ontology-service: A Web Ontology Language repository from IDEAconsult

#OpenTox Ontology service

Download

ontology-0.0.4-SNAPSHOT.war

##Deployment

Copy ontology.war under webapps directory of the servlet container. The application should be accessible at

##Build

mvn package -P release -P tdb -P noaa -P extended

###Maven dependency:

<dependency>
  <groupId>org.opentox</groupId>
  <artifactId>ontology</artifactId>
  <version>0.0.4-SNAPSHOT</version>
  <type>war</type>
</dependency>

##Configuration:

Does not use MySQL database. Uses Jena TDB for persistent storage (file based), which is automatically generated on deploy.

*WEB-INF/classes/org/opentox/config/config.properties

#tdb or sdb 
persistence=${jena.persistence}
#where to store TDB files. Default is java temporary directory
tdb=${tdb.folder}

*WEB-INF/classes/org/opentox/config/aa.properties

aa.opensso=${aa.opensso}
aa.policy=${aa.policy}
aa.enabled=${aa.enabled}

##Query examples

###Retrieve all classification algorithms:

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Algorithm ?x ?y
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Classification>.
	}

###All regression algorithms:

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Algorithm ?x ?y
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Regression>.
	}

###All clustering algorithms

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Algorithm ?x ?y
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Clustering>.
	}

###Single target algorithms

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Algorithm ?x ?y
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#SingleTarget>.
	}

###Lazy learning AND single target

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Algorithm ?x ?y
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#SingleTarget>.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#LazyLearning>.
	}

###Supervised learning algorithms

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Algorithm ?x ?y
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Supervised>.
	}

###All rule-based algorithms

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Algorithm ?x ?y
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Rules>.
	}

###All Models, build by rule-based algorithms

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Model
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Rules>.
        ?Model rdf:type ot:Model.
        ?Model ot:algorithm ?Algorithm. 
	}

###All models, built by clustering algorithms

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Model
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Clustering>.
        ?Model rdf:type ot:Model.
        ?Model ot:algorithm ?Algorithm. 
	}

###All models, built by regression algorithms and display predicted variables

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Model  ?Predicted
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Regression>.
        ?Model rdf:type ot:Model.
        ?Model ot:algorithm ?Algorithm. 
        ?Model ot:predictedVariables ?Predicted.
	}

###All models, predicting Endpoints (of certain type)

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Model ?endpoint
	where {
	?Algorithm rdf:type ot:Algorithm.
        ?Algorithm rdf:type <http://www.opentox.org/algorithmTypes.owl#Rules>.
        ?Model rdf:type ot:Model.
        ?Model ot:algorithm ?Algorithm. 
        ?Model ot:predictedVariables ?Predicted.
        ?Predicted owl:sameAs ?endpoint.
        ?endpoint rdf:type otee:Endpoints.
	}

###Select models, predicting Eye irritation/corrosion


PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select DISTINCT  ?Model
	where {
        ?Model rdf:type ot:Model.
        ?Model ot:predictedVariables ?Predicted.
        ?Predicted owl:sameAs <http://www.opentox.org/echaEndpoints.owl#Eye_irritation/corrosion>.

	}

Top level of endpoints ontology

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Endpoints 
	where {
	?Endpoints rdfs:subClassOf otee:Endpoints
	}

###Human health endpoints

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
	select ?Endpoints 
	where {
	?Endpoints rdfs:subClassOf otee:HumanHealthEffects 
	}

###All features same as http://www.opentox.org/echaEndpoints.owl#Endpoint Carcinogenicity

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX dc:<http://purl.org/dc/elements/1.1/#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
select ?Feature ?SameAS
		where {
	        ?Feature owl:sameAs otee:Carcinogenicity
		}

###Blue Obelisk ontology ####All Molecular descriptors

PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX bo:<http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#>
select ?x 
		where {
	        ?x rdf:type bo:MolecularDescriptor
		}

##Note OpenTox ontology service code is imported from https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/ontology-service

ideaconsult/ontology-service

#OpenTox Ontology service

Download

Top level of endpoints ontology