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-rw-r--r--bh20sequploader/bh20seq-schema.yml26
-rw-r--r--bh20sequploader/bh20seq-shex.rdf6
-rw-r--r--bh20simplewebuploader/templates/demo.html11
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>