoff, Shawn Bowers, Chris Mungall, Damian Gessler, many others
- Current Funding National Science Foundation
(DEB–1020868 to CW)
- Software Redland RDF Libraries, redstore, L
A
T EX, GraphViz, Protege, xqilla, GNU gawk
SLIDE 17 References
Baskauf, S. J. 2010. Organization of occurrence-related biodiversity resources based on the process of their creation and the role of individual organisms as resource relationship nodes. Biodiversity Informatics 7:17– 44. Horridge, M., 2009. A Practical Guide To Building OWL Ontologies Using Prot´ eg´ e 4 and CO-ODE Tools (Edi- tion 1.2). Technical report, The University Of Manchester. URL http://owl.cs.manchester.ac.uk/tutorials/ protegeowltutorial/.
