project.xml 25.1 KB
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<project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="common.os.prefix" value="common"/>

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  <sources>
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    <!-- First gff and then fasta if you want to have the sequence available -->
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    <source name="LegioParis-gff" type="legiolist-gff" version="4.1.1" dump="true">
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      <property name="gff3.taxonId" value="297246"/>
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      <property name="gff3.seqDataSourceName" value="LegioList LegioParis"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
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      <property name="gff3.seqClsName" value="Chromosome"/>
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      <property name="gff3.dataSetTitle" value="LegioList Legionella pneumophila str. Paris genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LegioParis_10-05-2012_LegioList/"/>
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    </source>
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    <source name="LegioParis-chromosome-fasta" type="fasta" version="4.1.1" dump="true">
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      <property name="fasta.taxonId" value="297246"/>
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
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      <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Paris chromosome sequence"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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      <property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.fasta"/>
    </source>
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    <source name="LegioParis-protein-gene" type="legiolist-gene-prot" version="4.1.1" dump="true">
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      <property name="legiolist.taxid" value="297246"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="LegioParis_10-05-2012_LegioList-prot-gene.tsv"/>
    </source>


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    <source name="LegioParis-protein-fasta" type="fasta" version="4.1.1" dump="true">
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      <property name="fasta.taxonId" value="297246"/>
      <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="LegioParis_10-05-2012_LegioList.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>

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    <source name="Lfallonii-gff" type="legiolist-gff" version="4.1.1" dump="true">
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      <property name="gff3.taxonId" value="96230"/>
      <property name="gff3.seqDataSourceName" value="LegioList Lfalloni"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella fallonii genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lfallonii"/>
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    </source>
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    <source name="Lfallonii-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
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      <property name="fasta.dataSetTitle" value="LegioList Legionella fallonii chromosome sequence"/>
      <property name="fasta.taxonId" value="96230"/>
      <property name="fasta.includes" value="Lfallonii.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>

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    <source name="Lfallonii-protein-gene" type="legiolist-gene-prot" version="4.1.1">
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      <property name="legiolist.taxid" value="96230"/>
      <property name="legiolist-gene-prot.dataSetTitle" value="LegioList Legionella fallonii proteins"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="Lfallonii-prot-gene.tsv"/>
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    </source>

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    <source name="Lfallonii-protein-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.taxonId" value="96230"/>
      <property name="fasta.dataSetTitle" value="Legiolist Lfallonii protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="Lfallonii.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>
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    <source name="Lhackeliae-gff" type="legiolist-gff" version="4.1.1">
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      <property name="gff3.taxonId" value="449"/>
      <property name="gff3.seqDataSourceName" value="LegioList Legionella hackeliae"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella hackeliae genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lhackeliae"/>
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    </source>
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    <source name="Lhackeliae-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
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      <property name="fasta.dataSetTitle" value="LegioList Legionella hackeliae chromosome sequence"/>
      <property name="fasta.taxonId" value="449"/>
      <property name="fasta.includes" value="Lhackeliae.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>

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    <source name="Lhackeliae-protein-gene" type="legiolist-gene-prot" version="4.1.1">
      <property name="legiolist.taxid" value="449"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="Lhackeliae-prot-gene.tsv"/>
    </source>


    <source name="Lhackeliae-protein-fasta" type="fasta" version="4.1.1">
      <property name="fasta.taxonId" value="449"/>
      <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="Lhackeliae.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>





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    <source name="Lmicadei-gff" type="legiolist-gff" version="4.1.1">
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      <property name="gff3.taxonId" value="451"/>
      <property name="gff3.seqDataSourceName" value="LegioList Legionella micdadei"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella micdadei genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lmicadei"/>
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    </source>
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    <source name="Lmicadei-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
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      <property name="fasta.dataSetTitle" value="LegioList Legionella micdadei chromosome sequence"/>
      <property name="fasta.taxonId" value="451"/>
      <property name="fasta.includes" value="Lmicadei.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>


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    <source name="Lmicadei-protein-gene" type="legiolist-gene-prot" version="4.1.1">
      <property name="legiolist.taxid" value="451"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="Lmicadei-prot-gene.tsv"/>
    </source>


