Parsing GSEA gmt files

README.md

@@ -123,6 +123,9 @@ To create a tab delimited file from a GSEA result, where FDR < 0.25
 You can convert the tabular format to RDF by using the included
 bioruby-table tool.
 
+To convert GMT input files to RDF use ./templates/gsea/gsea_gmt.erb.
+
+
 ### Mapping Affymetrix probes to sequence information, through R/Bioconductor
 
 [R/Bioconductor](http://www.bioconductor.org/) contains a lot of

templates/gsea/gsea_gmt.erb

@@ -0,0 +1,22 @@
+# Template for generating RDF triples from GSEA GMT files
+#
+#   env INFILE=c2.all.v3.0.symbols.gmt erb templates/gsea/gsea_gmt.rdf
+#
+<%= File.read(File.dirname(__FILE__)+'/preamble.rdf')  %>
+
+<%
+   File.open(ENV["INFILE"]).each_line do |line|
+     fields = line.split
+     if fields[9] == 'Y'
+       gene = fields.first
+       (species,source) = gene.scan(/(\w\w)_(CDS|DNA|EST)/)[0]
+       id = BioRdf::Turtle.mangle_identifier(gene)
+       m = gene.match(/\.\w\w\w:(\S+)$/)
+       gene = m[1] if m
+%>
+  :<%= id %>  :gene_name   "<%= gene %>" .
+  :<%= id %>  :species     "<%= species %>" .
+  :<%= id %>  :source      "<%= source %>" .
+  :<%= id %>  :signalP   true .
+<%  end 
+  end %>

templates/gsea/preamble.rdf

@@ -0,0 +1,6 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix hgnc: <http://identifiers.org/hgnc.symbol/> .
+@prefix : <http://biobeat.org/rdf/gsea#> .
+

test/data/parsers/gsea/gsea_gmt_example.gmt

@@ -0,0 +1,4 @@
+TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP  http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP.html S100P C20ORF114 DTL AHCTF1  LOC100132169  CDH1  GLCCI1  STK4  ZNF678  TTC3  EPB41L3 SLC1A2  LAMP2 B3GALNT1 HIST1H3B  CKS2  MEX3C OSBPL10 CPB1  RAB11FIP1 FAM54A
+TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN  http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN.html ASPN  SEC24A  NEAT1 VTCN1 MAOB  MID1  C5ORF54
+TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP.html  ASPN  GNA13 CTHRC1  AEBP1 PRC1  AGTPBP1 PRRX1 POSTN ZEB1  ENPEP LRRC15  UXS1  SSR1  EDNRA CX CR4 FBXO28  COL12A1 GPX8  TIE1  LOX COL11A1 RAP2C C5AR1 MICAL2  CILP  LYZ IFI44 THY1  SPAG9 INHBA BGN RAB18 PLXDC1  COL1A2  VCAN COL1A1  ADAM12  PLXNC1  COL3A1  ASAP1 TAGAP DOCK1 CD69  FLJ38379  COMP  FNDC1 COL6A3  HSPA6 WIPF1 LAMB1 UBTD2 THBS2 FN1 SMCHD1 FBN1  LOC645513 IGF1  SPARC COL5A2  COL5A1  MXRA5 RGS1  SULF2 NARG1 SFRP2 SULF1 ZNF117
+