diff options
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 26 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 6 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/demo.html | 11 |
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> |