source: trunk/flymine/project.xml @ 29409

<project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="source.location" location="../bio/sources/"/>
  <property name="source.location" location="../bio/sources/flymine"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="flymine.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="organisms" value="7227"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.FlyBaseProcessor org.intermine.bio.dataconversion.StockProcessor"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
    </source>
    <source name="chado-db-flybase-dpse" type="chado-db">
      <property name="source.db.name" value="flybase"/>
      <property name="organisms" value="7237"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.FlyBaseProcessor"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
    </source>
    <source name="chado-db-flybase-others" type="chado-db" dump="true">
      <property name="source.db.name" value="flybase"/>
      <property name="organisms" value="Dana Dere Dgri Dmoj Dper Dsec Dsim Dvir Dwil Dyak"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.FlyBaseProcessor"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
    </source>

    <source name="wormbase-identifiers" type="wormbase-identifiers">
      <property name="src.data.dir" location="/micklem/data/worm-identifiers/current"/>
    </source>
    <source name="ensembl-hgnc" type="ensembl-hgnc">
     <property name="src.data.dir" location="/micklem/data/ensembl-ids/current"/>
    </source> 
   <source name="ncbi-gene" type="ncbi-gene">
     <property name="src.data.dir" location="/micklem/data/ncbi/current/"/>
     <property name="organisms" value="9606"/>
    </source>
   <source name="mgi-identifiers" type="mgi-identifiers">
      <property name="src.data.dir" location="/micklem/data/mgi-identifiers/current"/>
    </source>
   <source name="rgd-identifiers" type="rgd-identifiers">
      <property name="src.data.dir" location="/micklem/data/rgd-identifiers/current"/>
    </source>

    <!-- uniprot must be processed immediately after chado -->
    <source name="uniprot" type="uniprot" dump="true">
      <property name="uniprot.organisms" value="7227 6239 7165 9606 10090 10116 46245 7230 7240 7244 7245 7217 7220 7222 7234 7260 7238 559292"/>
      <property name="src.data.dir" location="/micklem/data/uniprot/current"/>
      <property name="createinterpro" value="true"/>
    </source>

    <source name="uniprot-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227 6239 7165 4932 9606 10090 10116 46245 7230 7240 7244 7245 7217 7220 7222 7234 7260 7238"/>
      <property name="fasta.className" value="org.intermine.model.bio.Protein"/>
      <property name="fasta.classAttribute" value="primaryAccession"/>
      <property name="fasta.dataSetTitle" value="UniProt data set"/>
      <property name="fasta.dataSourceName" value="UniProt"/>
      <property name="src.data.dir" location="/micklem/data/uniprot/current"/>
      <property name="fasta.includes" value="uniprot_sprot_varsplic.fasta"/>
      <property name="fasta.sequenceType" value="protein" />
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.UniProtFastaLoaderTask"/>
    </source>
     <source name="drosophila-homology" type="drosophila-homology">
      <property name="src.data.dir" location="/micklem/data/flybase/homology/current"/>
      <property name="src.data.dir.includes" value="*.tsv"/>
    </source>
    <source name="anopheles-identifiers" type="anopheles-identifiers">
      <property name="src.data.dir" location="/micklem/data/anopheles-identifiers/current"/>
    </source>
    <source name="uniprot-keywords" type="uniprot-keywords">
      <property name="src.data.dir" location="/micklem/data/uniprot/current"/>
      <property name="src.data.dir.includes" value="keywlist.xml"/>
    </source>
    <source name="rnai" type="rnai">
      <property name="src.data.dir" location="/micklem/data/flymine/rnai/current"/>
    </source>
    <source name="arbeitman-items-xml" type="arbeitman-items-xml">
      <property name="src.data.file" location="/micklem/data/flymine/mage/arbeitman/arbeitman-tgt-items.xml"/>
    </source>
    <source name="bdgp-clone" type="bdgp-clone">
      <property name="src.data.dir" location="/micklem/data/flymine/bdgp-clones"/>
      <property name="src.data.dir.includes" value="dgc2flybase.txt"/>
    </source>

