Hi Syed, I've seen quite a few Biomart Formatters, but unfortunately none for JSON.
Do you have some hints on how to get JSON returned from biomart ? I did not find any useful info in the archives ( I came a cross a processor="JSON" statement but I'm unsure if that's the right way ). http://code.google.com/p/massspecdb/source/browse/trunk/code/biomart-perl/lib/BioMart/Formatter/ I'm looking for something like a BioMart::Formatter::JSON module which returns my response as JSON string, with the attribute name as key. My current query looks like this : /martservice?query=<Query virtualSchemaName = "default" formatter="CSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > <Dataset name = "hsapiens_gene_ensembl" interface = "default" > <Filter name = "gene_id" value = "GeneID:0001"/> <Attribute name = "gene_id" /> <Attribute name = "external_gene_id" /> <Attribute name = "chromosome_name" /> <Attribute name = "strand" /> <Attribute name = "start_position" /> <Attribute name = "end_position" /><Attribute name = "description" /> <Attribute name = "canonical_transcript_stable_id" /> <Attribute name = "ccds" /> </Dataset> </Query> Is there a way to tune this to get JSON or do I have to write my very own Biomart::Formatter::JSON for this ? If so, do you have any hints and do I have to register it somewhere so it get's called ? Any hint welcome, Jan
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