From f4ed46dae20abe5147871495ede2d6ac2b0854bc Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 15 Jul 2020 14:30:56 +0100
Subject: Add RDF output

---
 bh20sequploader/bh20seq-schema.yml       |  9 +++++++--
 bh20sequploader/bh20seq-shex.rdf         | 24 +++++++++++++++++-------
 doc/blog/using-covid-19-pubseq-part5.org |  2 ++
 3 files changed, 26 insertions(+), 9 deletions(-)

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 29ac22c..c690e8a 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -23,16 +23,21 @@ $graph:
       type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_001167
+    attribution_name:
+      doc: Attribution NAME related to data license
+      type: string?
+      jsonldPredicate:
+          _id: https://creativecommons.org/ns#attributionName
     attribution_url:
       doc: Attribution URL related to data license
       type: string?
       jsonldPredicate:
-          _id: https://creativecommons.org/ns#Work
+          _id: https://creativecommons.org/ns#attributionURL
     attribution_source:
       doc: Attribution source URL related to data license
       type: string?
       jsonldPredicate:
-          _id: https://creativecommons.org/ns#Work
+          _id: https://creativecommons.org/ns#attributionSource
 
 - name: hostSchema
   type: record
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 965229c..c48267d 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -1,6 +1,7 @@
 PREFIX : <https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#>
 PREFIX MainSchema: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
 PREFIX hostSchema: <http://biohackathon.org/bh20-seq-schema#hostSchema/>
+PREFIX cc:  <http://creativecommons.org/ns#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX sio: <http://semanticscience.org/resource/>
@@ -15,10 +16,11 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
   MainSchema:submitter @:submitterShape ;
   MainSchema:technology @:technologyShape ;
   MainSchema:virus @:virusShape;
+  MainSchema:license @:licenseShape;
 }
 
 :hostShape  {
-  	efo:EFO_0000532 [ obo:NCBITaxon_~ ] ;
+    efo:EFO_0000532 [ obo:NCBITaxon_~ ] ;
     sio:SIO_000115 xsd:string ?;
     obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 obo:PATO_0001340] ?;
     obo:PATO_0000011 xsd:integer ?;
@@ -32,14 +34,14 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
 
 :sampleShape  {
     sio:SIO_000115 xsd:string;
-	  evs:C25164 xsd:string;
-	  obo:GAZ_00000448 [wikidata:~] ;
+    evs:C25164 xsd:string;
+    obo:GAZ_00000448 [wikidata:~] ;
     obo:OBI_0001895 xsd:string ?;
     obo:NCIT_C41206 xsd:string ?;
     obo:OBI_0001479 IRI {0,2};
     obo:OBI_0001472 xsd:string ?;
     sio:SIO_001167 xsd:string ?;
-	edam:data_2091 IRI {0,3};
+    edam:data_2091 IRI {0,3};
 }
 
 :submitterShape {
@@ -47,7 +49,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
     sio:SIO_000116 xsd:string *;
     sio:SIO_000172 xsd:string ?;
     obo:NCIT_C37984 xsd:string ?;
-  	obo:NCIT_C37900 xsd:string ?;
+    obo:NCIT_C37900 xsd:string ?;
     efo:EFO_0001741 xsd:string ?;
     obo:NCIT_C42781 xsd:string ?;
     obo:NCIT_C19026 xsd:string ?;
@@ -63,6 +65,14 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
 }
 
 :virusShape{
-	edam:data_1875 [ obo:NCBITaxon_~ ] ;
-  	sio:SIO_010055 xsd:string ?;
+    edam:data_1875 [ obo:NCBITaxon_~ ] ;
+    sio:SIO_010055 xsd:string ?;
 }
+
+:licenseShape{
+    cc:License xsd:string;
+    sio:SIO_001167 xsd:string ?;
+    cc:attributionName xsd:string ?;
+    cc:attributionURL xsd:string ?;
+    cc:attributionSource xsd:string ?;
+}
\ No newline at end of file
diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org
index aa06d5e..cb11f43 100644
--- a/doc/blog/using-covid-19-pubseq-part5.org
+++ b/doc/blog/using-covid-19-pubseq-part5.org
@@ -125,4 +125,6 @@ To add the new fields to the form we have to modify it a little. If we
 go to the upload form we need to add the license box. The schema is
 loaded in [[https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229][main.py]] in the 'generate_form' function.
 
+With this [[https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3][patch]] the website adds the license input fields on the form.
+
 /Note: work in progress/
-- 
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