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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 Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013. The first thing I want to communicate:. Semantics != Ontologies. Semantics = Ontologies ?.

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Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013

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  1. Using Darwin Core as a Model:An Ontologically Minimalist Approach to Publishing Occurrence Data in RDF Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013

  2. The first thing I want to communicate: Semantics != Ontologies

  3. Semantics = Ontologies ? • Semantics • Semiotics • Linguistics • Psychology • Ontology • Philosophy • Computer Science

  4. 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.

  5. What’s green? • Def 1:

  6. What’s green? • Def2: 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?

  7. Occurrence Occurrence_ID Latitude Longitude Scientific Name Vernacular Name Occurrence Location Occurrence_ID Location_ID URI DateTimeDateTime IndividualOrganism_ID URI Location_ID URI Latitude float Longitude float Datum URI Identification Identification_ID Individual_ID URI Taxon URI Identified_by URI Taxon Taxon_ID Scientific Name Vernacular Name Authorship Year etc.

  8. There are many ways to think about biodiversity data.

  9. Thing #2 that I want to communicate Darwin Core (as it is) can be used as a light weight “ontology”.

  10. Don’t try this at home

  11. Thing #3 How to minimize the amount of ontology in the Core.

  12. Example: Material Sample dwctype:MaterialSample (roughly?) corresponds to OBI:Specimen.

  13. <owl:Classrdf:about=http://purl.obolibrary.org/obo/OBI_0100051> <owl:Classrdf:about=http://purl.obolibrary.org/obo/OBI_0100051> <owl:equivalentClass> <owl:Class> <owl:intersectionOfrdf:parseType="Collection"> <rdf:Descriptionrdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/> <owl:Restriction> <owl:onPropertyrdf:resource="http://purl.obolibrary.org/obo/BFO_0000087"/> <owl:someValuesFromrdf:resource="http://purl.obolibrary.org/obo/OBI_0000112"/> </owl:Restriction> </owl:intersectionOf> </owl:Class> </owl:equivalentClass> <rdfs:subClassOfrdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>

  14. <owl:disjointWithrdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/> <owl:disjointWithrdf: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>

  15. curl -L -H "Accept: application/rdf+xml" http://rs.tdwg.org/dwc/dwctype/MaterialSample | grep OBI <rdf:Descriptionrdf:about="http://rs.tdwg.org/dwc/dwctype/MaterialSample"> <rdfs:labelxml:lang="en-US">MaterialSample</rdfs:label> <rdfs:commentxml: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:isDefinedByrdf:resource="http://rs.tdwg.org/dwc/dwctype/"/> <dcterms:issued>2013-03-28</dcterms:issued> <dcterms:modified>2013-09-26</dcterms:modified> <rdf:typerdf:resource="http://www.w3.org/2000/01/rdf-schema#Class"/> <dcterms:hasVersionrdf:resource="http://rs.tdwg.org/dwc/dwctype/history/ #MaterialSample-2013-06-24"/> <dcam:memberOfrdf:resource="http://rs.tdwg.org/dwc/terms/DwCType"/> <rdfs:subClassOfrdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/> <dwcattributes:status>recommended</dwcattributes:status> <dwcattributes:decisionrdf:resource="http://rs.tdwg.org/dwc/terms/history/decisions/ Decision_2013-10-09_12"/> <dwcattributes:abcdEquivalence>DataSets/DataSet/Units/Unit</dwcattributes:abcdEquivalence> </rdf:Description>

  16. curl -L -H "Accept: application/rdf+xml" http://rs.tdwg.org/dwc/dwctype/MaterialSample | grep OBI <rdf:Descriptionrdf:about="http://rs.tdwg.org/dwc/dwctype/MaterialSample"> <rdfs:subClassOfrdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/> </rdf:Description>

  17. 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?

  18. 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.

  19. My suggestion? • Assertions that tie Core terms to upper ontologies should be asserted in a separate document. E.g. <rdf:Descriptionrdf:about="http://rs.tdwg.org/dwc/dwctype/MaterialSample"> <rdfs:subClassOfrdf: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.

  20. Thank you for paying attention! Question, comments, and criticism to @xjsachs joel.sachs@agr.gc.ca

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