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Add data provenence statements to the auspice view
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j23414 committed Nov 16, 2024
1 parent 70fbe18 commit d46f0e5
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6 changes: 6 additions & 0 deletions phylogenetic/defaults/auspice_config.json
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{
"title": "Washington Focused West Nile Virus Build",
"data_provenance": [
{
"name": "GenBank",
"url": "https://www.ncbi.nlm.nih.gov/genbank/"
}
],
"colorings": [
{"key": "gt", "title": "Genotype", "type": "categorical"},
{"key": "num_date", "title": "Sampling Date", "type": "continuous"},
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6 changes: 6 additions & 0 deletions phylogenetic/defaults/auspice_config_global.json
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@@ -1,5 +1,11 @@
{
"title": "Global West Nile Virus Build",
"data_provenance": [
{
"name": "GenBank",
"url": "https://www.ncbi.nlm.nih.gov/genbank/"
}
],
"colorings": [
{"key": "gt", "title": "Genotype", "type": "categorical"},
{"key": "num_date", "title": "Sampling Date", "type": "continuous"},
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5 changes: 5 additions & 0 deletions phylogenetic/defaults/description.md
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@@ -1,3 +1,8 @@
We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.

Special thanks to individuals at the [Northwest Pathogen Genomics Center of Excellence](https://github.com/NW-PaGe) and [Grubaugh lab](https://grubaughlab.com/) for comments, code and suggestions.

We curate sequence data and metadata from NCBI as starting point for our analyses. For global lineage designations, we query [pathoplexus](https://pathoplexus.org/) for lineage assignments and exclusively work with NCBI-sourced records at this time. Curated sequences and metadata are available as flat files at:

* [data.nextstrain.org/files/workflows/WNV/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/WNV/sequences.fasta.zst)
* [data.nextstrain.org/files/workflows/WNV/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/WNV/metadata.tsv.zst)

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