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GoogleCodeExporter commented 8 years ago

Hi all,

Your work is great and I couldn't wait to get started with it.
So I just started playing around with the Biological SPARQL queries you provide 
in the paper.

1. I selected the Lung methylation end-point. 
http://digital3.path.uab.edu/sparql
2. I ran the query:
PREFIX tcga: <http://tcga.deri.ie/schema/> 
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
SELECT DISTINCT ?patient avg(xsd:decimal(?methylationKRAS)) as ?avgMethKRAS
WHERE
{
?patientURI tcga:bcr_patient_barcode   ?patient.
?patientURI tcga:result   ?recordNo.
?recordNo tcga:chromosome   "12".
?recordNo tcga:position   ?position.
?recordNo tcga:beta_valu   ?methylationKRAS.
FILTER (xsd:decimal(?position)>=25386768 && xsd:decimal(?position)<25403863)
}

3. And I get an empty result set

Hope you can help out, best,
Joep

Original issue reported on code.google.com by joe...@gmail.com on 3 Dec 2014 at 9:34

GoogleCodeExporter commented 8 years ago

Hi Joep,

Thank you for your interest in our work. There is a small issue with the query. 
Please replace  tcga:beta_valu  with tcga:beta_value in the fifth triple 
pattern. The query is now syntactically correct. However, it may results in 
transaction time out as we imposed an execution timeout of 1 min for all the 
http://digital{x}.path.uab.edu/sparql SPARQL endpoints. Should you have further 
queries, Please don't hesitate to contact us. 

Best Regards,
Saleem
saleem.muhammd@gmail.com

Original comment by saleem.m...@gmail.com on 3 Dec 2014 at 12:50

GoogleCodeExporter commented 8 years ago

Thanks for the pointer.
Copy pasted from the pdf but apparently that character was missing.
Please close the issue as it is clearly a user error.
It might however be useful to add a note to the SPARQL endpoint overview about 
the timeout.

Cheers,
Joep

Original comment by joe...@gmail.com on 3 Dec 2014 at 1:29

rezacsedu / topfed

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