    <source name="Lmicadei-protein-fasta" type="fasta" version="4.1.1">
      <property name="fasta.taxonId" value="451"/>
      <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="Lmicadei.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>



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    <source name="Long_Mage-gff" type="legiolist-gff" version="4.1.1">
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      <property name="gff3.taxonId" value="661367"/>
      <property name="gff3.seqDataSourceName" value="LegioList Legionella longbeachae NSW150"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella longbeachae NSW150 genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Long_Mage"/>
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    </source>
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    <source name="Long_Mage-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
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      <property name="fasta.dataSetTitle" value="LegioList Legionella longbeachae NSW150 chromosome sequence"/>
      <property name="fasta.taxonId" value="661367"/>
      <property name="fasta.includes" value="Long_Mage.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>

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    <source name="Long_Mage-protein-gene" type="legiolist-gene-prot" version="4.1.1">
      <property name="legiolist.taxid" value="661367"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="Long_Mage-prot-gene.tsv"/>
    </source>

    <source name="Long_Mage-protein-fasta" type="fasta" version="4.1.1">
      <property name="fasta.taxonId" value="661367"/>
      <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="Long_Mage.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>

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    <source name="Lorraine-gff" type="legiolist-gff" version="4.1.1">
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      <property name="gff3.taxonId" value="1046632"/>
      <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Lorraine genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/Lorraine"/>
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    </source>
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    <source name="lorraine-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
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      <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Lorraine chromosome sequence"/>
      <property name="fasta.taxonId" value="1046632"/>
      <property name="fasta.includes" value="Lorraine.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>


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    <source name="Lorraine-protein-gene" type="legiolist-gene-prot" version="4.1.1">
      <property name="legiolist.taxid" value="1046632"/>
      <property name="legiolist-gene-prot.dataSetTitle" value="LegioList Lorraine proteins"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="Lorraine-prot-gene.tsv"/>
    </source>


    <source name="Lorraine-protein-fasta" type="fasta" version="4.1.1">
      <property name="fasta.taxonId" value="1046632"/>
      <property name="fasta.dataSetTitle" value="Legiolist Lorraine protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="Lorraine.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>



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    <source name="LpAlcoy-gff" type="legiolist-gff" version="4.1.1">
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      <property name="gff3.taxonId" value="423212"/>
      <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila 2300/99 Alcoy"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella pneumophila 2300/99 Alcoy genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpAlcoy"/>
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    </source>
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    <source name="LpAlcoy-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
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      <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila 2300/99 Alcoy chromosome sequence"/>
      <property name="fasta.taxonId" value="423212"/>
      <property name="fasta.includes" value="LpAlcoy.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>


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    <source name="LpAlcoy-protein-gene" type="legiolist-gene-prot" version="4.1.1">
      <property name="legiolist.taxid" value="423212"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="LpAlcoy-prot-gene.tsv"/>
    </source>


    <source name="LpAlcoy-protein-fasta" type="fasta" version="4.1.1">
      <property name="fasta.taxonId" value="423212"/>
      <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="LpAlcoy.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>





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    <source name="LpCorby-gff" type="legiolist-gff" version="4.1.1">
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      <property name="gff3.taxonId" value="400673"/>
      <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Corby"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella pneumophila str. Corby genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpCorby"/>
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    </source>
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    <source name="LpCorby-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
      <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Corby chromosome sequence"/>
      <property name="fasta.taxonId" value="400673"/>
      <property name="fasta.includes" value="LpCorby.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>
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    <source name="LpCorby-protein-gene" type="legiolist-gene-prot" version="4.1.1">
      <property name="legiolist.taxid" value="400673"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="LpCorby-prot-gene.tsv"/>
    </source>


    <source name="LpCorby-protein-fasta" type="fasta" version="4.1.1">
      <property name="fasta.taxonId" value="400673"/>
      <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="LpCorby.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>



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    <source name="LpLens-gff" type="legiolist-gff" version="4.1.1">
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      <property name="gff3.taxonId" value="297245"/>
      <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila str. Lens"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella pneumophila str. Lens genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpLens"/>
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    </source>
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    <source name="LpLens-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
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      <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila str. Lens chromosome sequence"/>
      <property name="fasta.taxonId" value="297245"/>
      <property name="fasta.includes" value="LpLens.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>

