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

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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

The first thing I want to communicate:

Semantics != Ontologies


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 green

What’s green?

  • Def 1:


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?


Joel sachs formal models track of the semantics for biodiversity symposium tdwg 2013

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.


Joel sachs formal models track of the semantics for biodiversity symposium tdwg 2013

There are many ways to think about biodiversity data.


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”.


Don t try this at home

Don’t try this at home


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.


Joel sachs formal models track of the semantics for biodiversity symposium tdwg 2013

<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"/>


Joel sachs formal models track of the semantics for biodiversity symposium tdwg 2013

<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>


Joel sachs formal models track of the semantics for biodiversity symposium tdwg 2013

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>


Joel sachs formal models track of the semantics for biodiversity symposium tdwg 2013

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

[email protected]


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