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CanCoGen field tweak
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sample collection date unit rename
illumina novaSeq parent
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Damion Dooley committed Feb 17, 2021
1 parent cddc0d5 commit 81113b7
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Showing 4 changed files with 40 additions and 46 deletions.
2 changes: 1 addition & 1 deletion script/main.js
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Expand Up @@ -11,7 +11,7 @@
* main.html?template=test_template
*
*/
const VERSION = '0.13.13';
const VERSION = '0.13.14';
const TEMPLATES = {
'CanCOGeN Covid-19': {'folder': 'canada_covid19', 'status': 'published'},
'PHAC Dexa (ALPHA)': {'folder': 'phac_dexa', 'status': 'draft'},
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53 changes: 28 additions & 25 deletions template/canada_covid19/data.js
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Expand Up @@ -437,10 +437,10 @@ var DATA = [
}
},
{
"fieldName": "sample collection date unit",
"fieldName": "sample collection date precision",
"capitalize": "",
"ontology_id": "",
"datatype": "",
"datatype": "select",
"source": "",
"dataStatus": null,
"xs:minInclusive": "",
Expand All @@ -455,6 +455,11 @@ var DATA = [
"field": "Precision of date collected"
}
]
},
"vocabulary": {
"year": {},
"month": {},
"day": {}
}
},
{
Expand Down Expand Up @@ -3270,6 +3275,9 @@ var DATA = [
"Illumina iSeq": {
"Illumina iSeq 100": {}
},
"Illumina NovaSeq": {
"Illumina NovaSeq 6000": {}
},
"Illumina MiniSeq": {},
"Illumina MiSeq": {},
"Illumina NextSeq": {},
Expand Down Expand Up @@ -3415,7 +3423,7 @@ var DATA = [
"examples": "/User/Documents/RespLab/Data/ncov123assembly.fasta"
},
{
"fieldName": "consensus sequence name",
"fieldName": "consensus sequence method name",
"capitalize": "",
"ontology_id": "",
"datatype": "xs:token",
Expand All @@ -3426,10 +3434,17 @@ var DATA = [
"requirement": "required",
"description": "The name of the consensus sequence.",
"guidance": "Provide the name and version number of the consensus sequence.",
"examples": "Ivar"
"examples": "Ivar",
"exportField": {
"CNPHI": [
{
"field": "consensus sequence"
}
]
}
},
{
"fieldName": "consensus sequence version",
"fieldName": "consensus sequence method version",
"capitalize": "",
"ontology_id": "",
"datatype": "xs:decimal",
Expand All @@ -3440,7 +3455,14 @@ var DATA = [
"requirement": "required",
"description": "The version of the software used to generate the consensus sequence.",
"guidance": "Provide the version of the software used to generate the consensus sequence.",
"examples": "1.3"
"examples": "1.3",
"exportField": {
"CNPHI": [
{
"field": "consensus sequence"
}
]
}
},
{
"fieldName": "breadth of coverage value",
Expand Down Expand Up @@ -4053,24 +4075,5 @@ var DATA = [
}
}
]
},
{
"fieldName": "Illumina NovaSeq",
"children": [
{
"fieldName": "Illumina NovaSeq 6000",
"capitalize": "",
"ontology_id": "OBI_0002630",
"datatype": "",
"source": "",
"dataStatus": null,
"xs:minInclusive": "",
"xs:maxInclusive": "",
"requirement": "",
"description": "",
"guidance": "",
"examples": ""
}
]
}
]
12 changes: 8 additions & 4 deletions template/canada_covid19/data.tsv
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Expand Up @@ -19,7 +19,7 @@ ID SC % AL rdfs:label@en AL IAO:0000115@en A IAO:0000119 SPLIT=| A
Sample collection and processing sequence submitter contact email xs:token The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca
Sample collection and processing sequence submitter contact address xs:token The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address
Sample collection and processing sample collection date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date sample collection date
Sample collection and processing sample collection date unit Precision of date collected
Sample collection and processing sample collection date precision select Precision of date collected
Sample collection and processing sample received date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20
Sample collection and processing geo_loc_name (country) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country geo_loc_name
Sample collection and processing geo_loc_name (province/territory) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province geo_loc_name
Expand Down Expand Up @@ -103,8 +103,8 @@ Risk Factor: A variable associated with an increased risk of disease or infectio
Bioinformatics and QC metrics dehosting method xs:token The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper
Bioinformatics and QC metrics consensus sequence filename xs:token The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. ncov123assembly.fasta
Bioinformatics and QC metrics consensus sequence filepath xs:token The filepath of the consesnsus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/RespLab/Data/ncov123assembly.fasta
Bioinformatics and QC metrics consensus sequence name xs:token required The name of the consensus sequence. Provide the name and version number of the consensus sequence. Ivar
Bioinformatics and QC metrics consensus sequence version xs:decimal required The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3
Bioinformatics and QC metrics consensus sequence method name xs:token required The name of the consensus sequence. Provide the name and version number of the consensus sequence. Ivar consensus sequence
Bioinformatics and QC metrics consensus sequence method version xs:decimal required The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence
Bioinformatics and QC metrics breadth of coverage value xs:token The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95%
Bioinformatics and QC metrics depth of coverage value xs:token The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage
Bioinformatics and QC metrics depth of coverage threshold xs:token The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x
Expand Down Expand Up @@ -159,6 +159,10 @@ GAZ_00002576 geo_loc_name (province/territory) Yukon Yukon Terri
UO:0000035 host age unit month month
UO:0000036 host age unit year year

