Example

HGNC.xml:

<?xml version="1.0" encoding="ISO-8859-1"?>
<!--
<!DOCTYPE ControlFile SYSTEM "ControlFile.dtd">
 -->

<ControlFile xmlns = "http://Grinder.ucsc.edu"
          xmlns:xsi = "http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation = "http://Grinder.ucsc.edu
                           ControlFile.xsd"
>

   <UserKeywords>
      <Keyword>
         <Key>{Base Dir}</Key>
         <Definition>/Grad School/Thesis/(Data Files)/</Definition>
<!--
         <Definition>/cse/grads/gregd/Thesis/Data Files/</Definition>
 -->
      </Keyword>
   </UserKeywords>

   <DataFile>{Base Dir}HGNC.tab</DataFile>
   <FTP>http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl</FTP>

   <IgnoreLines>1</IgnoreLines>
   <IgnoreIfColumn>
      <Column>4</Column>
<!--   <IgnoreIfContains>Withdrawn</IgnoreIfContains> -->
      <IgnoreIfIsNot>Approved</IgnoreIfIsNot>
   </IgnoreIfColumn>

   <KeyDefinitions>
      <Key>
         <Name>HGCN_ID</Name>
         <Definition>{Col 1-HGNC:}</Definition>
      </Key>

      <Key>
         <Name>ApprovedSymbol</Name>
         <Definition>{Col 2}</Definition>
      </Key>

      <Key>
         <Name>MGD_ID</Name>
         <Definition>{Col 8-MGI:}</Definition>
      </Key>

      <Key>
         <Name>RefSeqID</Name>
         <Definition splitter = ", ">{Col 9}</Definition>
      </Key>

      <Key>
         <Name>EnsemblID</Name>
         <Definition>{Col 15}</Definition>
      </Key>
   </KeyDefinitions>

   <Keyspace>
      <Name>RefSeq mRNA IDs</Name>
      <Species>Human</Species>
      <Description>RefSeq mRNA IDs via the HUGO Gene Nomenclature Committee</Description>
      <Type><RNA_Probe/></Type>
      <URL>http://www.gene.ucl.ac.uk/nomenclature/</URL>
      <FTP>http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl</FTP>
      <KeyInfo>
         <KeyName>RefSeqID</KeyName>
         <KeyDescription>{Col 3}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>HGNC ID</Name>
      <Species>Human</Species>
      <Description>HUGO Gene Nomenclature Committee Unique IDs</Description>
      <Type><Gene/></Type>
      <URL>http://www.gene.ucl.ac.uk/nomenclature/</URL>
      <FTP>http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl</FTP>
      <KeyInfo>
         <KeyName>HGCN_ID</KeyName>
         <KeyDescription>{Col 3}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>HGNC Approved Symbol</Name>
      <Species>Human</Species>
      <Description>HUGO Gene Nomenclature Committee Approved Symbol</Description>
      <Type><Gene/></Type>
      <URL>http://www.gene.ucl.ac.uk/nomenclature/</URL>
      <FTP>http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl</FTP>
      <KeyInfo>
         <KeyName>ApprovedSymbol</KeyName>
         <KeyDescription>{Col 3}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>MGD IDs</Name>
      <Species>Mouse</Species>
      <Description>MGD IDs via the HUGO Gene Nomenclature Committee</Description>
      <Type><Gene/></Type>
      <URL>http://www.gene.ucl.ac.uk/nomenclature/</URL>
      <FTP>http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl</FTP>
      <KeyInfo>
         <KeyName>MGD_ID</KeyName>
         <KeyDescription>{Col 3}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Mapping>
      <Name>HGNC</Name>
      <Description>HUGO Gene Nomenclature Committee Mappings</Description>
      <URL>http://www.gene.ucl.ac.uk/nomenclature/</URL>
      <FTP>http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl</FTP>
      <MapData>
         <MapPair>
            <SourceKeyspace>HGNC ID</SourceKeyspace>
            <SourceKeys>HGCN_ID</SourceKeys>
            <TargetKeyspace>HGNC Approved Symbol</TargetKeyspace>
            <TargetKeys>ApprovedSymbol</TargetKeys>
            <Bidirectional/>
            <Multiplicity>1-1</Multiplicity>
            <SourceDescription>HGNC Mapping created Item</SourceDescription>
            <TargetDescription>HGNC Mapping created Item</TargetDescription>
         </MapPair>
      </MapData>
   </Mapping>

   <Mapping>
      <Name>HGNC</Name>
      <Description>HUGO Gene Nomenclature Committee Mappings</Description>
      <MapData>
         <MapPair>
            <SourceKeyspace>HGNC Approved Symbol</SourceKeyspace>
            <SourceKeys>ApprovedSymbol</SourceKeys>
            <TargetKeyspace>RefSeq mRNA IDs</TargetKeyspace>
            <TargetKeys>RefSeqID</TargetKeys>
            <Bidirectional/>
            <Multiplicity>1-M</Multiplicity>
            <SourceDescription>HGNC Mapping created Item</SourceDescription>
            <TargetDescription>HGNC Mapping created Item</TargetDescription>
         </MapPair>
      </MapData>
   </Mapping>

   <Mapping>
      <Name>HGNC</Name>
      <Description>HUGO Gene Nomenclature Committee Mappings</Description>
      <MapData>
         <MapPair>
            <SourceKeyspace>HGNC Approved Symbol</SourceKeyspace>
            <SourceKeys>ApprovedSymbol</SourceKeys>
            <TargetKeyspace>MGD IDs</TargetKeyspace>
            <TargetKeys>MGD_ID</TargetKeys>
            <Bidirectional/>
            <Multiplicity>1-1</Multiplicity>
            <SourceDescription>HGNC Mapping created Item</SourceDescription>
            <TargetDescription>HGNC Mapping created Item</TargetDescription>
         </MapPair>
      </MapData>
   </Mapping>


</ControlFile>

-- Main.gregd - 17 Jul 2007