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.

Thank you for paying attention!

Question, comments, and criticism to

@[email protected]