From 2d201e156d530e5e912252c4300245da382b846e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 16 May 2020 10:14:13 -0500
Subject: Counting number of sequences
---
doc/blog/using-covid-19-pubseq-part1.org | 31 +++++++++++++++++++++++++++----
1 file changed, 27 insertions(+), 4 deletions(-)
(limited to 'doc/blog')
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org
index 617a01d..4b7ddc6 100644
--- a/doc/blog/using-covid-19-pubseq-part1.org
+++ b/doc/blog/using-covid-19-pubseq-part1.org
@@ -75,8 +75,10 @@ these identifiers throughout.
* Predicates
-Lets look at all the predicates in the dataset by pasting
-the following in a SPARQL end point http://sparql.genenetwork.org/sparql/
+To explore an RDF dataset, the first query we can do is open and gets
+us a list. Lets look at all the predicates in the dataset by pasting
+the following in a SPARQL end point
+http://sparql.genenetwork.org/sparql/
#+begin_src sql
select distinct ?p
@@ -86,9 +88,19 @@ select distinct ?p
#+end_src
you can ignore the openlink and w3 ones. To reduce results to a named
-graph set the default graph to
+graph set the default graph.
+To get a [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=select+distinct+%3Fg%0D%0A%7B%0D%0A++++GRAPH+%3Fg+%7B%3Fs+%3Fp+%3Fo%7D%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][list of graphs]] in the dataset, first do
+
+#+begin_src sql
+select distinct ?g
+{
+ GRAPH ?g {?s ?p ?o}
+}
+#+end_src
+
+Limiting search to metadata add
http://covid-19.genenetwork.org/graph/metadata.ttl in the top input
-box. There you can find a predicate for submitter that looks like
+box. Now you can find a [[http://sparql.genenetwork.org/sparql/?default-graph-uri=http%3A%2F%2Fcovid-19.genenetwork.org%2Fgraph%2Fmetadata.ttl&query=select+distinct+%3Fp%0D%0A%7B%0D%0A+++%3Fo+%3Fp+%3Fs%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][predicate]] for submitter that looks like
http://biohackathon.org/bh20-seq-schema#MainSchema/submitter.
To list all submitters, try
@@ -131,6 +143,17 @@ by University of Washington is
is http://arvados.org/keep:00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta
(note the ID may have changed so pick one with above query).
+Now we got this far, lets [[http://sparql.genenetwork.org/sparql/?default-graph-uri=http%3A%2F%2Fcovid-19.genenetwork.org%2Fgraph%2Fmetadata.ttl&query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+%28COUNT%28distinct+%3Fdataset%29+as+%3Fnum%29%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter%0D%0A%7D+&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][count the datasets]] submitted with
+
+#+begin_src sql
+PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+select (COUNT(distinct ?dataset) as ?num)
+{
+ ?dataset pubseq:submitter ?id .
+ ?id ?p ?submitter
+}
+#+end_src
+
* Fetch submitter info and other metadata
--
cgit v1.2.3