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    <source name="LpLens-protein-gene" type="legiolist-gene-prot" version="4.1.1">
      <property name="legiolist.taxid" value="297245"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="LpLens-prot-gene.tsv"/>
    </source>


    <source name="LpLens-protein-fasta" type="fasta" version="4.1.1">
      <property name="fasta.taxonId" value="297245"/>
      <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="LpLens.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>

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    <source name="LpPhila-gff" type="legiolist-gff" version="4.1.1">
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      <property name="gff3.taxonId" value="272624"/>
      <property name="gff3.seqDataSourceName" value="LegioList Legionella pneumophila subsp. pneumophila str. Philadelphia 1"/>
      <property name="gff3.dataSourceName" value="LegioList"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="Legionella pneumophila subsp. pneumophila str. Philadelphia 1 genome annotation"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/gff/clean/LpPhila"/>
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    </source>
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    <source name="LpPhila-chromosome-fasta" type="fasta" version="4.1.1">
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      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="LegioList"/>
      <property name="fasta.dataSetTitle" value="LegioList Legionella pneumophila subsp. pneumophila str. Philadelphia 1 chromosome sequence"/>
      <property name="fasta.taxonId" value="272624"/>
      <property name="fasta.includes" value="LpPhila.fasta"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/fasta"/>
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    </source>
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    <source name="LpPhila-protein-gene" type="legiolist-gene-prot" version="4.1.1">
      <property name="legiolist.taxid" value="272624"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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      <property name="src.data.dir.includes" value="LpPhila-prot-gene.tsv"/>
    </source>


    <source name="LpPhila-protein-fasta" type="fasta" version="4.1.1">
      <property name="fasta.taxonId" value="272624"/>
      <property name="fasta.dataSetTitle" value="Legiolist protein sequence"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.suffix" value="protein" />
      <property name="fasta.includes" value="LpPhila.faa"/>
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/genome/protein"/>
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    </source>
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    <!-- <source name="uniprot" type="uniprot">
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      <property name="uniprot.organisms" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
      <property name="src.data.dir" location="/home/rplanel/projects/legiolist-intermine/data/legiolist/genomes/uniprot"/>
      <property name="creatego" value="true"/>
      <property name="creategenes" value="true"/>
      <property name="allowduplicates" value="false"/>
      <property name="loadfragments" value="true"/>
      <property name="loadtrembl" value="true"/>
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    </source> -->
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    <source name="legiolist-homology" type="legiolist-homology" version="4.1.1">
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data/"/>
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      <property name="src.data.dir.includes" value="table_orthos.txt"/>
      <property name="legiolistTaxids" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
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    </source>
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    <source name="entrez-organism" type="entrez-organism">
      <property name="src.data.file" location="organisms.xml"/>
    </source>

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    <source name="so" type="so">
      <property name="src.data.file" location="so.obo" />
      <property name="licence" value="https://creativecommons.org/licenses/by/4.0/"/>
    </source>

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    <source name="go" type="go">
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      <property name="src.data.file" location="/home/intermine/intermine/data/pre-process-data/go-basic.obo"/>
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    </source>


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    <!-- <source name="pubmed-gene" type="pubmed-gene">
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      <property name="src.data.dir" location="/home/intermine/intermine/data/pre-process-data"/>
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      <property name="pubmed.organisms" value="272624 297246 297245 400673 423212 1046632 661367 451 449 96230"/>
      <property name="src.data.dir.includes" value="gene2pubmed"/>
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    </source> -->
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    <source name="update-publications" type="update-publications" dump="true">
      <property name="src.data.file" location="publications.xml"/>
      <!-- <property name="loadFullRecord" value="true"/> -->
    </source>

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  </sources>

  <post-processing>
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    <post-process name="create-references"/>
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    <post-process name="create-chromosome-locations-and-lengths"/>
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    <post-process name="do-sources" />
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    <post-process name="populate-child-features"/>
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    <post-process name="create-location-range-index"/>
    <post-process name="create-overlap-view" />
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    <post-process name="create-search-index" />
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    <post-process name="create-autocomplete-index" />
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    <post-process name="transfer-sequences"/>
    <post-process name="create-attribute-indexes" />
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    <post-process name="summarise-objectstore" />

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  </post-processing>
</project>