<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="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="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="uniprot.organisms" value="7227 6239 7165 9606 10090 10116 46245 7230 7244 7217 7220 7222 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.taxonId" value="7227 6239 7165 4932 9606 10090 10116 46245 7230 7244 7217 7220 7222 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="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 9606 10090 10116 7955 6239 4932"/>
     </source>
    <source name="ensembl-core" type="ensembl-core">
     <property name="src.data.dir" location="/micklem/data/ensembl/anopheles_gambiae/current_core"/>
     <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="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="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="uberon" type="uberon">
      <property name="src.data.file" location="/micklem/data/uberon/current/uberon.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="go-annotation" type="ontology-annotation">
      <property name="ontologyfile" location="/micklem/data/go-annotation/current/gene_ontology.obo"/><commit_msg>use original GO source<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="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="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="uniprot.organisms" value="7227 6239 7165 9606 10090 10116 46245 7230 7244 7217 7220 7222 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.taxonId" value="7227 6239 7165 4932 9606 10090 10116 46245 7230 7244 7217 7220 7222 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="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 9606 10090 10116 7955 6239 4932"/>
     </source>
    <source name="ensembl-core" type="ensembl-core">
     <property name="src.data.dir" location="/micklem/data/ensembl/anopheles_gambiae/current_core"/>
     <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="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="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="uberon" type="uberon">
      <property name="src.data.file" location="/micklem/data/uberon/current/uberon.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="go-annotation" type="go-annotation">
      <property name="ontologyfile" location="/micklem/data/go-annotation/current/gene_ontology.obo"/>
{'fraction_non_alphanumeric': 0.1711139347734011, 'fraction_numerical': 0.042354934349851756, 'mean_word_length': 3.832748538011696, 'pattern_counts': {'":': 0, '<': 281, '<?xml version=': 0, '>': 281, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 10}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 6, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6771787', 'n_tokens_mistral': 5967, 'n_tokens_neox': 5312, 'n_words': 880}