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| author | Pjotr Prins | 2020-05-16 12:08:57 -0500 |
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| committer | Pjotr Prins | 2020-05-16 12:08:57 -0500 |
| commit | d0060bc74ee1f4bffdf89af4cfaa3ffa0c96b3e5 (patch) | |
| tree | b55dfc341837b648dfadb8b4acf8c58a631d0c19 /doc | |
| parent | 89dbb86a7efa9badf0fbccdf467eaae43fb9a9f4 (diff) | |
| parent | f1d0f4faa2cc4496f5e0df679db0e716ceeac5b2 (diff) | |
| download | bh20-seq-resource-d0060bc74ee1f4bffdf89af4cfaa3ffa0c96b3e5.tar.gz bh20-seq-resource-d0060bc74ee1f4bffdf89af4cfaa3ffa0c96b3e5.tar.lz bh20-seq-resource-d0060bc74ee1f4bffdf89af4cfaa3ffa0c96b3e5.zip | |
Merge branch 'master' of github.com:pjotrp/bh20-seq-resource
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part1.org | 8 |
1 files changed, 5 insertions, 3 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org index 4b7ddc6..bca885d 100644 --- a/doc/blog/using-covid-19-pubseq-part1.org +++ b/doc/blog/using-covid-19-pubseq-part1.org @@ -138,10 +138,12 @@ select distinct ?dataset ?submitter } #+end_src -which reads a bit better. We can also see the datasets. One of them submitted -by University of Washington is -is http://arvados.org/keep:00fede2c6f52b053a14edca01cfa02b7+126/sequence.fasta +which reads a bit better. We can also see the [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0Aselect+distinct+%3Fdataset+%3Fsubmitter%0D%0A%7B%0D%0A+++%3Fdataset+pubseq%3Asubmitter+%3Fid+.%0D%0A+++%3Fid+%3Fp+%3Fsubmitter%0D%0A%7D%0D%0A&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][submitted sequences]]. One +of them submitted by University of Washington is +http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/sequence.fasta (note the ID may have changed so pick one with above query). +To see the submitted metadata replace sequence.fasta with metadata.yaml +http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/metadata.yaml 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 |