The BioBricks Foundation:Standards/Technical/PoBoL/Owl Draft 0.2
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Draft version 0.2 of PoBoL:
This draft adds "restrictions" that state what properties (dnaSequence, prefix, etc.) a certain class (Biobrick, BiobrickFormat, etc.) is guaranteed to have.
Source
- Generated in Protege as OWL (XML)
- translated to Turtle using [1],
- hand-polished
Issues:
- subParts properties: how can we state that subParts should point to a collection of BasicBiobrick?
- naming: more specific names like, for example, 'biobrickPrefix' rather than 'prefix'?
- Biobrick family: could also be formulated as 'SuperBiobrick' (aka an abstract super class of Biobrick)
Files
Media:Pobol_rdf_draft_0.2.turtle.owl
Draft Ontology in Turtle/N3 Format:
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix foaf: <http://xmlns.com/foaf/0.1#> . @prefix bbf: <http://www.biobricks.org/rdf/0.1#> . ###################################################### ## Definition of Biobrick Class and core Properties ## bbf:Biobrick rdf:type owl:Class ; rdfs:comment "description of a Biobrick"^^xsd:string ; rdfs:label "Biobrick"^^xsd:string ; rdfs:subClassOf owl:Thing ; rdfs:subClassOf [ rdf:type owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty bbf:format ] ; rdfs:subClassOf [ rdf:type owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty bbf:dnaSequence ] . bbf:dnaSequence rdf:type owl:InverseFunctionalProperty , owl:FunctionalProperty ; rdfs:domain bbf:Biobrick ; rdfs:label "sequence"^^xsd:string ; rdfs:range xsd:string . bbf:format rdf:type owl:InverseFunctionalProperty , owl:FunctionalProperty ; rdfs:domain bbf:Biobrick ; rdfs:label "format"^^xsd:string ; rdfs:range bbf:BiobrickFormat . ## Biobrick level2 properties bbf:author rdf:type owl:ObjectProperty ; rdfs:domain bbf:Biobrick ; rdfs:range foaf:Person . # http://xmlns.com/foaf/spec/#term_Person bbf:date rdf:type owl:FunctionalProperty ; rdfs:domain bbf:Biobrick ; rdfs:range xsd:date . bbf:shortDescription rdf:type owl:FunctionalProperty ; rdfs:domain bbf:Biobrick ; rdfs:range xsd:string . bbf:longDescription rdf:type owl:FunctionalProperty ; rdfs:domain bbf:Biobrick ; rdfs:range xsd:string . bbf:reference rdf:type owl:ObjectProperty ; rdfs:domain bbf:Biobrick ; rdfs:range xsd:string . bbf:family rdf:type owl:ObjectProperty ; rdfs:comment "group of related Biobricks to which this one belongs"^^xsd:string ; rdfs:domain bbf:Biobrick ; rdfs:label "family"^^xsd:string ; rdfs:range bbf:BiobrickFamily . ####################################################### ## Basic and Composite Biobrick-subclass and properties bbf:BiobrickBasic rdf:type owl:Class ; rdfs:subClassOf bbf:Biobrick ; rdfs:subClassOf [ rdf:type owl:Restriction ; owl:cardinality "0"^^xsd:int ; owl:onProperty bbf:subParts ] ; owl:disjointWith bbf:BiobrickComposite . bbf:BiobrickComposite rdf:type owl:Class ; rdfs:subClassOf bbf:Biobrick ; rdfs:subClassOf [ rdf:type owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty bbf:subParts ] ; owl:disjointWith bbf:BiobrickBasic . bbf:subParts rdf:type owl:InverseFunctionalProperty , owl:FunctionalProperty ; rdfs:comment "a list of basic Biobricks this Biobrick is made of"^^xsd:string ; rdfs:domain bbf:Biobrick ; rdfs:label "Biobrick Composition"^^xsd:string . ############################ ## Other Biobrick subclasses bbf:BiobrickVector rdf:type owl:Class ; rdfs:subClassOf bbf:Biobrick . bbf:isCircular rdf:type owl:FunctionalProperty ; rdfs:comment "circular DNA flag"^^xsd:string ; rdfs:domain bbf:BiobrickVector ; rdfs:label "is circular?"