Ricardo Pereira Software Engineer TDWG Infrastructure Project (TIP)
Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013
description
Transcript of Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013
![Page 1: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/1.jpg)
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
![Page 2: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/2.jpg)
The first thing I want to communicate:
Semantics != Ontologies
![Page 3: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/3.jpg)
Semantics = Ontologies ?
• Semantics– Semiotics– Linguistics– Psychology
• Ontology– Philosophy– Computer Science
![Page 4: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/4.jpg)
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.
![Page 5: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/5.jpg)
What’s green?
• Def 1:
![Page 6: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/6.jpg)
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?
![Page 7: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/7.jpg)
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
![Page 8: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/8.jpg)
There are many ways to think about biodiversity data.
![Page 9: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/9.jpg)
Thing #2 that I want to communicate
Darwin Core (as it is) can be used as a light weight “ontology”.
![Page 10: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/10.jpg)
![Page 11: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/11.jpg)
![Page 12: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/12.jpg)
![Page 13: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/13.jpg)
![Page 14: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/14.jpg)
![Page 15: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/15.jpg)
Don’t try this at home
![Page 16: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/16.jpg)
Thing #3
How to minimize the amount of ontology in the Core.
![Page 17: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/17.jpg)
Example: Material Sample
dwctype:MaterialSample (roughly?) corresponds to OBI:Specimen.
![Page 18: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/18.jpg)
<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"/>
![Page 19: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/19.jpg)
![Page 20: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/20.jpg)
![Page 21: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/21.jpg)
<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>
![Page 22: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/22.jpg)
![Page 23: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/23.jpg)
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>
![Page 24: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/24.jpg)
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>
![Page 25: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/25.jpg)
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?
![Page 26: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/26.jpg)
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.
![Page 27: Joel Sachs Formal Models track of the Semantics for Biodiversity Symposium TDWG 2013](https://reader036.fdocuments.in/reader036/viewer/2022062410/56816511550346895dd78c46/html5/thumbnails/27.jpg)
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.