Joachim; Thanks very much for the help. I'm copying in the BioMart users list as well.
> > SPARQL-Exception:The following principal mart did not return results: > > Can any of the BioMart folks point me in the right direction? > To understand your problem, I assume you did the following: > 1. Go to http://bm-test.res.oicr.on.ca:9085/ > 2. Click on "Advanced" under "Database Search" > 3. Select "Simple Mutations" > 4. Choose dataset, filters and attributes (let's say, 'Breast Cancer' with > attributes 'Cancer type', 'Chromosome', 'Mutation ID', 'Donor ID' > 5. Clicked on the "SPARQL" button to get the SPARQL query that returns the > same resultset Exactly right -- that's how I got the SPARQL to submit. > I then copied the query with an added "LIMIT 10" into a file called > "snp_config.sparql" and ran "./biomart_sparql.rb -h > bm-test.res.oicr.on.ca > -p 9085" which queries the mart with the HTTP GET request I am doing the equivalent but with the Python SPARQL wrapper (http://sparql-wrapper.sourceforge.net/). I dug into this more because it should work based on your feedback. I had some of the prefixes of the query messed up, which was causing the issue. Awesome, now I've got a basic query working and can move forward. Thanks so much for the help: https://github.com/chapmanb/bcbb/blob/master/semantic/biomart.py > If you want to query other attributes, you can have a look at the > ontology via (for example) Protege by loading the ontology from > http://bm-test.res.oicr.on.ca:9085/martsemantics/snp_config/ontology Thanks for this -- I will dig into the query builder plan more tomorrow. Can you explain how the attributes are named? It looks like there are 4 parts in each: - mart name - feature group (?) - where the feature is derived from (?) - attribute name attribute:snp__simple_somatic_mutation__dm__consequence_type attribute:snp__feature__main__chromosome What I'd like to do is semi-automate the name creation so users can select based on attribute name in the API. Is there any easy way to query for the first 3 values based on the attribute name? Thanks again, Brad _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
