Update metadata description on policies page

[scottcain]

On https://virusseq-dataportal.ca/policies, the Contextual Metadata: list should be updated with this:

Study id- a unique identifier for each data provider Specimen collector sample ID- a unique identifier for each sequenced specimen GISAID accession- the GISAID accession number assigned to the sequence Sample collected by- the name of the agency that collected the original sample Sequence submitted by- the name of the agency that generated the sequence Sample collection date- the date on which the sample was collected Geo_loc_name (country)- the country where the sample was collected Geo_loc_name (state/province/territory)- the province/territory where the sample was collected Organism- Taxonomic name of the organism Isolate- Identifier of the specific isolate Fasta header name- fasta file identifier of the isolate Purpose of sampling- the reason that the sample was collected Purpose of sampling details- the description of why the sample was collected, providing specific details Anatomical material- A substance obtained from an anatomical part of an organism e.g. tissue, blood Anatomical part- An anatomical part of an organism e.g. oropharynx Body product- A substance excreted/secreted from an organism e.g. feces, urine, sweat Environmental material- A substance obtained from the natural or man-made environment e.g. soil, water, sewage Environmental site- An environmental location may describe a site in the natural or built environment e.g. metal can, hospital Collection device- The instrument or container used to collect the sample e.g. swab Collection method- The process used to collect the sample e.g. phlebotamy, necropsy Host (scientific name)- The taxonomic, or scientific name of the host Host disease- The name of the disease experienced by the host Host age- Age of host at the time of sampling Host age unit- The unit used to measure the host age, in either months or years Host age bin- Age of host at the time of sampling, expressed as an age group Host gender- The gender of the host at the time of sample collection Purpose of sequencing- The reason that the sample was sequenced Purpose of sequencing details- The description of why the sample was sequenced providing specific details Sequencing instrument- The model of the sequencing instrument used Sequencing protocol- The protocol used to generate the sequence Raw sequence data processing method- The names of the software and version number used for raw data processing e.g. removing barcodes, filtering etc Dehosting method- The method used to remove host reads from the pathogen sequence Consensus sequence software name- The name of software used to generate the consensus sequence Consensus sequence software version- The version of the software used to generate the consensus sequence Breadth of coverage value- The percentage of the reference genome covered by the sequenced data, to a prescribed depth Depth of coverage value- The average number of reads representing a given nucleotide in the reconstructed sequence Reference genome accession- A persistent, unique identifier of a genome database entry Bioinformatics protocol- A description of the overall bioinformatics strategy used Gene name- The name of the gene used in the diagnostic RT-PCR test Diagnostic_pcr_ct_value- The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test Lineage name- The name of the lineage assigned to a squenced sample Lineage analysis software name- The name of the software used to determine the lineage Lineage analysis software version- The version of the software used to determine the lineage Lineage analysis software data version- A version number that represents both pangolin-data version number Scorpio call- A software that performs snp-based calling of VOCs, mainly serious constellations of reoccurring phylogenetically-independent origin Scorpio version- The version of scorpio software to determine the lineage

[justincorrigible]

Changes made and reviewable in dev at https://portal.dev.cancogen.cancercollaboratory.org/policies Will promote to prod once reviewed/approved

[scottcain]

@justincorrigible Unfortunately, I can't see the dev site; want to post a screenshot?

[justincorrigible]

Here we go!

[scottcain]

@justincorrigible Thanks! It can go into the next release in which it's convenient to put it.

[justincorrigible]

Changes deployed to prod. Please feel free to close the ticket upon validation 👍

[scottcain]

Thanks @justincorrigible