Yaml and ShEx changes

3 files changed, 17 insertions, 26 deletions

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 0be5a50..de0de7d 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -185,10 +185,10 @@ $graph:
   type: record
   fields:
     sample_sequencing_technology:
-      doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION)
+      doc: Technology device that was used to sequence the sample (e.g Sanger, Nanopore MiniION)
       type: string[]
       jsonldPredicate:
-        _id: http://purl.obolibrary.org/obo/OBI_0600047
+        _id: http://purl.obolibrary.org/obo/NCIT_C153598
         _type: "@id"
         noLinkCheck: true
     assembly_method:
@@ -198,7 +198,7 @@ $graph:
         _id: http://purl.obolibrary.org/obo/GENEPIO_0000090
         _type: "@id"
     alignment_protocol:
-      doc: Field for additional information on the pipeline applied to obtain the assembly
+      doc: Protocol which provides detailed instructions to obtain the assembly
       type: string?
       jsonldPredicate:
         _id: http://www.ebi.ac.uk/efo/EFO_0004917
@@ -217,42 +217,42 @@ $graph:
   type: record
   fields:
     authors:
-      doc: Name(s) of the author(s)
+      doc: Name(s) of the author(s) of the sequence data in the scientific publication
       type: string[]
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C42781
     submitter_name:
-      doc: Name of the submitter(s)
+      doc: Name of the submitter(s) of the sequence data
       type: string[]?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000116
     submitter_address:
-      doc: Address of the submitter
+      doc: Address of the submitter of the sequence data
       type: string?
       jsonldPredicate:
           _id: http://semanticscience.org/resource/SIO_000172
     originating_lab:
-      doc: Laboratory where the sample originates from sample
+      doc: Laboratory name or identifier where the sample to sequence was produced
       type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C37984
     lab_address:
-      doc: Address of the laboratory
+      doc: Address of the laboratory where the sample was produced
       type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C25407
     provider:
-      doc: Provider of the sample
+      doc: Name or identifier of the provider of the sample
       type: string?
       jsonldPredicate:
           _id: http://purl.obolibrary.org/obo/NCIT_C37900
     submitter_sample_id:
-      doc: Identifer given to the sample by the submitter
+      doc: Identifier given to the sample by the submitter
       type: string?
       jsonldPredicate:
-          _id: http://purl.obolibrary.org/obo/NCIT_C25364
+          _id: http://purl.obolibrary.org/obo/NCIT_C164332
     publication:
-      doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...)
+      doc: Reference to the scientifc publication of the sequence (e.g. DOI, pubmed ID, ...)
       type: string?
       jsonldPredicate:
         _id: http://purl.obolibrary.org/obo/NCIT_C19026
@@ -260,7 +260,7 @@ $graph:
       doc: ORCID of the submitter as a full URI, e.g. https://orcid.org/0000-0002-1825-0097
       type: string[]?
       jsonldPredicate:
-          _id: http://semanticscience.org/resource/SIO_000115
+          _id: http://purl.obolibrary.org/obo/APOLLO_SV_00000496
           _type: "@id"
           noLinkCheck: true
     additional_submitter_information:
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 69bd7f4..e22ad60 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -56,14 +56,14 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
     obo:NCIT_C37984 xsd:string ?;       #(originating_lab) Laboratory, optional, string
     obo:NCIT_C25407  xsd:string ?;      #(lab address), Address, optional, string
     obo:NCIT_C37900 xsd:string ?;       #(provider), Provider, optional, string
-    obo:NCIT_C25364 xsd:string ?;       #(submitter_sample_id), identifier, optional, string
+    obo:NCIT_C164332 xsd:string ?;       #(submitter_sample_id), Sample identifier, optional, string
     obo:NCIT_C19026 xsd:string ?;       #(publication), Scientific Publication, optional string
-    sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/ {0,10};   #(submitter_orcid) identifier, optional but given regular expression
+    obo:APOLLO_SV_00000496 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/ {0,10};   #(submitter_orcid) identifier, optional but given regular expression
     sio:SIO_001167 xsd:string ?;        #(additional_submitter_information), comment, optional string
 }
 
 :technologyShape CLOSED {
-    obo:OBI_0600047 IRI {1,3} ;         #(sample_sequencing_technology), sequencing assay, optional
+    obo:NCIT_C153598 IRI {1,3} ;         #(sample_sequencing_technology), DNA Sequencing, mandatory
     obo:GENEPIO_0000090 [obo:GENEPIO_0001628 obo:GENEPIO_0002028 ] ;    #(assembly method), assembly method, mandatory, one of the two
     efo:EFO_0004917 xsd:string ?;        #(alignment_protocol), high throughput sequence alignment protocol, optional
     obo:FLU_0000848 xsd:double OR xsd:integer {0,3};    #(sequence coverage) sequence coverage, optional
diff --git a/bh20simplewebuploader/templates/demo.html b/bh20simplewebuploader/templates/demo.html
index 75bc0e2..1edca00 100644
--- a/bh20simplewebuploader/templates/demo.html
+++ b/bh20simplewebuploader/templates/demo.html
@@ -1,13 +1,11 @@
 <!DOCTYPE html>
 <html>
   {% include 'header.html' %}
-  {% include 'mapheader.html' %}
   <body>
     {% include 'banner.html' %}
     {% include 'menu.html' %}
 
-    <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences!</p>
-
+    <p>The Virtuoso database contains <span id="CounterDB"></span> public sequences! The examples here should provide a starting point to explore our data in our public <a href="http://sparql.genenetwork.org/sparql">SPARQL endpoint</a> or via <a href="https://covid-19-sparql.expasy.org/">SIB COVID-19 Integrated Knowledgebase</a>. See also our documentation <a href="http://127.0.0.1:5000/blog?id=using-covid-19-pubseq-part1">here</a> for more information!</p>
     <!--
     <div class="search">
       <input id="search-input" type="search" placeholder="FASTA uri" required>
@@ -22,7 +20,6 @@
 
     <section class="search-section">
       <div class="filter-options" action="#">
-        <p>[Demo] Display content sequences by: </p>
         <div>
           <button class="button" onclick="fetchSEQCountBySpecimen()">Count by Specimen source</button>
           <button class="button" onclick="fetchSEQCountByLocation()">Count by Location</button>
@@ -37,9 +34,6 @@
     <div id="loader" class="loader invisible">
     </div>
 
-    <section id="map_view" class="map">
-      <div id="mapid"></div>
-    </section>
 
     <section>
       <div id="table"></div>
@@ -61,9 +55,6 @@
                   span.appendChild(txt);
               });
       });
-
-     drawMap()
-
     </script>
 
   </body>