Cleanup open build config

1. Replace "GENBANK" with "GenBank" per NCBI style in data_provenance 2. Drop "GenBank" from title as it will appear immediately below in byline 3. Update description mainly to warn against scooping data generators
nextstrain · Jun 26, 2021 · 6b78079 · 6b78079
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commit 6b78079
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Showing 9 changed files with 30 additions and 30 deletions.
diff --git a/nextstrain_profiles/nextstrain-open/africa_auspice_config.json b/nextstrain_profiles/nextstrain-open/africa_auspice_config.json
@@ -8,7 +8,7 @@
   ],
   "data_provenance": [
     {
-      "name": "GENBANK",
+      "name": "GenBank",
       "url": "https://www.ncbi.nlm.nih.gov/genbank/"
     }
   ],
@@ -101,4 +101,4 @@
     "entropy",
     "frequencies"
   ]
-}
+}
diff --git a/nextstrain_profiles/nextstrain-open/asia_auspice_config.json b/nextstrain_profiles/nextstrain-open/asia_auspice_config.json
@@ -8,7 +8,7 @@
   ],
   "data_provenance": [
     {
-      "name": "GENBANK",
+      "name": "GenBank",
       "url": "https://www.ncbi.nlm.nih.gov/genbank/"
     }
   ],
@@ -101,4 +101,4 @@
     "entropy",
     "frequencies"
   ]
-}
+}
diff --git a/nextstrain_profiles/nextstrain-open/builds.yaml b/nextstrain_profiles/nextstrain-open/builds.yaml
@@ -34,37 +34,37 @@ builds:
   global:
     subsampling_scheme: nextstrain_region_global
     auspice_config: nextstrain_profiles/nextstrain-open/global_auspice_config.json
-    title: Genomic epidemiology of GenBank SARS-CoV-2 genomes, global subsampling
+    title: Genomic epidemiology of SARS-CoV-2 with global subsampling
   africa:
     subsampling_scheme: nextstrain_region
     region: Africa
     auspice_config: nextstrain_profiles/nextstrain-open/africa_auspice_config.json
-    title: Genomic epidemiology of GenBank SARS-CoV-2 genomes focused on Africa
+    title: Genomic epidemiology of SARS-CoV-2 with Africa-focused subsampling
   asia:
     subsampling_scheme: nextstrain_region
     region: Asia
     auspice_config: nextstrain_profiles/nextstrain-open/asia_auspice_config.json
-    title: Genomic epidemiology of GenBank SARS-CoV-2 genomes focused on Asia
+    title: Genomic epidemiology of SARS-CoV-2 with Asia-focused subsampling
   europe:
     subsampling_scheme: nextstrain_region
     region: Europe
     auspice_config: nextstrain_profiles/nextstrain-open/europe_auspice_config.json
-    title: Genomic epidemiology of GenBank SARS-CoV-2 genomes focused on Europe
+    title: Genomic epidemiology of SARS-CoV-2 with Europe-focused subsampling
   north-america:
     subsampling_scheme: nextstrain_region
     region: North America
     auspice_config: nextstrain_profiles/nextstrain-open/north-america_auspice_config.json
-    title: Genomic epidemiology of GenBank SARS-CoV-2 genomes focused on North America
+    title: Genomic epidemiology of SARS-CoV-2 with North America-focused subsampling
   oceania:
     subsampling_scheme: nextstrain_region
     region: Oceania
     auspice_config: nextstrain_profiles/nextstrain-open/oceania_auspice_config.json
-    title: Genomic epidemiology of GenBank SARS-CoV-2 genomes focused on Oceania
+    title: Genomic epidemiology of SARS-CoV-2 with Oceania-focused subsampling
   south-america:
     subsampling_scheme: nextstrain_region
     region: South America
     auspice_config: nextstrain_profiles/nextstrain-open/south-america_auspice_config.json
-    title: Genomic epidemiology of GenBank SARS-CoV-2 genomes focused on South America
+    title: Genomic epidemiology of SARS-CoV-2 with South America-focused subsampling
 
 
 # remove S dropout sequences and sequences without division label in US

diff --git a/nextstrain_profiles/nextstrain-open/europe_auspice_config.json b/nextstrain_profiles/nextstrain-open/europe_auspice_config.json
@@ -8,7 +8,7 @@
   ],
   "data_provenance": [
     {
-      "name": "GENBANK",
+      "name": "GenBank",
       "url": "https://www.ncbi.nlm.nih.gov/genbank/"
     }
   ],
@@ -101,4 +101,4 @@
     "entropy",
     "frequencies"
   ]
-}
+}
diff --git a/nextstrain_profiles/nextstrain-open/global_auspice_config.json b/nextstrain_profiles/nextstrain-open/global_auspice_config.json
@@ -8,7 +8,7 @@
   ],
   "data_provenance": [
     {
-      "name": "GENBANK",
+      "name": "GenBank",
       "url": "https://www.ncbi.nlm.nih.gov/genbank/"
     }
   ],
@@ -101,4 +101,4 @@
     "entropy",
     "frequencies"
   ]
-}
+}
diff --git a/nextstrain_profiles/nextstrain-open/nextstrain_description.md b/nextstrain_profiles/nextstrain-open/nextstrain_description.md
@@ -6,34 +6,34 @@ There are hundreds of thousands of complete SARS-CoV-2 genomes available on open
 
 Site numbering and genome structure uses [Wuhan-Hu-1/2019](https://www.ncbi.nlm.nih.gov/nuccore/MN908947) as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 8 &times; 10^-4 subs per site per year. Full details on bioinformatic processing can be found [here](https://github.com/nextstrain/ncov).
 