UO:0000035 sample collection date precision year
UO:0000036 sample collection date precision month
UO:0000033 sample collection date precision day

OBI:0000895 biomaterial extracted RNA (total) total RNA extract total RNA extract RNA extract OBI:0000880
OBI:0000869 biomaterial extracted RNA (poly-A) polyA RNA extract polyA RNA extract, poly-A RNA extract RNA extract OBI:0000880
OBI:0002627 biomaterial extracted RNA (ribo-depleted) ribosomal RNA-depleted RNA extract ribo-depleted RNA extract RNA extract OBI:0000880
Expand Down Expand Up @@ -1021,7 +1025,7 @@ OBI_0002048 Illumina Illumina HiSeq 3000 illumina hiseq 3000
OBI_0002049 Illumina Illumina HiSeq 4000 illumina hiseq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html HiSeq 4000 DNA sequencer OBI_0400103
Illumina Illumina iSeq
http://www.ebi.ac.uk/efo/EFO_0008635 Illumina iSeq Illumina iSeq 100 illumina iseq 100 The Illumina iSeq 100 is a benchtop sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions, gene expression analysis and 16S metagenomic sequencing. https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008635&viewMode=All&siblings=true iSeq 100 high throughput sequencer http://www.ebi.ac.uk/efo/EFO_0002699
Illumina NovaSeq
Illumina Illumina NovaSeq
OBI_0002630 Illumina NovaSeq Illumina NovaSeq 6000 illumina novaseq 6000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run) http://www.illumina.com/systems/sequencing-platforms/novaseq.html NovaSeq 6000 DNA sequencer OBI_0400103
http://www.ebi.ac.uk/efo/EFO_0008636 Illumina Illumina MiniSeq illumina miniseq The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina and an output upto 8Gb. https://www.illumina.com/systems/sequencing-platforms/miniseq/specifications.html MiniSeq high throughput sequencer http://www.ebi.ac.uk/efo/EFO_0002699
OBI_0002003 Illumina Illumina MiSeq MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf illumina miseq DNA sequencer OBI_0400103
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19 changes: 3 additions & 16 deletions template/canada_covid19/reference.html
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Expand Up @@ -192,7 +192,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission


<tr>
<td class="label">sample collection date unit</td>
<td class="label">sample collection date precision</td>
<td></td>
<td></td>
<td></td>
Expand Down Expand Up @@ -855,7 +855,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission


<tr>
<td class="label">consensus sequence name</td>
<td class="label">consensus sequence method name</td>
<td>The name of the consensus sequence.</td>
<td>Provide the name and version number of the consensus sequence.</td>
<td>Ivar</td>
Expand All @@ -864,7 +864,7 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission


<tr>
<td class="label">consensus sequence version</td>
<td class="label">consensus sequence method version</td>
<td>The version of the software used to generate the consensus sequence.</td>
<td>Provide the version of the software used to generate the consensus sequence.</td>
<td>1.3</td>
Expand Down Expand Up @@ -1153,19 +1153,6 @@ <h2>CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission
<td>None</td>
</tr>


<tr class="section">
<td colspan="5"><h3>Illumina NovaSeq</h3></td>
</tr>

<tr>
<td class="label">Illumina NovaSeq 6000</td>
<td></td>
<td></td>
<td></td>
<td>None</td>
</tr>

</table>

</tbody>
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