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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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slide1

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

semantics ontologies
Semantics = Ontologies ?
  • Semantics
    • Semiotics
    • Linguistics
    • Psychology
  • Ontology
    • Philosophy
    • Computer Science
ontologies as a vehicle for semantics
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 green1
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?

slide7

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.

thing 2 that i want to communicate
Thing #2 that I want to communicate

Darwin Core (as it is) can be used as a light weight “ontology”.

thing 3
Thing #3

How to minimize the amount of ontology in the Core.

example material sample
Example: Material Sample

dwctype:MaterialSample (roughly?) corresponds to OBI:Specimen.

slide18

<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"/>

slide21

<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>

slide23

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>

slide24

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>

on the one hand
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
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
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.
thank you for paying attention
Thank you for paying attention!

Question, comments, and criticism to

@xjsachs

joel.sachs@agr.gc.ca