    <source name="long-oligo" type="long-oligo" dump="true">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="MRNA"/>
      <property name="src.data.dir" location="/micklem/data/flymine/long-oligo"/>
    </source>

    <source name="ensembl" type="ensembl">
     <property name="src.data.dir" location="/micklem/data/ensembl/current"/>
     <property name="src.data.dir.includes" value="7165.xml"/>
    </source>

    <source name="interpro" type="interpro">
      <property name="src.data.dir" location="/micklem/data/interpro/current"/>
    </source>

    <source name="omim" type="omim">
      <property name="src.data.dir" location="/micklem/data/metabolic/omim/test"/>
    </source>
    <source name="kegg-pathway" type="kegg-pathway">
      <property name="src.data.dir" location="/micklem/data/kegg/current"/>
      <property name="kegg.organisms" value="7227"/>
    </source>
<!--
    <source name="kegg-orthologues" type="kegg-orthologues">
      <property name="src.data.dir" location="/micklem/data/kegg/orthologues"/>
      <property name="kegg.organisms" value="7227 9606 4932 6239 7955 10090 10116"/>
    </source>
-->
    <source name="flyatlas" type="flyatlas">
      <property name="src.data.dir" location="/micklem/data/flyatlas/current"/>
    </source>
    <source name="anoph-expr" type="anoph-expr">
      <property name="src.data.dir" location="/micklem/data/flymine/anoph-expr"/>
      <property name="src.data.dir.includes" value="E-TABM-186-processed-data-1343527732.txt"/>
      <property name="geneFile" value="/micklem/data/flymine/anoph-expr/reporter_gene_mappingFile.txt"/>
    </source>

    <source name="treefam" type="treefam">
      <property name="src.data.dir" location="/micklem/data/treefam/current"/>
      <property name="src.data.dir.includes" value="ortholog.txt.table"/>
      <property name="geneFile" value="/micklem/data/treefam/current/genes.txt.table"/>
      <property name="treefam.organisms" value="7227 7165"/>
      <property name="treefam.homologues" value="9606 10090 10116 7955 6239 4932"/>
    </source>

    <source name="ensembl-compara" type="ensembl-compara">
      <property name="src.data.dir" location="/micklem/data/ensembl-compara/current"/>
      <property name="ensemblcompara.organisms" value="7227"/>
      <property name="ensemblcompara.homologues" value="6239 9606 10090 10116"/>
    </source>
    <source name="anoest" type="anoest">
      <property name="dataSourceName" value="VectorBase"/>
      <property name="dataSetTitle" value="AnoEST clusters"/>
      <property name="source.db.name" value="anoest"/>
    </source>
    <source name="pdb" type="pdb">
      <property name="src.data.dir" location="/micklem/data/pdb/current"/>
      <property name="pdb.organisms" value="7227"/>
    </source>
    <source name="psi-mi-ontology" type="psi-mi-ontology">
      <property name="src.data.file" location="/micklem/data/psi/ontology/current/psi-mi.obo"/>
    </source>
    <source name="so" type="so">
      <property name="src.data.file" location="../../bio/sources/so/so.obo"/>
    </source>
    <source name="go" type="go" dump="true">
      <property name="src.data.file" location="/micklem/data/go-annotation/current/gene_ontology.obo"/>
    </source>
<!--
    <source name="uberon" type="uberon">
      <property name="src.data.file" location="/micklem/data/old_shared_data/uberon/uberon.obo"/>
    </source>
-->
    <source name="go-annotation" type="ontology-annotation">
      <property name="ontologyfile" location="/micklem/data/go-annotation/current/gene_ontology.obo"/>
      <property name="src.data.dir" location="/micklem/data/go-annotation/flymine"/>
      <property name="ontologyPrefix" value="GO"/>
    </source>
    
    <source name="flybase-expression" type="flybase-expression">
      <property name="src.data.dir" location="/micklem/data/modMine_flyRNAseq"/>
      <property name="src.data.dir.includes" value="HTD_modENCODE_BinData_2010-10-05.txt"/>
      <property name="flybaseExpressionLevelsFile" location="/micklem/data/modMine_flyRNAseq/BinLOOKUP_modENCODE_FlyAtlas.txt"/>
    </source>

