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Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part1.org')
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1 files changed, 12 insertions, 11 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org index 5a749d6..0fd5589 100644 --- a/doc/blog/using-covid-19-pubseq-part1.org +++ b/doc/blog/using-covid-19-pubseq-part1.org @@ -5,18 +5,8 @@ # C-c C-t task rotate # RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png -#+HTML_LINK_HOME: http://covid19.genenetwork.org #+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" /> -As part of the COVID-19 Biohackathon 2020 we formed a working group -to create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for -Corona virus sequences. The general idea is to create a repository -that has a low barrier to entry for uploading sequence data using best -practices. I.e., data published with a creative commons 4.0 (CC-4.0) -license with metadata using state-of-the art standards and, perhaps -most importantly, providing standardised workflows that get triggered -on upload, so that results are immediately available in standardised -data formats. * Table of Contents :TOC:noexport: - [[#what-does-this-mean][What does this mean?]] @@ -261,7 +251,6 @@ Now we know how to get at the origin we can do it the other way round and fetch all sequences referring to Washington state #+begin_src sql - select ?seq ?sample { ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . @@ -272,6 +261,18 @@ select ?seq ?sample which lists 300 sequences originating from Washington state! Which is almost half of the set coming out of GenBank. +Likewise to list all sequences from Turkey we can find the wikidata +entity is [[https://www.wikidata.org/wiki/Q43][Q43]]: + +#+begin_src sql +select ?seq ?sample +{ + ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q43> +} +#+end_src + + * Discussion The public sequence uploader collects sequences, raw data and |