<commit_before><project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="source.location" location="../bio/sources/"/>
  <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="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" >
      <property name="source.db.name" value="flybase"/>
      <property name="organisms" value="Dmoj Dana Dsim Dvir 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="chado-db-wormbase-c_elegans" type="chado-db" dump="true">
      <property name="source.db.name" value="wormbase"/>
      <property name="organisms" value="6239"/>
      <property name="dataSourceName" value="WormBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.WormBaseProcessor"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.GenomeDBConverter"/>
    </source>
    <!-- see flymine
    <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>
   
    <!-- 46245=pse 7217=anan 7230=moj 7244=virilis 7245=yokuba 7240=simulans -->
    <!-- 6238=briggsae 31234=remanei 135651=brenneri 281687=japonica -->
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="7227 6239 46245 7230 7244 7245 6238 31234 135651 281687"/>
      <property name="src.data.dir" location="/micklem/data/uniprot/current"/>
      <property name="createinterpro" value="true"/>
    </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="uniprot-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227 6239 7230 46245 7244 7245 6238 31234 135651 281687"/>
      <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>

<!--    ADDED FOR r20 -->
    <source name="rnai" type="rnai" dump="true">
       <property name="src.data.dir" location="/micklem/data/flymine/rnai/current"/>
    </source>
<!--
    <property name="src.data.dir" location="/micklem/data/wormbase-rnai/current"/>
    <source name="flyrnai-screens" type="flyrnai-screens">
      <property name="src.data.dir" location="/micklem/data/drsc/current"/>
      <property name="src.data.dir.includes" value="RNAi_all_hits*"/>
      <property name="screenDetailsFile" location="/micklem/data/drsc/current/RNAi_screen_details"/>
    </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 6239"/>
    </source>
    -->
    
    <!-- Added r28 
    <source name="flyatlas" type="flyatlas">
      <property name="src.data.dir" location="/micklem/data/flyatlas/current"/>
    </source>
    -->        
    <!-- Added r25 -->
    <source name="ensembl-compara" type="ensembl-compara">
      <property name="src.data.dir" location="/micklem/data/ensembl-compara/current"/>
      <property name="ensemblcompara.organisms" value="7227 6239"/>
      <property name="ensemblcompara.homologues" value="9606 10090"/>
    </source>
    
    <source name="reactome" type="biopax">
      <property name="src.data.dir" location="/micklem/data/reactome/current"/>
      <property name="biopax.organisms" value="7227 6239"/>
      <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/current"/>
      <property name="biopax.organisms" value="7227 6239"/>
      <property name="biopax.datasourcename" value="Reactome"/>
      <property name="biopax.datasetname" value="FlyReactome data set"/>
      <property name="biopax.curated" value="true"/>
    </source>
<!-- END -->

    <source name="interpro" type="interpro" >
      <property name="src.data.dir" location="/micklem/data/interpro/current"/>
    </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="psi-intact" type="psi">
        <property name="src.data.dir" location="/micklem/data/psi/intact/current"/>
        <property name="intact.organisms" value="7227 6239 7230 46245 7240 7244 7245 6238 31234 135651 281687"/>
    </source>
    <source name="biogrid" type="biogrid" dump="true">
        <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 46245"/>
    </source>
    <source name="so" type="so">
      <property name="src.data.file" location="../../bio/sources/so/so.obo"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="/micklem/data/go-annotation/current/gene_ontology.obo"/>
    </source>
    <source name="go-annotation" type="ontology-annotation" dump="true">
      <property name="ontologyfile" location="/micklem/data/go-annotation/current/gene_ontology.obo"/>
      <property name="src.data.dir" location="/micklem/data/go-annotation/modmine"/>
      <property name="src.data.dir.includes" value="*/gene_association*"/>
    </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-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="flybase-dmel-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.includes" value="dmel-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila melanogaster"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
    </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-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"/><commit_msg>modified go-annotation setting (new set up)<commit_after><project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="source.location" location="../bio/sources/"/>
  <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="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" >
      <property name="source.db.name" value="flybase"/>
      <property name="organisms" value="Dmoj Dana Dsim Dvir 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="chado-db-wormbase-c_elegans" type="chado-db" dump="true">
      <property name="source.db.name" value="wormbase"/>
      <property name="organisms" value="6239"/>
      <property name="dataSourceName" value="WormBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.WormBaseProcessor"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.GenomeDBConverter"/>
    </source>
    <!-- see flymine
    <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>
   
