GeoExample

Geo GPL96.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>{Sep}</Key>
         <Definition> /// </Definition>
      </Keyword>
      <Keyword>
         <Key>{Base Dir}</Key>
         <Definition>/Grad School/Thesis/(Data Files)/</Definition>
<!--
         <Definition>/projects/sysbio/map/Data/Expression/Any/Geo/Remote/</Definition>
 -->
      </Keyword>
   </UserKeywords>

   <DataFile>{Base Dir}GPL96_family.soft.gz</DataFile>
<!--
   <FTP>Get Geo Location and fill in here</FTP>
 -->

   <Ignore>!</Ignore>
   <Ignore>^</Ignore>
   <Ignore>#</Ignore>
   <IgnoreLines>1</IgnoreLines>
   <DoneIfBeginsWith>^sample =</DoneIfBeginsWith>

   <KeyDefinitions>
      <Key>
         <Name>Affymetrix Probe Set ID</Name>
         <Definition>{Col 1}</Definition>
      </Key>

      <Key>
         <Name>GenBank Accession Number</Name>
         <Definition>{Col 2}</Definition>
      </Key>

      <Key>
         <Name>UniGene Accession Number</Name>
         <Definition>{Col 4}</Definition>
      </Key>

      <Key>
         <Name>LocusLink Accession Number</Name>
         <Definition splitter = "{Sep}">{Col 5}</Definition>
      </Key>

      <Key>
         <Name>UniGene Gene Symbol</Name>
         <Definition splitter = "{Sep}">{Col 7}</Definition>
      </Key>

      <Key>
         <Name>Ensembl ID</Name>
         <Definition splitter = "{Sep}">{Col 16}</Definition>
      </Key>

      <Key>
         <Name>SwissProt</Name>
         <Definition splitter = "{Sep}">{Col 17}</Definition>
      </Key>

      <Key>
         <Name>EC</Name>
         <Definition splitter = "{Sep}">{Col 18-EC:}</Definition>
      </Key>

      <Key>
         <Name>OMIM</Name>
         <Definition splitter = "{Sep}">{Col 19}</Definition>
      </Key>

      <Key>
         <Name>RefSeq Protein IDs</Name>
         <Definition splitter = "{Sep}">{Col 20}</Definition>
      </Key>

      <Key>
         <Name>RefSeq Transcript IDs</Name>
         <Definition splitter = "{Sep}">{Col 21}</Definition>
      </Key>
   </KeyDefinitions>

   <Keyspace>
      <Name>Affymetrix Probe Set IDs</Name>
      <Species>Human</Species>
      <Description>Affymetrix Probe Set IDs</Description>
      <Type><DNA_Probe/></Type>
      <URL>https://www.netaffx.com/LinkServlet?array=U133&amp;probeset=</URL>
      <FTP>https://www.netaffx.com/LinkServlet?array=U133&amp;probeset=</FTP>
      <KeyInfo>
         <KeyName>Affymetrix Probe Set ID</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>GenBank Accession Numbers</Name>
      <Species>Human</Species>
      <Description>GenBank Accession Numbers via Affymetrix</Description>
      <Type><Gene/></Type>
      <URL>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&amp;db=Nucleotide&amp;term=</URL>
      <FTP>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&amp;db=Nucleotide&amp;term=</FTP>
      <KeyInfo>
         <KeyName>GenBank Accession Number</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>UniGene Accession Numbers</Name>
      <Species>Human</Species>
      <Description>UniGene Accession Numbers</Description>
      <Type><Gene/></Type>
      <URL>http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&amp;CID=</URL>
      <FTP>http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&amp;CID=</FTP>
      <KeyInfo>
         <KeyName>UniGene Accession Number</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>UniGene Gene Symbols</Name>
      <Species>Human</Species>
      <Description>UniGene Gene Symbols via Affymetrix</Description>
      <Type><Gene/></Type>
      <URL></URL>
      <FTP></FTP>
      <KeyInfo>
         <KeyName>UniGene Gene Symbol</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>LocusLink Accession Numbers</Name>
      <Species>Human</Species>
      <Description>LocusLink Accession Numbers via Affymetrix</Description>
      <Type><Gene/></Type>
      <URL>http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=</URL>
      <FTP>http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=</FTP>
      <KeyInfo>
         <KeyName>LocusLink Accession Number</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>Ensembl IDs</Name>
      <Species>Human</Species>
      <Description>Ensembl IDs via Affymetrix</Description>
      <Type><Gene/></Type>
      <KeyInfo>
         <KeyName>Ensembl ID</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>SwissProt</Name>
      <Species>Human</Species>
      <Description>SwissProt Protein identifiers via Affymetrix</Description>
      <Type><Protein/></Type>
      <KeyInfo>
         <KeyName>SwissProt</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>EC</Name>
      <Species>Human</Species>
      <Description>Enzyme Commission family numbers via Affymetrix</Description>
      <Type><Categorization/></Type>
      <KeyInfo>
         <KeyName>EC</KeyName>
         <KeyDescription></KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>OMIM</Name>
      <Species>Human</Species>
      <Description>OMIM: Online Mendelian Inheritance in Man accession number</Description>
      <Type><Categorization/></Type>
      <URL>http://www.ncbi.nlm.nih.gov:80/entrez/dispomim.cgi?id=</URL>
      <FTP>http://www.ncbi.nlm.nih.gov:80/entrez/dispomim.cgi?id=</FTP>
      <KeyInfo>
         <KeyName>OMIM</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>RefSeq Protein IDs</Name>
      <Species>Human</Species>
      <Description>RefSeq Protein IDs via Affymetrix</Description>
      <Type><Protein/></Type>
      <KeyInfo>
         <KeyName>RefSeq Protein IDs</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Keyspace>
      <Name>RefSeq Transcript IDs</Name>
      <Species>Human</Species>
      <Description>RefSeq Transcript IDs via Affymetrix</Description>
      <Type><Protein/></Type>
      <KeyInfo>
         <KeyName>RefSeq Transcript IDs</KeyName>
         <KeyDescription>{Col 6} : {Col 12}</KeyDescription>
      </KeyInfo>
   </Keyspace>

   <Mapping>
      <Name>Affymetrix GPL96 Mappings</Name>
      <Description>Mappings from Affymetrix, via GPL96 on GEO</Description>
      <MapData>
         <MapFamily>
            <KeyspaceName>Affymetrix Probe Set IDs</KeyspaceName>
            <KeyName>Affymetrix Probe Set ID</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>GenBank Accession Numbers</KeyspaceName>
            <KeyName>GenBank Accession Number</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>UniGene Accession Numbers</KeyspaceName>
            <KeyName>UniGene Accession Number</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>UniGene Gene Symbols</KeyspaceName>
            <KeyName>UniGene Gene Symbol</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>LocusLink Accession Numbers</KeyspaceName>
            <KeyName>LocusLink Accession Number</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>Ensembl IDs</KeyspaceName>
            <KeyName>Ensembl ID</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>SwissProt</KeyspaceName>
            <KeyName>SwissProt</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>EC</KeyspaceName>
            <KeyName>EC</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>OMIM</KeyspaceName>
            <KeyName>OMIM</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>RefSeq Protein IDs</KeyspaceName>
            <KeyName>RefSeq Protein IDs</KeyName>
         </MapFamily>

         <MapFamily>
            <KeyspaceName>RefSeq Transcript IDs</KeyspaceName>
            <KeyName>RefSeq Transcript IDs</KeyName>
         </MapFamily>
      </MapData>
   </Mapping>

</ControlFile>

-- Main.gregd - 20 Dec 2007