Changeset 552

Timestamp:

12/04/11 13:09:58 (6 months ago)

Author:

martijn

Message:

Improved HDMB script: InChI keys and info properties

Location:

trunk/dbbuilder/src/org/bridgedb/util/hmdb

Files:

• Hmdb2Gdb.java (modified) (4 diffs)
• ParseHmdb.java (modified) (2 diffs)

trunk/dbbuilder/src/org/bridgedb/util/hmdb/Hmdb2Gdb.java

@@ -23 +23 @@
 import java.io.InputStreamReader;
 import java.io.LineNumberReader;
+import java.text.SimpleDateFormat;
+import java.util.Date;
 import java.util.zip.ZipFile;
 
@@ -112 +114 @@
                 simpleGdb.createGdbTables();
                 simpleGdb.preInsert();
+                
+                String dateStr = new SimpleDateFormat("yyyyMMdd").format(new Date());
+                simpleGdb.setInfo("BUILDDATE", dateStr);
+                simpleGdb.setInfo("DATASOURCENAME", "HMDB");
+                simpleGdb.setInfo("DATASOURCEVERSION", "metabocards_" + dateStr);
+                simpleGdb.setInfo("DATATYPE", "Metabolite");
+                simpleGdb.setInfo("SERIES", "standard_metabolite");
     }
 
@@ -152 +161 @@
                         error += simpleGdb.addLink (ref, right);
                 }
-
+                
+                if (c.inchi != null)
+                {
+                        error += simpleGdb.addAttribute(ref, "InChI", c.inchi);
+                }
+                
                 if (c.idKegg != null) for (String id : c.idKegg)
                 {
@@ -162 +176 @@
                 if (c.idChebi != null) for (String id : c.idChebi)
                 {
-                        Xref right = new Xref (id, BioDataSource.CHEBI);
+                        Xref right = new Xref ("CHEBI:" + id, BioDataSource.CHEBI);
                         error += simpleGdb.addGene(right);
                         error += simpleGdb.addLink(ref, right);

trunk/dbbuilder/src/org/bridgedb/util/hmdb/ParseHmdb.java

@@ -81 +81 @@
                                 smiles = value;
                         }
+                        else if (key.equals("inchi_identifier"))        
+                        {
+                                inchi = value;
+                        }
                 }
 
@@ -94 +98 @@
                 String smiles = null;
                 String[] synonyms = null;
+                String inchi = null;
         }