-The analysis on this page uses data from completely open sources, such that we can make input data and intermediate files available for further analysis (see below).
-But be aware that not all regions are well represented in open data bases and some of the above trees might lack recent data from particular geographic regions.
-We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequence and metadata for sharing their work in open databases. A full listing of all originating and submitting laboratories is available below. An attribution table is available by clicking on "Download Data" at the bottom of the page and then clicking on "Strain Metadata" in the resulting dialog box.
+The analysis on this page uses data from NCBI GenBank as a source following Open Data principles, such that we can make input data and intermediate files available for further analysis (see below). Open Data is data that can be freely used, re-used and redistributed by anyone - subject only, at most, to the requirement to attribute and sharealike. But be aware that not all regions are well represented in open databases and some of the above trees might lack recent data from particular geographic regions.
+
+We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work in open databases. 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. An attribution table is available by clicking on "Download Data" at the bottom of the page and then clicking on "Strain Metadata" in the resulting dialog box.
 
 To maximize the utility and visibility of these generously shared data, we provide preprocessed files that can serve as a starting point for additional analyses.
 
 ### All sequences and metadata
 
+#### Ingested and parsed data
+
  * [sequences.fasta.gz](https://data.nextstrain.org/files/ncov/open/sequences.fasta.gz)
  * [metadata.tsv.gz](https://data.nextstrain.org/files/ncov/open/metadata.tsv.gz)
 
-
-### Pre-processed file
+#### Pre-processed files
 
  * [aligned.fasta.xz](https://data.nextstrain.org/files/ncov/open/aligned.fasta.xz)
  * [filtered.fasta.xz](https://data.nextstrain.org/files/ncov/open/filtered.fasta.xz)
  * [masked.fasta.xz](https://data.nextstrain.org/files/ncov/open/masked.fasta.xz)
  * [mutation-summary.tsv.xz](https://data.nextstrain.org/files/ncov/open/mutation-summary.tsv.xz)
 
- ### Subsampled sequences and intermediate files
+### Subsampled sequences and intermediate files
 
-The files below exist for the `global` and the regional builds (`asia`, `africa`, `europe`, `north-america`, `oceania`, `south-america`).
+The files below exist for the `global` and the regional builds (`africa`, `asia`, `europe`, `north-america`, `oceania` and `south-america`).
 The links below refer to the `global` build, substitute `global` with the desired region in the links if necessary
 
- * [aligned.fasta.xz](https://data.nextstrain.org/files/ncov/open/global/aligned.fasta.xz)
  * [sequences.fasta.xz](https://data.nextstrain.org/files/ncov/open/global/sequences.fasta.xz)
  * [metadata.tsv.xz](https://data.nextstrain.org/files/ncov/open/global/metadata.tsv.xz)
+ * [aligned.fasta.xz](https://data.nextstrain.org/files/ncov/open/global/aligned.fasta.xz)
  * [auspice tree](https://data.nextstrain.org/files/ncov/open/global/global.json)
  * [auspice root sequence](https://data.nextstrain.org/files/ncov/open/global/global_root-sequence.json)
  * [auspice tip frequencies](https://data.nextstrain.org/files/ncov/open/global/global_tip-frequencies.json)
-
diff --git a/nextstrain_profiles/nextstrain-open/north-america_auspice_config.json b/nextstrain_profiles/nextstrain-open/north-america_auspice_config.json
@@ -8,7 +8,7 @@
   ],
   "data_provenance": [
     {
-      "name": "GENBANK",
+      "name": "GenBank",
       "url": "https://www.ncbi.nlm.nih.gov/genbank/"
     }
   ],
@@ -101,4 +101,4 @@
     "entropy",
     "frequencies"
   ]
-}
+}
diff --git a/nextstrain_profiles/nextstrain-open/oceania_auspice_config.json b/nextstrain_profiles/nextstrain-open/oceania_auspice_config.json
@@ -8,7 +8,7 @@
   ],
   "data_provenance": [
     {
-      "name": "GENBANK",
+      "name": "GenBank",
       "url": "https://www.ncbi.nlm.nih.gov/genbank/"
     }
   ],
@@ -101,4 +101,4 @@
     "entropy",
     "frequencies"
   ]
-}
+}
diff --git a/nextstrain_profiles/nextstrain-open/south-america_auspice_config.json b/nextstrain_profiles/nextstrain-open/south-america_auspice_config.json
@@ -8,7 +8,7 @@
   ],
   "data_provenance": [
     {
-      "name": "GENBANK",
+      "name": "GenBank",
       "url": "https://www.ncbi.nlm.nih.gov/genbank/"
     }
   ],
@@ -101,4 +101,4 @@
     "entropy",
     "frequencies"
   ]
-}
+}