From bef48abab5e8596703dd825b2d920ea25314d868 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 26 Oct 2020 10:23:00 +0000 Subject: Update blog --- doc/blog/using-covid-19-pubseq-part1.html | 257 ++++++++++++++++++++---------- doc/blog/using-covid-19-pubseq-part1.org | 57 +++++-- 2 files changed, 224 insertions(+), 90 deletions(-) (limited to 'doc/blog') diff --git a/doc/blog/using-covid-19-pubseq-part1.html b/doc/blog/using-covid-19-pubseq-part1.html index deeb749..454eeb5 100644 --- a/doc/blog/using-covid-19-pubseq-part1.html +++ b/doc/blog/using-covid-19-pubseq-part1.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + COVID-19 PubSeq - query metadata (part 1) @@ -40,7 +40,7 @@ } pre.src { position: relative; - overflow: visible; + overflow: auto; padding-top: 1.2em; } pre.src:before { @@ -195,50 +195,26 @@ @@ -248,20 +224,20 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 What does this mean?

+
+

1 What does this mean?

This means that when someone uploads a SARS-CoV-2 sequence using one @@ -313,11 +289,11 @@ initiative!

-
-

2 Fetch sequence data

+
+

2 Fetch sequence data

-The latest run of the pipeline can be viewed here. Each of these +The latest run of the pipeline can be viewed here. Each of these generated files can just be downloaded for your own use and sharing! Data is published under a Creative Commons 4.0 attribution license (CC-BY-4.0). This means that, unlike some other 'public' resources, @@ -338,8 +314,8 @@ these identifiers throughout.

-
-

3 Predicates

+
+

3 Predicates

To explore an RDF dataset, the first query we can do is open and gets @@ -452,8 +428,8 @@ Run this -

4 Fetch submitter info and other metadata

+
+

4 Fetch submitter info and other metadata

To get datasets with submitters we can do the above @@ -558,26 +534,94 @@ PREFIX sio: <http://semanticscience.org/resource/"> sio: <http://semantics

-Run query. +Run this query.

This query tells us the sample was submitted "2020-03-21" and originates from http://www.wikidata.org/entity/Q30, i.e., the USA and is a biospecimen collected from the back of the throat by swabbing. -We can track it back to the original GenBank submission using the -http://identifiers.org/insdc/MT326090.1 link. +We have also added country and label data to make it a bit easier to +view/query the database and place the sequence on the map. We use +wikidata entities for disambiguation. By using 'Q30' for the USA we +don't have to figure out the different ways people spell the name. To +get from the wikidata entity to a human readable form we provide a +country name translation for convenience. For example when the +predicate is http://purl.obolibrary.org/obo/GAZ_00000448 we can do +

+ +
+
PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+PREFIX sio: <http://semanticscience.org/resource/>
+select distinct ?sample ?geoname
+{
+   ?sample sio:SIO_000115 "MT326090.1" .
+   ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo .
+   ?geo rdfs:label ?geoname .
+}
+
+
+ +

+Which will show the geoname spelled out as 'United States'.

-We have also added country and label data to make it a bit easier -to view/query the database and place the sequence on the map. +For this sample we can also track it back to the original GenBank +submission using the listed http://identifiers.org/insdc/MT326090.1 +link.

-
-

5 Fetch all sequences from Washington state

+ +
+

5 Fetch all sequences from Washington state

Now we know how to get at the origin we can do it the other way round @@ -585,19 +629,72 @@ and fetch all sequences referring to Washington state

-
select ?seq ?sample
+
select ?date ?name ?identifier ?seq
 {
     ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample .
-    ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223>
-}
+
+    ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> .
+    ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
+    ?sample <http://semanticscience.org/resource/SIO_000115> ?name .
+    ?sample <http://edamontology.org/data_2091"><http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample .
+
+    ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> .
+    ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date .
+    ?sample <http://semanticscience.org/resource/SIO_000115> ?name .
+    ?sample <http://edamontology.org/data_2091> ?identifier .
+} order by ?date

-which lists 300 sequences originating from Washington state! Which in +Run query +

+ +

+Which shows the date and links to NCBI and raw sequence data in FASTA format, +e.g. +

+ +
+"date"  "name"  "identifier"  "seq"
+"2020-01-15"  "MT252760.1"  "http://identifiers.org/insdc/MT252760.1#sequence"  "http://collections.lugli.arvadosapi.com/c=0164784cba5e3e39b7ba8d83fdc92649+126/sequence.fasta"
+"2020-01-15"  "MT252720.1"  "http://identifiers.org/insdc/MT252720.1#sequence"  "http://collections.lugli.arvadosapi.com/c=0387a3e47dd8a0c9ea0a4a21931f6308+126/sequence.fasta"
+(...)
+
+ + +

+The query lists 300 sequences originating from Washington state! Which in April was almost half of the set coming out of GenBank.