    <!-- 46245=pse 7217=anan 7230=moj 7244=virilis 7245=yokuba 7240=simulans -->
    <!-- 6238=briggsae 31234=remanei 135651=brenneri 281687=japonica -->
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="7227 6239 46245 7230 7244 7245 6238 31234 135651 281687"/>
      <property name="src.data.dir" location="/micklem/data/uniprot/current"/>
      <property name="createinterpro" value="true"/>
    </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="uniprot-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227 6239 7230 46245 7244 7245 6238 31234 135651 281687"/>
      <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>

<!--    ADDED FOR r20 -->
    <source name="rnai" type="rnai" dump="true">
       <property name="src.data.dir" location="/micklem/data/flymine/rnai/current"/>
    </source>
<!--
    <property name="src.data.dir" location="/micklem/data/wormbase-rnai/current"/>
    <source name="flyrnai-screens" type="flyrnai-screens">
      <property name="src.data.dir" location="/micklem/data/drsc/current"/>
      <property name="src.data.dir.includes" value="RNAi_all_hits*"/>
      <property name="screenDetailsFile" location="/micklem/data/drsc/current/RNAi_screen_details"/>
    </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 6239"/>
    </source>
    -->
    
    <!-- Added r28 
    <source name="flyatlas" type="flyatlas">
      <property name="src.data.dir" location="/micklem/data/flyatlas/current"/>
    </source>
    -->        
    <!-- Added r25 -->
    <source name="ensembl-compara" type="ensembl-compara">
      <property name="src.data.dir" location="/micklem/data/ensembl-compara/current"/>
      <property name="ensemblcompara.organisms" value="7227 6239"/>
      <property name="ensemblcompara.homologues" value="9606 10090"/>
    </source>
    
    <source name="reactome" type="biopax">
      <property name="src.data.dir" location="/micklem/data/reactome/current"/>
      <property name="biopax.organisms" value="7227 6239"/>
      <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/current"/>
      <property name="biopax.organisms" value="7227 6239"/>
      <property name="biopax.datasourcename" value="Reactome"/>
      <property name="biopax.datasetname" value="FlyReactome data set"/>
      <property name="biopax.curated" value="true"/>
    </source>
<!-- END -->

    <source name="interpro" type="interpro" >
      <property name="src.data.dir" location="/micklem/data/interpro/current"/>
    </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="psi-intact" type="psi">
        <property name="src.data.dir" location="/micklem/data/psi/intact/current"/>
        <property name="intact.organisms" value="7227 6239 7230 46245 7240 7244 7245 6238 31234 135651 281687"/>
    </source>
    <source name="biogrid" type="biogrid" dump="true">
        <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 46245"/>
    </source>
    <source name="so" type="so">
      <property name="src.data.file" location="../../bio/sources/so/so.obo"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="/micklem/data/go-annotation/current/gene_ontology.obo"/>
    </source>
    <source name="go-annotation" type="go-annotation" dump="true">
      <property name="ontologyfile" location="/micklem/data/go-annotation/current/gene_ontology.obo"/>
      <property name="src.data.dir" location="/micklem/data/go-annotation/modmine"/>
      <property name="ontologyPrefix" value="GO"/>
    </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-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="flybase-dmel-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.intermine.model.bio.Gene"/>
      <property name="fasta.includes" value="dmel-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/micklem/data/flybase/fasta/current"/>
      <property name="fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila melanogaster"/>
      <property name="fasta.dataSourceName" value="FlyBase"/>
    </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-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"/>
{'fraction_non_alphanumeric': 0.1711024720893142, 'fraction_numerical': 0.027711323763955343, 'mean_word_length': 3.7023670025779234, 'pattern_counts': {'":': 0, '<': 337, '<?xml version=': 0, '>': 337, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 4}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5588611', 'n_tokens_mistral': 6977, 'n_tokens_neox': 6394, 'n_words': 1008}