* molgenis3_3 is not connected to svn (probably after helios installation) .  molgenis4pheno is working.
 * New molgenis project in molgenis4phenotypeWorkspaceHeliosCocoa32 with name  molgenis  ...and it's working with molgenis4pheno

== External Ontology ==
(see relative message including Pedro Lopes, '''Richard Cyganiak) '''

=== How  to connect multiple semantic systems, some using [http://www4.wiwiss.fu-berlin.de/bizer/D2RQ/spec/#specification D2R] and some purely semantic : ===
 * learn basics of D2RQ mapping language, modify the mapping file that you probably created using generate-[[BR]]mapping.  This is probably the file that lives in molgenis_distro (generated by d2rq) : WebContent/WEB-INF/molgenis-rdf-mapping.n3

=== For instance how to define mappings that explicitly say that a table column corresponds to an element of the FOAF ontology ? ===
 * In the mapping file there is a class map corresponding to each table . Find the right class map . below the class map ,there is a property bridge for each column .

{{{
@prefix map: <file:///stdout#> .
@prefix db: <> .
@prefix vocab: <http://localhost:8080/molgenis_distro/vocab/resource/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix d2rq: <http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#> .
@prefix jdbc: <http://d2rq.org/terms/jdbc/> .
@prefix d2r: <http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/config.rdf#> .

<> a d2r:Server;
    rdfs:label "D2R Server";
    d2r:baseURI <http://localhost:8080/pheno/>;
    d2r:port 8080;
    d2r:documentMetadata [
        rdfs:comment "This comment is custom document metadata.";
    ];
	d2r:vocabularyIncludeInstances true;    
    .# Should be jndi loaded!
map:database a d2rq:Database;
	d2rq:jdbcDriver "com.mysql.jdbc.Driver";
	d2rq:jdbcDSN "jdbc:mysql://localhost/bbmri";
	d2rq:username "molgenis";
	d2rq:password "molgenis";
	jdbc:autoReconnect "true";
	jdbc:zeroDateTimeBehavior "convertToNull";
	.
# Entity Investigation
map:Investigation a d2rq:ClassMap;
	d2rq:dataStorage map:database;
	d2rq:uriPattern "Investigation/@@Investigation.id@@";
	d2rq:class vocab:Investigation;
	d2rq:classDefinitionLabel "";
	d2rq:classDefinitionComment " Investigation defines self-contained units of study. For example: Framingham study. Optionally a description and an accession to a data source can be provided. Each Investigation has a unique name and a group of subjects of observation (ObservableTarget), traits of observation (ObservableFeature), results (in ObservedValues), and optionally actions (Protocols, ProtoclApplications). Maps to XGAP/FuGE Investigation, MAGE-TAB Experiment and METABASE:Study. ";
	.	.................................................................................................................................................
	.	.................................................................................................................................................
	.	.................................................................................................................................................
map:Investigation_description a d2rq:PropertyBridge;
	d2rq:belongsToClassMap map:Investigation;
	d2rq:property vocab:Investigation_description;
	d2rq:propertyDefinitionLabel "description";
	d2rq:propertyDefinitionComment "(Optional) Rudimentary meta data about the Investigation";
	d2rq:column "Investigation.description";
	d2rq:datatype xsd:text;
	.
}}}
 * Find the right class map. Below the class map, there's a property bridge for each column. Find the right one.
 * '''Change its !d2rq:property value to the FOAF term, e.g., foaf:name.'''
 * '''You also have to make sure that the FOAF namespace is declared in the @prefix section at the very beginning of the file.'''

=== When there is a table column whose values map elements from the !DailyMed D2R database? ===
 * Instead of mapping the column to a literal with !d2rq:column, use a !d2rq:uriPattern that produces URIs that match the URIs in the other dataset.

= next todos: =
 * '''Change its !d2rq:property value to the FOAF term, e.g., !foaf:name.'''
 * '''You also have to make sure that the FOAF namespace is declared in the @prefix section at the very beginning of the file.'''