Sirisha Gollapudi wrote:
Hi,
I'm trying to use Biomart to access Reactome data. I have added the
REACTOME (CSHL US) database under Biomart service in Taverna, and
selected the pathway dataset. I wanted to retrieve all the rice
pathways, by setting "Limit to Species" to Oryza sativa. For the
attributes I chose Pathway name, Pathway Stable ID and Pathway DB_ID.
However after constructing this, the count returns "0 genes" - but the
same query on the Biomart section of the Reactome site
(http://www.reactome.org/cgi-bin/mart) returns 447 entries.
I've attached the workflow - if there are any Biomart/Reactome experts
who can enlighten me, that would be great :)
Hi Sirisha,
There seems to some inconsistency with one of the attribute identifiers.
The configuration file that Taverna uses to generate the query
(http://www.reactome.org:5555/biomart/martservice?type=configuration&dataset=pathway)
specifies "pathway_DB_ID" as the attribute identifier. This results in
an error from Biomart "Attribute pathway_DB_ID NOT FOUND".
If I generate the same query from the website the the attribute
identifier is "pathway_db_id".
As a workaround you could manually change "pathway_DB_ID" to
"pathway_db_id" in the scufl file.
I've copied this to the Biomart list, hopefully the Reactome mart
maintainer can update the config file for this dataset.
David.
--
David Withers
School of Computer Science, University of Manchester,
Oxford Road, Manchester, M13 9PL, UK.
+44 (0)161 275 0683