@@ -624,8 +721,8 @@ Run -

6 Discussion

+
+

6 Discussion

The public sequence uploader collects sequences, raw data and @@ -636,8 +733,8 @@ referenced in publications and origins are citeable.

-
-

7 Acknowledgements

+
+

7 Acknowledgements

The overall effort was due to magnificent freely donated input by a @@ -652,7 +749,7 @@ Garrison this initiative would not have existed!

-
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-26 Wed 05:02. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-10-26 Mon 05:21.
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org index e41952d..78d9f19 100644 --- a/doc/blog/using-covid-19-pubseq-part1.org +++ b/doc/blog/using-covid-19-pubseq-part1.org @@ -62,7 +62,7 @@ initiative! * Fetch sequence data -The latest run of the pipeline can be viewed [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][here]]. Each of these +The latest run of the pipeline can be viewed [[http://covid19.genenetwork.org/status][here]]. Each of these generated files can just be downloaded for your own use and sharing! Data is published under a [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 attribution license]] (CC-BY-4.0). This means that, unlike some other 'public' resources, @@ -241,16 +241,36 @@ select distinct ?sample ?p ?o } #+end_src -Run [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0APREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0D%0Aselect+distinct+%3Fsample+%3Fp+%3Fo%0D%0A%7B%0D%0A+++%3Fsample+sio%3ASIO_000115+%22MT326090.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][query]]. +Run this [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0APREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0D%0Aselect+distinct+%3Fsample+%3Fp+%3Fo%0D%0A%7B%0D%0A+++%3Fsample+sio%3ASIO_000115+%22MT326090.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][query]]. This query tells us the sample was submitted "2020-03-21" and originates from http://www.wikidata.org/entity/Q30, i.e., the USA and is a biospecimen collected from the back of the throat by swabbing. -We can track it back to the original GenBank [[http://identifiers.org/insdc/MT326090.1#sequence][submission]] using the -http://identifiers.org/insdc/MT326090.1 link. +We have also added country and label data to make it a bit easier to +view/query the database and place the sequence on the [[http://covid19.genenetwork.org/][map]]. We use +wikidata entities for disambiguation. By using 'Q30' for the USA we +don't have to figure out the different ways people spell the name. To +get from the wikidata entity to a human readable form we provide a +country name [[https://github.com/arvados/bh20-seq-resource/blob/72369b2e2e3cd881be2bd648a61e1449ffe34875/semantic_enrichment/countries.ttl#L306][translation]] for convenience. For example when the +predicate is http://purl.obolibrary.org/obo/GAZ_00000448 we can do + +#+begin_src sql +PREFIX pubseq: +PREFIX sio: +select distinct ?sample ?geoname +{ + ?sample sio:SIO_000115 "MT326090.1" . + ?sample ?geo . + ?geo rdfs:label ?geoname . +} +#+end_src + +Which will show the geoname spelled out as 'United States'. + +For this sample we can also track it back to the original GenBank +[[http://identifiers.org/insdc/MT326090.1#sequence][submission]] using the listed http://identifiers.org/insdc/MT326090.1 +link. -We have also added country and label data to make it a bit easier -to view/query the database and place the sequence on the [[http://covid19.genenetwork.org/][map]]. * Fetch all sequences from Washington state @@ -258,14 +278,31 @@ 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 +select ?date ?name ?identifier ?seq { ?seq ?sample . - ?sample -} + + ?sample . + ?sample ?date . + ?sample ?name . + ?sample ?identifier . +} order by ?date #+end_src -which lists 300 sequences originating from Washington state! Which in +Run [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=select+%3Fdate+%3Fname+%3Fidentifier+%3Fseq%0D%0A%7B%0D%0A++++%3Fseq+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2Fsample%3E+%3Fsample+.%0D%0A%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGAZ_00000448%3E+%3Chttp%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223%3E+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25164%3E+%3Fdate+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000115%3E+%3Fname+.%0D%0A++++%3Fsample+%3Chttp%3A%2F%2Fedamontology.org%2Fdata_2091%3E+%3Fidentifier+.%0D%0A%7D+order+by+%3Fdate&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][query]] + +Which shows the date and links to NCBI and raw sequence data in FASTA format, +e.g. + +#+begin_example +"date" "name" "identifier" "seq" +"2020-01-15" "MT252760.1" "http://identifiers.org/insdc/MT252760.1#sequence" "http://collections.lugli.arvadosapi.com/c=0164784cba5e3e39b7ba8d83fdc92649+126/sequence.fasta" +"2020-01-15" "MT252720.1" "http://identifiers.org/insdc/MT252720.1#sequence" "http://collections.lugli.arvadosapi.com/c=0387a3e47dd8a0c9ea0a4a21931f6308+126/sequence.fasta" +(...) +#+end_example + + +The query lists 300 sequences originating from Washington state! Which in April was almost half of the set coming out of GenBank. Likewise to list all sequences from Turkey we can find the wikidata -- cgit v1.2.3