The BioBricks Foundation:Standards/Technical/PoBoL/Owl Draft 0.1

@prefix bbf:  <http://www.biobricks.org/rdf/0.1#> .
@prefix formats: <http://www.biobricks.org/rdfformats/0.1#> .
@prefix knightlab:    <http://xxx/knight/people#> .
@prefix endylab:    <http://xxx/knight/people#> .
@prefix :  <#> .

:BBa_P1010
       bbf:dnaSequence    "ATGXX";
       bbf:format      formats:1_0;

       bbf:shortDescription    "ccdb death switch";
       bbf:longDescription     "a negative selection marker";
       bbf:author              knightlab:tom;
       bbf:author              endylab:drew;
       .
       
@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 :  <http://www.biobricks.org/rdf/0.1#> .

## Definition of Biobrick Class and core Properties

:Biobrick
       a        owl:Class;
       rdfs:subClassOf  owl:Thing;
       rdfs:label       "Biobrick";
       rdfs:comment     "description of a Biobrick";
       .

:dnaSequence
       a       owl:InverseFunctionalProperty;
       a       owl:FunctionalProperty;
       rdfs:domain       :Biobrick;
       rdfs:range        xsd:string;
       rdfs:label       "sequence";
       .

:format
       a       owl:InverseFunctionalProperty;
       a       owl:FunctionalProperty;
       rdfs:domain       :Biobrick;
       rdfs:range        :BiobrickFormat;
       rdfs:label        "format";
       .

:subParts
       a       owl:InverseFunctionalProperty;
       a       owl:FunctionalProperty;
       rdfs:domain       :Biobrick;
#        rdfs:range       xsd:collection; ## haven't found the type for "collection of x" yet.
       rdfs:label       "Biobrick Composition";
       rdfs:comment     "a list of basic Biobricks this Biobrick is made of";
       .

:family
       a       owl:ObjectProperty;
       rdfs:domain      :Biobrick;
       rdfs:range       :BiobrickFamily;
       rdfs:label       "family";
       rdfs:comment     "group of related Biobricks to which this one belongs";
       .

       ## Definition of add-on Biobrick Properties

:author
       a        owl:ObjectProperty;
       rdfs:range       foaf:Person; # http://xmlns.com/foaf/spec/#term_Person
       rdfs:domain      :Biobrick;
       .

:date
       a       owl:FunctionalProperty;
       rdfs:range       xsd:date;
       rdfs:domain      :Biobrick;
       .

:reference
       a        owl:ObjectProperty;
       rdfs:range      xsd:string;  # PMID? DOI?
       rdfs:domain      :Biobrick;
       .

:shortDescription
       a       owl:FunctionalProperty;
       rdfs:range       xsd:string;
       rdfs:domain      :Biobrick;
       .

:longDescription
       a       owl:FunctionalProperty;
       rdfs:range       xsd:string;
       rdfs:domain      :Biobrick;
       .

## Definition of Biobrick physical Format class and properties

:BiobrickFormat
       a        owl:Class;
       rdfs:subClassOf  owl:Thing;
       rdfs:label       "Biobrick Format";
       rdfs:comment     "Biobrick Physical Assembly Format";
       .

:prefix
       a       owl:ObjectProperty;
       a       owl:FunctionalProperty;
       rdfs:range       xsd:string;
       rdfs:comment     "standard prefix sequence";
       rdfs:label       "Biobrick prefix";
       .

:suffix
       a       owl:ObjectProperty;
       a       owl:FunctionalProperty;
       rdfs:range       xsd:string;
       rdfs:comment     "standard suffix sequence";
       rdfs:label       "Biobrick suffix";
       .

:shortDescription       rdfs:domain     :BiobrickFormat. # described above
:longDescription        rdfs:domain     :BiobrickFormat.

## Biobrick subclasses

:BiobrickBasic
       a       owl:Class;
       rdfs:subClassOf  :Biobrick;
       .

:BiobrickComposite
       a       owl:Class;
       rdfs:subClassOf  :Biobrick;
       .

:BiobrickVector
       a       owl:Class;
       rdfs:subClassOf  :Biobrick;
       .

:isCircular
       a       owl:FunctionalProperty;
       rdfs:range       xsd:boolean;
       rdfs:domain      :BiobrickVector;
       rdfs:comment     "circular DNA flag";
       rdfs:label       "is circular?";
       .

:SelectiveMarker
       a       owl:Class;
       rdfs:subClassOf  :Biobrick;
       .

## Physical DNA class and properties

:DNA
       a       owl:Class;
       rdfs:subClassOf owl:Thing;
       rdfs:comment     "description of an actual piece of DNA";
       rdfs:label       "Physical DNA";
       .

:vector
       a       owl:FunctionalProperty;
       rdfs:domain      :DNA;
       rdfs:range       :Vector;
       rdfs:label       "vector";
       .

:insert
       a       owl:FunctionalProperty;
       rdfs:domain      :DNA;
       rdfs:range       :Biobrick;
       rdfs:label       "insert";
       rdfs:comment     "biobrick embedded in a vector";
       .

## minimal Sample description

:Sample
       a       owl:Class;
       rdfs:subClassOf owl:Thing;
       rdfs:comment     "description of a sample in a freezer or elsewhere";
       rdfs:label       "sample";
       .

:date   rdfs:domain     :Sample .  # defined in more detail above

:dna
       a       owl:FunctionalProperty;
       a       owl:InverseFunctionalProperty;
       rdfs:domain      :Sample;
       rdfs:range       :DNA;
       rdfs:label       "physical DNA";
       rdfs:comment     "DNA content of a sample";
       .

## Biobrick Family

:BiobrickFamily
       a       owl:Class;
       rdfs:subClassOf owl:Thing;
       rdfs:comment     "description of a group of related Biobricks";
       rdfs:label       "Biobrick Family";
       .

:name
       a       owl:FunctionalProperty;
       a       owl:InverseFunctionalProperty;
       rdfs:domain      :BiobrickFamily;
       rdfs:range       xsd:string;
       rdfs:label       "name";
       rdfs:comment     "a name";
       .

:subFamilyOf
       a       owl:ObjectProperty;
       rdfs:domain      :BiobrickFamily;
       rdfs:range       :BiobrickFamily;
       rdfs:label       "super Family";
       rdfs:comment     "0 or more parent families";
       .

:shortDescription       rdfs:domain     :BiobrickFamily. # as defined above
:longDescription        rdfs:domain     :BiobrickFamily.
:author                 rdfs:domain     :BiobrickFamily.
:date                   rdfs:domain     :BiobrickFamily.
:reference              rdfs:domain     :BiobrickFamily.