    <source name="flyreg" type="flyreg">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="src.data.dir" location="/micklem/data/redfly/current/tfbs"/>
      <property name="src.data.dir.includes" value="tfbs_dump.gff"/>
    </source>
    <source name="redfly" type="redfly">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="src.data.dir" location="/micklem/data/redfly/current/crm"/>
      <property name="src.data.dir.includes" value="crm_dump.gff"/>
    </source>

    <source name="fly-fish" type="fly-fish">
      <property name="src.data.dir" location="/micklem/data/flymine/flyfish"/>
      <property name="src.data.dir.includes" value="annotation_matrix_filter_3.csv"/>
    </source>
    <source name="flybase-dmel-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila melanogaster"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dpse-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7237"/>
      <property name="fasta.dataSetTitle"
                value="FlyBase fasta data set for Drosophila pseudoobscura pseudoobscura"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dpse-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dana-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7217"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila ananassae"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dana-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dere-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7220"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila erecta"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dere-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dgri-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7222"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila grimshawi"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dgri-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dmoj-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7230"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila mojavensis"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmoj-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dper-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7234"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila persimilis"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dper-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dsec-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7238"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila sechellia"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dsec-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dsim-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7240"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila simulans"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dsim-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dvir-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7244"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila virilis"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dvir-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dwil-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7260"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila willistoni"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dwil-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dyak-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7245"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila yakuba"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dyak-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dmel-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila melanogaster"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dpse-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7237"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dpse-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila pseudoobscura pseudoobscura"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dana-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7217"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dana-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila ananassae"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dere-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7220"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dere-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila erecta"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dgri-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7222"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dgri-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila grimshawi"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dmoj-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7230"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmoj-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila mojavensis"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dper-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7234"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dper-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila persimilis"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dsec-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7238"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dsec-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila sechellia"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dsim-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7240"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dsim-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila simulans"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dvir-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7244"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dvir-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila virilis"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dwil-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7260"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dwil-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila willistoni"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dyak-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7245"/>
      <property name="fasta.className" value="org.intermine.model.bio.CDS"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dyak-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila yakuba"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dmel-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.intermine.model.bio.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila melanogaster"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dmel-3prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.intermine.model.bio.ThreePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-three_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila melanogaster"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    
    
    <source name="flybase-dpse-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7237"/>
      <property name="fasta.className" value="org.intermine.model.bio.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dpse-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila pseudoobscura pseudoobscura"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dpse-3prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7237"/>
      <property name="fasta.className" value="org.intermine.model.bio.ThreePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dpse-all-three_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila pseudoobscura pseudoobscura"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dgri-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7222"/>
      <property name="fasta.className" value="org.intermine.model.bio.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dgri-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila grimshawi"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dper-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7234"/>
      <property name="fasta.className" value="org.intermine.model.bio.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dper-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila persimilis"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dsec-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7238"/>
      <property name="fasta.className" value="org.intermine.model.bio.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dsec-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila sechellia"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dsim-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7240"/>
      <property name="fasta.className" value="org.intermine.model.bio.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dsim-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila simulans"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="flybase-dyak-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7245"/>
      <property name="fasta.className" value="org.intermine.model.bio.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dyak-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase data set for Drosophila yakuba"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
    </source>
    <source name="pubmed-gene" type="pubmed-gene" dump="true">
      <property name="src.data.dir" location="/micklem/data/pubmed/current"/>
      <property name="pubmed.organisms" value="7227 7165 6239 7240 7244 7245 7217 7220 7222 7234 7238 46245"/>
      <property name="src.data.dir.includes" value="gene2pubmed"/>
      <property name="infoFile" location="/micklem/data/pubmed/current/gene_info"/>
    </source>

    <source name="interpro-go" type="interpro-go">
      <property name="src.data.dir" location="/micklem/data/interpro/ontology/current"/>
    </source>

