Fix RDF schema problems with lane_number and species.

[htsworkflow.git] / htsworkflow / util / schemas / htsworkflow.turtle

diff --git a/htsworkflow/util/schemas/htsworkflow.turtle b/htsworkflow/util/schemas/htsworkflow.turtle
index 7319c0c1bb8bb8a14b32cb7a0436c8eaac42c0f9..8fe0362d32a33b721d72c112fc7093f80ad34067 100644 (file)
--- a/htsworkflow/util/schemas/htsworkflow.turtle
+++ b/htsworkflow/util/schemas/htsworkflow.turtle
@@ -14,10 +14,12 @@
     dc:title "HTS-Workflow ontology" ;
     a owl:Ontology .
 
-htswlib:Class a rdfs:Class .
+htswlib:Class rdfs:subClassOf rdfs:Class ;
+              a rdfs:Class .
+rdfs:Resource a rdfs:Class.
 
 htswlib:IlluminaFlowcell
-    a rdfs:Class, htswlib:Class ;
+    a rdfs:Class, htswlib:Class;
     rdfs:comment "information about a illumina flowcell" ;
     rdfs:label "Flowcell" .
 
@@ -69,7 +71,7 @@ htswlib:date
     rdfs:label "made on" ;
     rdfs:domain htswlib:IlluminaFlowcell ;
     rdfs:domain htswlib:Library ;
-    rdfs:range rdfs:Literal .
+    rdfs:range xsd:dateTime .
 
 htswlib:total_unique_locations
     a rdf:Property ;
@@ -77,7 +79,7 @@ htswlib:total_unique_locations
     rdfs:label "Unique locations" ;
     rdfs:domain htswlib:Library ;
     rdfs:domain htswlib:IlluminaLane ;
-    rdfs:range rdfs:Literal .
+    rdfs:range xsd:integer .
 
 htswlib:has_mappings
     a rdf:Property ;
@@ -193,6 +195,28 @@ htswlib:sequencer_name
     rdfs:domain htswlib:Sequencer ;
     rdfs:range rdfs:Literal .
 
+# lane properties
+htswlib:status
+   a rdf:Proprety ;
+   rdfs:comment "Operators opinion of lane status, e.g. were there spots in the pictures" ;
+   rdfs:label "Status" ;
+   rdfs:domain htswlib:IlluminaLane ;
+   rdfs:range htswlib:Literal .
+
+htswlib:cluster_estimate
+   a rdf:Proprety ;
+   rdfs:comment "Estimate of clusters per tile" ;
+   rdfs:label "Cluster Estimate" ;
+   rdfs:domain htswlib:IlluminaLane ;
+   rdfs:range htswlib:Literal .
+
+htswlib:pM
+   a rdf:Proprety ;
+   rdfs:comment "picoMolarity" ;
+   rdfs:label "picoMolarity" ;
+   rdfs:domain htswlib:IlluminaLane ;
+   rdfs:range htswlib:Literal .
+
 
 # library only properties
 htswlib:library_id
@@ -217,6 +241,13 @@ htswlib:library_type
     rdfs:domain htswlib:Library ;
     rdfs:range rdfs:Literal .
 
+htswlib:condition
+   a rdf:Property ;
+   rdfs:comment "Describes what treatment has been applied to the cells" ;
+   rdfs:label "Condition" ;
+   rdfs:domain htswlib:Library ;
+   rdfs:range rdfs:Literal .
+
 htswlib:stopping_point
     a rdf:Property ;
     rdfs:comment "Protocol stopping point" ;
@@ -243,7 +274,7 @@ htswlib:gel_cut
     rdfs:comment "The estimated fragment sizes cut from gel";
     rdfs:label "Gel Cut" ;
     rdfs:domain htswlib:Library ;
-    rdfs:range rdfs:Literal .
+    rdfs:range xsd:integer .
 
 htswlib:made_by
     a rdf:Property ;
@@ -282,12 +313,19 @@ htswlib:affiliation
 
 htswlib:species
     a rdf:Property ;
-    rdfs:comment "Scientific name of sample species" ;
+    rdfs:comment "A species class" ;
     rdfs:label "Species" ;
     rdfs:domain htswlib:Library ;
     #rdfs:domain htswlib:IlluminaLane;
     rdfs:range htswlib:Species .
 
+htswlib:species_name
+   a rdf:Property ;
+   rdfs:comment "Scientific name of sample species" ;
+   rdfs:label "Species name";
+   rdfs:domain htswlib:Species, htswlib:Library ;
+   rdfs:range xsd:string .
+
 htswlib:replicate
     a rdf:Property ;
     rdfs:comment "Which replicate this was" ;
@@ -301,7 +339,7 @@ htswlib:lane_number
     rdfs:comment "Which lane were we run in" ;
     rdfs:label "lane id" ;
     rdfs:domain htswlib:IlluminaLane ;
-    rdfs:range rdfs:Literal .
+    rdfs:range xsd:string .
 
 # FIXME: should this be note?
 htswlib:comment