TDWG Standards Roadmap Roger Hyam (Technical Architecture Group)
Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013
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Transcript of Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013
Using Darwin Core as a Model:An Ontologically Minimalist Approach to
Publishing Occurrence Data in RDF
Joel SachsFormal Models track of the Semantics for
Biodiversity Symposium TDWG 2013
The first thing I want to communicate:
Semantics != Ontologies
Semantics = Ontologies ?
• Semantics– Semiotics– Linguistics– Psychology
• Ontology– Philosophy– Computer Science
Ontologies as a vehicle for semantics
• Ontologies were the first choice for putting the “semantic” in semantic web.
• But ontologies aren’t the only way to supply semantics.
• Furthermore, ontologies can be a barrier to shared semantics, in a number of ways.
What’s green?
• Def 1:
What’s green?
• Def 2: Green is the portion of the electromagnetic spectrum with a wavelength between 520 – 570 nm.
What’s electromagnetic?What’s a spectrum?What’s a wavelength?What’s a nanomemter?
Occurrence_IDLocation_ID URIDateTime DateTimeIndividualOrganism_ID URI
Location_ID URILatitude floatLongitude floatDatum URI
Identification_IDIndividual_ID URITaxon URIIdentified_by URI
Occurrence_IDLatitudeLongitudeScientific NameVernacular Name
Taxon_IDScientific NameVernacular NameAuthorshipYearetc.
Occurrence
Location
Identification
Taxon
Occurrence
There are many ways to think about biodiversity data.
Thing #2 that I want to communicate
Darwin Core (as it is) can be used as a light weight “ontology”.
Don’t try this at home
Thing #3
How to minimize the amount of ontology in the Core.
Example: Material Sample
dwctype:MaterialSample (roughly?) corresponds to OBI:Specimen.
<owl:Class rdf:about=http://purl.obolibrary.org/obo/OBI_0100051><owl:equivalentClass>
<owl:Class> <owl:intersectionOf rdf:parseType="Collection"> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/> <owl:Restriction> <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000087"/> <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000112"/> </owl:Restriction> </owl:intersectionOf> </owl:Class> </owl:equivalentClass> <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/> <n0pred:IAO_0000602>(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] </n0pred:IAO_0000602> <n0pred:BFO_0000179>material</n0pred:BFO_0000179> <n0pred:BFO_0000180>MaterialEntity</n0pred:BFO_0000180> <n0pred:IAO_0000602>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] </n0pred:IAO_0000602> <n0pred:IAO_0000602>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] </n0pred:IAO_0000602>
curl -L -H "Accept: application/rdf+xml" http://rs.tdwg.org/dwc/dwctype/MaterialSample | grep OBI
<rdf:Description rdf:about="http://rs.tdwg.org/dwc/dwctype/MaterialSample"><rdfs:label xml:lang="en-US">MaterialSample</rdfs:label><rdfs:comment xml:lang="en-US">A resource describing the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed.</rdfs:comment><rdfs:isDefinedBy rdf:resource="http://rs.tdwg.org/dwc/dwctype/"/>
<dcterms:issued>2013-03-28</dcterms:issued><dcterms:modified>2013-09-26</dcterms:modified><rdf:type rdf:resource="http://www.w3.org/2000/01/rdf-schema#Class"/><dcterms:hasVersion rdf:resource="http://rs.tdwg.org/dwc/dwctype/history/ #MaterialSample-
2013-06-24"/><dcam:memberOf rdf:resource="http://rs.tdwg.org/dwc/terms/DwCType"/><rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/>
<dwcattributes:status>recommended</dwcattributes:status><dwcattributes:decision rdf:resource="http://rs.tdwg.org/dwc/terms/history/decisions/
Decision_2013-10-09_12"/><dwcattributes:abcdEquivalence>DataSets/DataSet/Units/Unit</dwcattributes:abcdEquivalence>
</rdf:Description>
curl -L -H "Accept: application/rdf+xml" http://rs.tdwg.org/dwc/dwctype/MaterialSample | grep OBI
<rdf:Description rdf:about="http://rs.tdwg.org/dwc/dwctype/MaterialSample">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/>
</rdf:Description>
On the one hand
• Nobody forces consuming application to ingest the OBI and BFO ontologies when they ingest Darwin Core.
• So what’s the big deal?
On the other hand
• Many semantic web clients automatically fetch and load referenced documents.– Especially if the documents are referenced with important
properties like rdfs:subClassOf
• It’s bad form (and slightly dangerous) to clutter a semantic web document with terms from unnecessary namespaces.
My suggestion?
• Assertions that tie Core terms to upper ontologies should be asserted in a separate document.
E.g.<rdf:Description rdf:about="http://rs.tdwg.org/dwc/dwctype/MaterialSample"> <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/></rdf:Description>
should be asserted in obi.owl, or dwc_obi.owl
• That way, those doing integration that depends on OBI axioms can ingest the appropriate descriptions.
• Those that don’t need the OBI axioms don’t have to worry about incorrect inference.– Keep in mind: There is no preferred upper ontology for science on the
semantic web.• BFO, Dolce, SUMO, UMBEL, NULO, etc.