<!-- text files, didn't see a gain from BioPAX 
    <source name="reactome" type="reactome">
      <property name="src.data.dir" location="/micklem/data/old_shared_data/reactome/current"/>
      <property name="reactome.organisms" value="7227 4932 6239"/>
    </source>
-->

    <source name="reactome" type="biopax">
      <property name="src.data.dir" location="/micklem/data/reactome/current"/>
      <property name="biopax.organisms" value="7227"/>
      <property name="biopax.datasourcename" value="Reactome"/>
      <property name="biopax.datasetname" value="Reactome data set"/>
      <property name="biopax.curated" value="false"/>
    </source>

    <source name="reactome-curated" type="biopax">
      <property name="src.data.dir" location="/micklem/data/reactome/curated"/>
      <property name="biopax.organisms" value="7227"/>
      <property name="biopax.datasourcename" value="Reactome"/>
      <property name="biopax.datasetname" value="FlyReactome data set"/>
      <property name="biopax.curated" value="true"/>
    </source>

    <source name="bdgp-insitu" type="bdgp-insitu">
      <property name="src.data.dir" location="/micklem/data/flymine/bdgp-insitu/current"/>
    </source>
    <source name="fly-anatomy-ontology" type="fly-anatomy-ontology">
      <property name="src.data.file" location="/micklem/data/ontologies/fly-anatomy/current/fly_anatomy.obo"/>
    </source>
    <source name="fly-development-ontology" type="fly-development-ontology">
      <property name="src.data.file" location="/micklem/data/ontologies/fly-development/current/fly_development.obo"/>
    </source>
    <source name="fly-misc-cvterms" type="fly-misc-cvterms">
      <property name="src.data.file" location="/micklem/data/ontologies/fly-cv/current/flybase_controlled_vocabulary.obo"/>
    </source>

    <source name="drosdel-gff" type="drosdel-gff">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="src.data.dir"
                location="/micklem/data/flymine/drosdel/2008-03-19/chromosome_structure_variations/"/>
    </source>

    <source name="miranda" type="miranda">
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.taxonId" value="7227"/>
      <property name="src.data.dir" location="/micklem/data/flymine/mirna/miranda/current"/>
      <property name="src.data.dir.includes" value="v5.gff.drosophila_melanogaster.gff"/>
    </source>
    <source name="psi-intact" type="psi" dump="true">
      <property name="src.data.dir" location="/micklem/data/psi/intact/current"/>
      <property name="intact.organisms" value="7227 6239 46245 7240 7244 7245"/>
    </source>

    <source name="biogrid" type="biogrid">
      <property name="src.data.dir" location="/micklem/data/biogrid/current"/>
      <property name="src.data.dir.includes" value="*psi25.xml"/>
      <property name="biogrid.organisms" value="7227 6239"/>
    </source>

    <source name="affy-probes" type="affy-probes">
      <property name="src.data.dir" location="/micklem/data/flymine/affy-probes/current"/>
      <property name="src.data.dir.includes" value="*.txt"/>
    </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="flymine-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="create-references" />
    <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"/>
    <post-process name="create-overlap-relations-flymine" dump="true"/>
    <post-process name="do-sources" />
    <post-process name="create-intron-features">
      <property name="organisms" value="7165"/>
    </post-process>
    <post-process name="create-bioseg-location-index"/>
    <post-process name="create-overlap-view" />
    <post-process name="create-attribute-indexes"/>
    <post-process name="summarise-objectstore"/>
    <post-process name="create-autocomplete-index"/>
    <post-process name="create-search-index"/>

    <!-- grant-db-production/
    TODO: Not really post processing but just has to be done sometime...
  <target name="grant-db-production" depends="prepare" - ->
    <!- - grant 'public' user select permission on production db - ->
    <taskdef name="grant" classname="org.intermine.task.GrantTask">
      <classpath refid="models.class.path"/>
    </taskdef>

    <grant database="db.production" user="PUBLIC" perm="SELECT"/>

  </target>
    -->
  </post-processing>

</project>