^^xsd:string ; rdfs:range xsd:boolean . bbf:SelectiveMarker rdf:type owl:Class ; rdfs:subClassOf bbf:Biobrick . ################################################ ## Biobrick physical Format class and properties bbf:BiobrickFormat rdf:type owl:Class ; rdfs:comment "Biobrick Physical Assembly Format"^^xsd:string ; rdfs:label "Biobrick Format"^^xsd:string ; rdfs:subClassOf owl:Thing ; rdfs:subClassOf [ rdf:type owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty bbf:suffix ] ; rdfs:subClassOf [ rdf:type owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty bbf:prefix ] ; rdfs:subClassOf [ rdf:type owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty bbf:selfScar ] . bbf:prefix rdf:type owl:ObjectProperty , owl:FunctionalProperty ; rdfs:comment "standard prefix sequence"^^xsd:string ; rdfs:domain bbf:BiobrickFormat ; rdfs:label "Biobrick prefix"^^xsd:string ; rdfs:range xsd:string . bbf:suffix rdf:type owl:ObjectProperty , owl:FunctionalProperty ; rdfs:comment "standard suffix sequence"^^xsd:string ; rdfs:domain bbf:BiobrickFormat ; rdfs:label "Biobrick suffix"^^xsd:string ; rdfs:range xsd:string . bbf:selfScar rdf:type owl:ObjectProperty, owl:FunctionalProperty ; rdfs:comment "the sequence left between two Biobricks of this Format after standard assembly"^^xsd:string ; rdfs:domain bbf:BiobrickFormat ; rdfs:range xsd:string . bbf:shortDescription rdfs:domain bbf:BiobrickFormat. # described above bbf:longDescription rdfs:domain bbf:BiobrickFormat. #################################### ## Physical DNA class and properties bbf:DNA rdf:type owl:Class ; rdfs:comment "description of an actual piece of DNA"^^xsd:string ; rdfs:label "Physical DNA"^^xsd:string . bbf:vector rdf:type owl:FunctionalProperty ; rdfs:domain bbf:DNA ; rdfs:label "vector"^^xsd:string . bbf:insert rdf:type owl:FunctionalProperty ; rdfs:comment "biobrick embedded in a vector"^^xsd:string ; rdfs:domain bbf:DNA ; rdfs:label "insert"^^xsd:string ; rdfs:range bbf:Biobrick . ############################# ## minimal Sample description bbf:Sample rdf:type owl:Class ; rdfs:comment "description of a sample in a freezer or elsewhere"^^xsd:string ; rdfs:label "sample"^^xsd:string . bbf:dna rdf:type owl:FunctionalProperty ; rdfs:comment "DNA content of a sample"^^xsd:string ; rdfs:domain bbf:Sample ; rdfs:label "physical DNA"^^xsd:string ; rdfs:range bbf:DNA . bbf:label rdf:type owl:ObjectProperty ; rdfs:comment "physical label on a sample or similar"^^<http://www.w3.org/2001/XMLSchema#string> ; rdfs:domain bbf:Sample ; rdfs:range <http://www.w3.org/2001/XMLSchema#string> . bbf:date rdfs:domain bbf:Sample . # defined in more detail above bbf:author rdfs:domain bbf:Sample . # defined in more detail above ################## ## Biobrick Family bbf:BiobrickFamily rdf:type owl:Class ; rdfs:comment "description of a group of related Biobricks"^^xsd:string ; rdfs:label "Biobrick Family"^^xsd:string . bbf:name rdf:type owl:InverseFunctionalProperty , owl:FunctionalProperty ; rdfs:comment "a name"^^xsd:string ; rdfs:domain bbf:BiobrickFamily ; rdfs:label "name"^^xsd:string ; rdfs:range xsd:string . bbf:subFamilyOf rdf:type owl:ObjectProperty ; rdfs:comment "0 or more parent families"^^xsd:string ; rdfs:domain bbf:BiobrickFamily ; rdfs:label "super Family"^^xsd:string ; rdfs:range bbf:BiobrickFamily . bbf:shortDescription rdfs:domain bbf:BiobrickFamily. # as defined above bbf:longDescription rdfs:domain bbf:BiobrickFamily. bbf:author rdfs:domain bbf:BiobrickFamily. bbf:date rdfs:domain bbf:BiobrickFamily. bbf:reference rdfs:domain bbf:BiobrickFamily.