Changeset 387

Timestamp:

06/01/10 06:07:37 (21 months ago)

Author:

AlexanderPico

Message:

Adding KEGG Genes and BioCyc? datasources

Location:

trunk/org.bridgedb.bio

Files:

• resources/org/bridgedb/bio/datasources.txt (modified) (2 diffs)
• src/org/bridgedb/bio/BioDataSource.java (modified) (4 diffs)

trunk/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.txt

@@ -1 +1 @@
 TAIR    A       http://www.arabidopsis.org/             AT1G35255       gene    Arabidopsis thaliana    1       urn:miriam:tair.locus
 Agilent Ag                      A_24_P98555     probe           0       Ag
+BioCyc  Bc      http://www.biocyc.org   http://www.biocyc.org/getid?id=$ID      EcoCyc:MON0-2657        gene            1       Bc
 BioGrid Bg      http://www.thebiogrid.org/                      probe           0       urn:miriam:biogrid
 Cint    C                               probe           0       C
@@ -48 +49 @@
 IPI     Ip              http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[IPI-acc:$ID]      IPI00020529     probe           0       Ip
 IRGSP Gene      Ir      http://rgp.dna.affrc.go.jp/IRGSP/               Os12g0561000    gene            1       Ir
+KEGG Genes      Kg      http://www.genome.jp/kegg/genes.html    http://www.genome.jp/dbget-bin/www_bget?$ID     ecj:JW5076      gene            1       Kg
 Entrez Gene     L       http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene        http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=$ID       1232    gene            1       urn:miriam:entrez.gene
 MGI     M       http://www.informatics.jax.org/ http://www.informatics.jax.org/searches/accession_report.cgi?id=$ID     MGI:2687328     gene    Mus musculus    1       urn:miriam:mgd

trunk/org.bridgedb.bio/src/org/bridgedb/bio/BioDataSource.java

@@ -42 +42 @@
         public static final DataSource BIOGRID = DataSource.register (
                 "Bg", "BioGrid").asDataSource();
+        public static final DataSource BIOCYC = DataSource.register (
+                "Bc", "BioCyc").asDataSource();
         public static final DataSource CINT = DataSource.register (
                 "C", "Cint").asDataSource();
@@ -133 +135 @@
         public static final DataSource IRGSP_GENE = DataSource.register (
                 "Ir", "IRGSP Gene").asDataSource();
+        public static final DataSource KEGG_GENES = DataSource.register (
+                "Kg", "KEGG Genes").asDataSource();
         public static final DataSource ENTREZ_GENE = DataSource.register (
                 "L", "Entrez Gene").asDataSource();
@@ -352 +356 @@
                                 Pattern.compile("ENSDARG\\d{11}")
                 );
-                DataSourcePatterns.registerPattern(
-                                BioDataSource.ENSEMBL_MTUBERCULOSIS,
-                                Pattern.compile("EBMYCG\\d{11}")
-                );
+                DataSourcePatterns.registerPattern(
+                                BioDataSource.ENSEMBL_MTUBERCULOSIS,
+                                Pattern.compile("EBMYCG\\d{11}")
+                );
                 DataSourcePatterns.registerPattern(
                                 BioDataSource.ENSEMBL_FRUITFLY, 
@@ -453 +457 @@
                                 Pattern.compile("C\\d+")
                 );
+                DataSourcePatterns.registerPattern(
+                                BioDataSource.KEGG_GENES,
+                                Pattern.compile("[a-z]{3}:.+")
+                );
+                DataSourcePatterns.registerPattern(
+                                BioDataSource.BIOCYC,
+                                Pattern.compile("(Meta|Eco)Cyc:.+")
+                );              
                 
                 ensemblBySpecies.put (Organism.BacillusSubtilis, ENSEMBL_BSUBTILIS);