Feature
We still need a way to access information about the Features. Defining Features as rdf:Property (predicates) makes impossible using them as rdf:Classes, which is necessary in many cases. Now Features are defined as owl:Classes.
- Feature URI is defined by dc:identifier (Dublin Core namespace)
... xmlns:dc="http://purl.org/dc/elements/1.1/" ... <dc:identifier rdf:datatype="&xsd;string" >http://myserice/feature/{featureid2}</dc:identifier>
- Feature name is defined by dc:title (Dublin Core namespace)
<dc:title rdf:datatype="&xsd;string">XLogP</dc:title>
- The origin of the Feature is defined by ot:hasSource (OpenTox namespace) element and can be Algorithm, Model or Dataset
- Links with other ontologies are established via RDF subclassing (rdf:type property), or owl:sameAs property.
Examples:
Features, defined as originated from a Dataset or Machine Learning Algorithm
<ot:Feature rdf:ID="MultiCellCall"> <dc:identifier rdf:datatype="&xsd;string" >http://myservice/feature/{featureid1}</dc:identifier> <dc:source rdf:datatype="&xsd;string" >http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_MultiCellCall</dc:source> <ot:hasSource rdf:resource="#DSSToxCPDBAS"/> </ot:Feature> <ot:Feature rdf:ID="MultiCellCallPredicted"> <dc:identifier rdf:datatype="&xsd;string" >http://myservice/feature/{featureid3}</dc:identifier> <ot:hasSource rdf:resource="#WekaJ48"/> </ot:Feature>
Feature, with a descriptor calculation algorithm , defined as a source.
<ot:Feature rdf:ID="XLogPDescriptor"> <dc:identifier rdf:datatype="&xsd;string" >http://myservice/feature/{featureid2}</dc:identifier> <dc:title rdf:datatype="&xsd;string">XLogP</dc:title> <ot:hasSource rdf:resource="#XLogPCalculation"/> </ot:Feature>
Features, which are defined as Carcinogenicity endpoints, according to ECHA endpoints ontology
:
<rdf:RDF xmlns="http://www.opentox.org/example/1.1#" xml:base="http://www.opentox.org/example/1.1" xmlns:ot="http://www.opentox.org/api/1.1#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:p3="&dc;#" xmlns:p2="http://www.opentox.org/algorithmTypes.owl#" xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#" xmlns:p1="http://www.w3.org/1998/Math/MathML" xmlns:otee="http://www.opentox.org/echaEndpoints.owl#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> <owl:Ontology rdf:about=""> <rdfs:comment rdf:datatype="&xsd;string" >An example of OpenTox resource ontology usage. Definition of example instances</rdfs:comment> <owl:imports rdf:resource="http://www.opentox.org/echaEndpoints.owl"/> <owl:imports rdf:resource="http://www.opentox.org/api/1.1"/> </owl:Ontology> <ot:Feature rdf:ID="CarcinogenicityLazar"> <dc:identifier rdf:datatype="&xsd;string">/feature/1</dc:identifier> <ot:hasSource rdf:resource="#Lazar"/> <owl:sameAs rdf:resource="http://www.opentox.org/echaEndpoints.owl#Carcinogenicity"/> </ot:Feature> <ot:Feature rdf:ID="CarcinogenicityToxtree"> <dc:identifier rdf:datatype="&xsd;string">/feature/2</dc:identifier> <ot:hasSource rdf:resource="#ToxtreeCarcinogenicity"/> <owl:sameAs rdf:resource="http://www.opentox.org/echaEndpoints.owl#Carcinogenicity"/> </ot:Feature> </rdf:RDF>
How this relationship is defined in Protege is illustrated below:
Feature upload code ...