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Diffstat (limited to 'doc')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part1.org | 74 |
1 files changed, 65 insertions, 9 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org index 647165d..d97660b 100644 --- a/doc/blog/using-covid-19-pubseq-part1.org +++ b/doc/blog/using-covid-19-pubseq-part1.org @@ -68,16 +68,72 @@ If you download the GFA or FASTA sequences you'll find sequences are named something like *keep:e17abc8a0269875ed4cfbff5d9897c6c+123/sequence.fasta* which refers to an internal Arvados Keep representation of the FASTA -sequence. Keep is content-addressable which means that +sequence. Keep is content-addressable which means that the value e17abc8a0269875ed4cfbff5d9897c6c uniquely identifies the file by its -contents. If the contents change, the identifier would change! We use +contents. If the contents change, the identifier changes! We use 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/ + +#+begin_src sql +select distinct ?p +{ + ?o ?p ?s +} +#+end_src + +you can ignore the openlink and w3 ones. To reduce results to a named +graph set the default graph to +http://covid-19.genenetwork.org/graph/metadata.ttl in the top input +box. There you can find a predicate for submitter that looks like +http://biohackathon.org/bh20-seq-schema#MainSchema/submitter. + +To list all submitters, try + +#+begin_src sql +select distinct ?s +{ + ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?s +} +#+end_src + +Oh wait, it returns things like nodeID://b76150! That is not helpful, +these are anonymous nodes in the graph. These point to another triple +and by + +#+begin_src sql +select distinct ?s +{ + ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?id . + ?id ?p ?s +} +#+end_src + +you get a list of all submitters including "University of Washington, +Seattle, WA 98109, USA". + +To lift the full URL out of the query you can use a header like + +#+begin_src sql +PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?submitter +{ + ?dataset pubseq:submitter ?id . + ?id ?p ?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 +(note the ID may have changed so pick one with above query). + + * Fetch submitter info and other metadata -We are interested in e17abc8a0269875ed4cfbff5d9897c6c and now we -want to get some metadata. We can use a SPARQL end point hosted at -http://sparql.genenetwork.org/sparql/. Paste in a query like #+begin_src sql select ?p ?s @@ -138,7 +194,7 @@ half of the set coming out of GenBank. The overall effort was due to magnificent freely donated input by a great number of people. I particularly want to thank Thomas Liener for the great effort he made with the ontology group in getting ontology's -and schema sorted! Peter Amstutz and Curii helped build the on-demand -compute and back-ends. Thanks also to Michael Crusoe for supporting -the CWL initiative. And without Erik Garrison this initiative would -not have existed! +and schema sorted! Peter Amstutz and [[https://arvados.org/][Arvados/Curii]] helped build the +on-demand compute and back-ends. Thanks also to Michael Crusoe for +supporting the [[https://www.commonwl.org/][Common Workflow Language]] initiative. And without Erik +Garrison this initiative would not have existed! |