biomart-client

Clojure library to query unRESTful BioMart web services.

Usage

Querying

(use '[biomart-client.utils :only (martservice-url)]
     '[biomart-client.query])

(def ms (martservice-url "http://www.i-dcc.org/biomart"))
;=> #'user/ms
;=> "http://www.i-dcc.org/biomart/martservice"

(query ms {:dataset "dcc"
           :filter  {:marker_symbol ["Art4" "Cbx1"]}
           :attrs   [:marker_symbol :mgi_accession_id]}))
;=> ({:mgi_accession_id "MGI:1202710", :marker_symbol "Art4"}
     {:mgi_accession_id "MGI:105369", :marker_symbol "Cbx1"})

(query ms {:count true} {:dataset "dcc"
                         :filter  {:marker_symbol '(art4 abcd1 cbx1)}
                         :attrs   [:mgi_accession_id]}))
;=> ({:count 3})

BioMart metadata

(use '[biomart-client.metadata])

(def r (registry ms))
(map :name (marts r))
;=> ("ikmc" "biomart" "htgt" "ikmc_unitrap" "emma_biomart"
     "Eurexpress Biomart" "europhenomeannotations" "ENSEMBL_MART_ENSEMBL"
     "ENSEMBL_MART_VEGA")

(datasets ms "ikmc")
;=> (("TableSet" "kermits" "IKMC Mouse Production" "1" "" "200" "50000" "default" "2011-03-24 16:09:13") ("TableSet" "omim" "OMIM (with MGI Mouse Orthologue Mappings)" "1" "" "200" "50000" "default" "2011-03-24 16:09:14") ("TableSet" "idcc_targ_rep" "IKMC Targeted Products" "1" "" "200" "50000" "default" "2011-03-24 16:09:13") ("TableSet" "dcc" "IKMC Projects / Alleles" "1" "" "200" "50000" "default" "2011-03-24 16:09:12"))

(map #(nth % 1) (datasets ms "ikmc"))
;=> ("kermits" "omim" "idcc_targ_rep" "dcc")

(def c (configuration ms "dcc"))
(default-attributes c)
;=> ("marker_symbol" "mgi_accession_id" "ikmc_project" "ikmc_project_id" "status" "mouse_available" "escell_available" "vector_available")

(map first (attributes ms "dcc"))
;=> ("marker_symbol" "marker_name" "mgi_accession_id" "secondary_mgi_accession_id" "synonym" "ensembl_gene_id" "vega_gene_id" "ncbi_gene_id" "ccds_id" "omim_id" "omim_description" "chromosome" "strand" "start" "end" "ikmc_project" "ikmc_project_id" "status" "mouse_available" "escell_available" "vector_available" "mgi_gene_traps" "tigm_gene_traps" "igtc" "imsr" "targeted_mutations" "other_mutations")

(def f (filters ms "dcc"))
(map first f)
;=> ("marker_symbol" "mgi_accession_id" "secondary_mgi_accession_id" "ensembl_gene_id" "vega_gene_id" "ncbi_gene_id" "ccds_id" "omim_id" "chromosome" "start" "end" "strand" "project" "ikmc_project_id" "mouse_available" "escell_available" "vector_available" "status" "regeneron_status")

Installation

Available from clojars.org; add:

[biomart-client "1.0.0-SNAPSHOT"]

to your project.clj

License

Copyright (C) 2010, Ray Miller ray@1729.org.uk.

THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE PUBLIC LICENSE, http://www.eclipse.org/org/documents/epl-v10.php.

ANY USE, REPRODUCTION OR DISTRIBUTION OF THE PROGRAM CONSTITUTES RECIPIENT’S ACCEPTANCE OF THIS AGREEMENT.

TODO

• Write more tests

• Deal with duplicate attrs in query parser? At the moment, for federated queries, an attribute in the second dataset will trample on data from the first dataset with the same attribute name.

• Implement work-around for boolean filters from Darren's Ruby library

  • see his dataset.rb class.