From 83d3f4d03ab8ef61773951c7686b4a70932a8eb5 Mon Sep 17 00:00:00 2001 From: James Hadfield Date: Mon, 6 Dec 2021 12:33:05 +1300 Subject: [PATCH] Fix broken URL in docs The nCoV docs were previously stored on the master branch of nextstrain/ncov and served via GitHub pages. The GitHub pages URLs are now set up as redirects, however this URL pointed to the file itself which has since moved. --- static-site/content/blog/2021-07-08-ncov-open-announcement.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/static-site/content/blog/2021-07-08-ncov-open-announcement.md b/static-site/content/blog/2021-07-08-ncov-open-announcement.md index da243f079..a1b4233cc 100644 --- a/static-site/content/blog/2021-07-08-ncov-open-announcement.md +++ b/static-site/content/blog/2021-07-08-ncov-open-announcement.md @@ -15,7 +15,7 @@ Our goal with Nextstrain is to harness the scientific and public health potentia ![gisaid_vs_open_map](img/gisaid_vs_open_map.png) **Fig 1.** Geographic distribution of samples included in "global" build with GISAID data and Open Data -Moving forward, we will be simultaneously curating and keeping continually updated analyses for GISAID data at [nextstrain.org/ncov/gisaid](https://nextstrain.org/ncov/gisaid) as well as Open Data at [nextstrain.org/ncov/open](https://nextstrain.org/ncov/open), where we are mirroring the pattern of one "global" build alongside six "regional" builds (Fig. 1). Open data is fetched from NCBI GenBank in a completely separate process from data fetched from GISAID. To maximize the utility and visibility of shared open datasets, we also provide preprocessed files that can serve as a starting point for additional analyses, including flat files of aligned sequences and curated metadata. Please see our [documentation](https://github.com/nextstrain/ncov/blob/master/docs/remote_inputs.md) on how to use these preprocessed files. Briefly, this allows Nextstrain build config files to point at URLs like [data.nextstrain.org/files/ncov/open/metadata.tsv.gz](https://data.nextstrain.org/files/ncov/open/metadata.tsv.gz), providing an automated starting point which lets users avoid having to click through a web interface to provision data. This should allow for more automated rebuilds of public health dashboards. Following Terms of Use, we keep GISAID data secure and only provide access to these intermediate data files for GenBank data. +Moving forward, we will be simultaneously curating and keeping continually updated analyses for GISAID data at [nextstrain.org/ncov/gisaid](https://nextstrain.org/ncov/gisaid) as well as Open Data at [nextstrain.org/ncov/open](https://nextstrain.org/ncov/open), where we are mirroring the pattern of one "global" build alongside six "regional" builds (Fig. 1). Open data is fetched from NCBI GenBank in a completely separate process from data fetched from GISAID. To maximize the utility and visibility of shared open datasets, we also provide preprocessed files that can serve as a starting point for additional analyses, including flat files of aligned sequences and curated metadata. Please see our [documentation](https://docs.nextstrain.org/projects/ncov/en/latest/reference/remote_inputs.html) on how to use these preprocessed files. Briefly, this allows Nextstrain build config files to point at URLs like [data.nextstrain.org/files/ncov/open/metadata.tsv.gz](https://data.nextstrain.org/files/ncov/open/metadata.tsv.gz), providing an automated starting point which lets users avoid having to click through a web interface to provision data. This should allow for more automated rebuilds of public health dashboards. Following Terms of Use, we keep GISAID data secure and only provide access to these intermediate data files for GenBank data. Please note that although data generators have generously shared data in an open fashion, _that does not mean there should be a free license to publish on this data_. At Nextstrain we strongly believe in appropriate credit and recognise that "scooping" can make future data generation harder and less appealing to share, and can be particularly problematic for scientists from low and middle income countries. Data generators should be cited where possible and collaborations should be sought in some circumstances. To facilitate such attribution, the open metadata includes links to the original records as well as author information where available. Please try to avoid scooping someone else's work, be mindful of what plans others might have, and reach out if uncertain.