<commit_before><project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="modmine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>
    <source name="chado-db-flybase-dmel" type="chado-db" dump="true">
      <property name="source.db.name" value="flybase"/>
      <property name="genus" value="Drosophila"/>
      <property name="species" value="melanogaster"/>
      <property name="taxonId" value="7227"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
    </source>
    <source name="chado-db-flybase-dpse" type="chado-db" dump="true">
      <property name="source.db.name" value="flybase"/>
      <property name="genus" value="Drosophila"/>
      <property name="species" value="pseudoobscura"/>
      <property name="taxonId" value="7237"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="dataSetTitle" value="FlyBase Drosophila pseudoobscura data set"/>
    </source>
    <source name="chado-db-wormbase-c_elegans" type="chado-db" dump="true">
      <property name="source.db.name" value="wormbase"/>
      <property name="genus" value="Caenorhabditis"/>
      <property name="species" value="elegans"/>
      <property name="taxonId" value="6239"/>
      <property name="dataSourceName" value="WormBase"/>
      <property name="dataSetTitle" value="WormBase C.elegans data set"/>
    </source>
    <source name="inparanoid-orthologue" type="orthologue" dump="true">
      <property name="src.data.dir" location="/shared/data/orthologues/inparanoid/current/"/>
    </source>
    <source name="entrez-organism" type="entrez-organism">
      <!-- this source finds the taxon ids in the objectstore, retrieves
           species name and genus from Entrez into an InterMine format XML
           file, loads that file into a target items DB, then into the final
           objectstore -->
      <property name="src.data.file" location="build/organisms.xml"/>
    </source>
    <source name="modmine-static" type="intermine-items-xml-file">
      <property name="src.data.file" location="datasets.xml"/>
    </source>
    <source name="update-publications" type="update-publications" dump="true">
      <!-- this source finds the publication ids (pubmed ids) in the
           objectstore, retrieves the details of the publication from Entrez
           into an InterMine format XML file, loads that file into a target
           items DB, then into the final objectstore -->
      <property name="src.data.file" location="build/publications.xml"/>
    </source>
  </sources>

  <post-processing>
    <post-process name="create-utr-references"/>
    <post-process name="calculate-locations"/>
    <post-process name="create-references" dump="true"/>
    <post-process name="make-spanning-locations"/>
    <post-process name="create-chromosome-locations-and-lengths"/>
    <post-process name="create-intergenic-region-features"/>
    <post-process name="transfer-sequences" dump="true"/>
    <post-process name="create-overlap-relations-flymine" dump="true"/>
    <post-process name="do-sources"/>

    <post-process name="set-collection-counts" dump="true"/>
    <post-process name="create-intron-features"/>
    <post-process name="synonym-update"/>
    <post-process name="create-attribute-indexes"/>
  </post-processing>

</project>

<commit_msg>Added sequence from fasta to modMine build.<commit_after><project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="modmine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>
    <source name="chado-db-flybase-dmel" type="chado-db" dump="true">
      <property name="source.db.name" value="flybase"/>
      <property name="genus" value="Drosophila"/>
      <property name="species" value="melanogaster"/>
      <property name="taxonId" value="7227"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
    </source>
<!--
    <source name="chado-db-flybase-dpse" type="chado-db" dump="true">
      <property name="source.db.name" value="flybase"/>
      <property name="genus" value="Drosophila"/>
      <property name="species" value="pseudoobscura pseudoobscura"/>
      <property name="taxonId" value="7237"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="dataSetTitle" value="FlyBase Drosophila pseudoobscura data set"/>
    </source>
-->
    <source name="chado-db-wormbase-c_elegans" type="chado-db" dump="true">
      <property name="source.db.name" value="wormbase"/>
      <property name="genus" value="Caenorhabditis"/>
      <property name="species" value="elegans"/>
      <property name="taxonId" value="6239"/>
      <property name="dataSourceName" value="WormBase"/>
      <property name="dataSetTitle" value="WormBase C.elegans data set"/>
    </source>
    <source name="inparanoid-orthologue" type="orthologue" dump="true">
      <property name="src.data.dir" location="/shared/data/orthologues/inparanoid/current/"/>
    </source>
    <source name="flybase-dmel-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Gene"/>
      <property name="fasta.classAttribute" value="organismDbId"/>
      <property name="fasta.includes" value="dmel-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_5_1/fasta"/>
    </source>
    <source name="flybase-dmel-translation-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Translation"/>
      <property name="fasta.classAttribute" value="organismDbId"/>
      <property name="fasta.includes" value="dmel-all-translation-*.fasta"/>
      <property name="fasta.sequenceType" value="protein"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_5_1/fasta"/>
    </source>
    <source name="flybase-dmel-transcript-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Transcript"/>
      <property name="fasta.classAttribute" value="organismDbId"/>
      <property name="fasta.includes" value="dmel-all-transcript-r*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_5_1/fasta"/>
    </source>
    <source name="flybase-dmel-chromosome-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Chromosome"/>
      <property name="fasta.includes" value="dmel-all-chromosome-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_5_1/fasta"/>
    </source>
    <source name="flybase-dmel-cds-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.idSuffix" value="-cds"/>
      <property name="fasta.className" value="org.flymine.model.genomic.CDS"/>
      <property name="fasta.includes" value="dmel-all-CDS-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_5_1/fasta"/>
    </source>
    <source name="wormbase-c_elegans-chromosome-fasta" type="fasta">
      <property name="fasta.taxonId" value="6239"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Chromosome"/>
      <property name="fasta.includes" value="*chromosome*.fasta"/>
      <property name="src.data.dir" location="/shared/data/wormbase/ws175"/>
    </source>
    <source name="entrez-organism" type="entrez-organism">
      <!-- this source finds the taxon ids in the objectstore, retrieves
           species name and genus from Entrez into an InterMine format XML
           file, loads that file into a target items DB, then into the final
           objectstore -->
      <property name="src.data.file" location="build/organisms.xml"/>
    </source>
    <source name="modmine-static" type="intermine-items-xml-file">
      <property name="src.data.file" location="datasets.xml"/>
    </source>
    <source name="update-publications" type="update-publications" dump="true">
      <!-- this source finds the publication ids (pubmed ids) in the
           objectstore, retrieves the details of the publication from Entrez
           into an InterMine format XML file, loads that file into a target
           items DB, then into the final objectstore -->
      <property name="src.data.file" location="build/publications.xml"/>
    </source>
  </sources>

  <post-processing>
    <post-process name="create-utr-references"/>
    <post-process name="calculate-locations"/>
    <post-process name="create-references" dump="true"/>
    <post-process name="make-spanning-locations"/>
    <post-process name="create-chromosome-locations-and-lengths"/>
    <post-process name="create-intergenic-region-features"/>
    <post-process name="transfer-sequences" dump="true"/>
    <post-process name="create-overlap-relations-flymine" dump="true"/>
    <post-process name="do-sources"/>

    <post-process name="set-collection-counts" dump="true"/>
    <post-process name="create-intron-features"/>
    <post-process name="synonym-update"/>
    <post-process name="create-attribute-indexes"/>
  </post-processing>

</project>


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