<commit_before><project type="bio">
  <property name="target.model" value="genomic"/>
  <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="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"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.FlyBaseChadoDBConverter"/>
    </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"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.FlyBaseChadoDBConverter"/>
    </source>
    <source name="wormbase-identifiers" type="wormbase-identifiers">
      <property name="src.data.dir" location="/shared/data/wormbase/current"/>
    </source>
    <source name="anopheles-identifiers" type="anopheles-identifiers">
      <property name="src.data.dir" location="/shared/data/anopheles/mappings"/>
      <property name="src.data.dir.includes" value="New_IDs*"/>
    </source>
    <source name="uniprot" type="uniprot" dump="true">
      <property name="uniprot.organisms" value="7227 7237 6239 180454 7460 4932 9606 10090"/>
      <property name="src.data.dir" location="/shared/data/uniprot/current"/>
      <property name="createinterpro" value="true"/>
      <property name="use.split.files" value="true"/>
    </source>
    <source name="uniprot-keywords" type="uniprot-keywords">
      <property name="src.data.dir" location="/shared/data/uniprot/current"/>
      <property name="src.data.dir.includes" value="keydef.xml"/>
    </source>
    <source name="rnai" type="rnai">
      <property name="src.data.dir" location="/shared/data/wormRNAi/wormbase_rnai/current"/>
    </source>
    <source name="mage" type="mage">
      <property name="src.data.dir" location="/shared/data/mage/arbeitman"/>
      <property name="quantitationtypes" value="Signal med ratio"/>
    </source>
    <source name="bdgp-clone" type="bdgp-clone">
      <property name="src.data.dir" location="/shared/data/bdgp_clones"/>
      <property name="src.data.dir.includes" value="dgc2flybase.txt"/>
    </source>
    <source name="long_oligo" type="long_oligo">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="MRNA"/>
      <property name="gff3.seqDataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/long_oligo"/>
    </source>
    <source name="drosdel-gff" type="drosdel-gff">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.seqDataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/liftover/drosdel/combined"/>
    </source>
    <source name="ensembl-anopheles" type="ensembl" dump="true">
      <property name="organism" value="AGP"/>
    </source>
    <source name="ensembl-apis-mellifera" type="ensembl" dump="true">
      <property name="organism" value="AM"/>
    </source>
    <source name="flyreg" type="flyreg">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.seqDataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/REDfly/current/tfbs/"/>
    </source>   
    <source name="interpro" type="interpro">      
      <property name="src.data.dir" location="/shared/data/interpro/current"/>
    </source>
    <source name="homophila" type="homophila">
      <property name="src.data.dir" location="/shared/data/homophila/current"/>
      <property name="src.data.dir.includes" value="homophila_matches.txt"/>
      <property name="diseasefile" location="/shared/data/homophila/current/homophila_diseases.txt"/>
      <property name="proteingenefile" location="/shared/data/homophila/current/protein_gene.txt"/>
    </source>
    <source name="tiling_path" type="tiling_path" dump="true">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.seqDataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/liftover/tiling_reordered/"/>
    </source>
    <source name="kegg-pathway" type="kegg-pathway">
      <property name="src.data.dir" location="/shared/data/kegg/current"/>
    </source>
    <source name="flyatlas" type="flyatlas">
      <property name="src.data.dir" location="/shared/data/flyatlas/current"/>
    </source>
    <source name="affy-probes" type="affy-probes">
      <property name="src.data.dir" location="/shared/data/affy-probes/current"/>
    </source>
    <source name="anoph-expr" type="anoph-expr">
      <property name="src.data.dir" location="/shared/data/anoph_expr"/>
      <property name="src.data.dir.includes" value="E-TABM-186-processed-data-1343527732.txt"/>
      <property name="genefile" value="/shared/data/anoph_expr/reporter_gene_mappingFile.txt"/>
    </source>
    <source name="tiffin" type="tiffin" dump="true">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.seqDataSourceName" value="Sanger"/>
      <property name="src.data.dir" location="/shared/data/tiffin/tiffin1.2"/>
    </source>
    <source name="tiffin-expression" type="tiffin-expression">
      <property name="src.data.dir" location="/shared/data/tiffin/"/>
      <property name="src.data.dir.includes" value="tiffin_ImaGo"/>
    </source>
    <source name="anoest" type="anoest">
      <property name="source.db.name" value="anoest"/>
    </source>
    <source name="protein_structure" type="protein_structure">
      <property name="src.data.dir" location="/shared/data/kenji/data/all/"/>
    </source>
    <source name="pdb" type="pdb">
      <property name="src.data.dir" location="/shared/data/pdb/current"/>
    </source>
    <source name="psi-intact" type="psi">
      <property name="src.data.dir" location="/shared/data/psi/intact/current"/>
      <property name="organisms" value="7227 6239 4932"/>
    </source>
    <source name="psi-mi-ontology" type="psi-mi-ontology">
      <property name="src.data.file" location="/shared/data/psi/ontology/current/psi-mi.obo"/>
    </source>
    <source name="go" type="go" dump="true">
      <property name="src.data.file" location="/shared/data/go-annotation/gene_ontology.obo"/>
    </source>
    <source name="go-annotation" type="go-annotation" dump="true">
      <property name="ontologyfile" location="/shared/data/go-annotation/gene_ontology.obo"/><commit_msg>Don't dump so often in flymine 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="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="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"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.FlyBaseChadoDBConverter"/>
    </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"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.FlyBaseChadoDBConverter"/>
    </source>
    <source name="wormbase-identifiers" type="wormbase-identifiers">
      <property name="src.data.dir" location="/shared/data/wormbase/current"/>
    </source>
    <source name="anopheles-identifiers" type="anopheles-identifiers">
      <property name="src.data.dir" location="/shared/data/anopheles/mappings"/>
      <property name="src.data.dir.includes" value="New_IDs*"/>
    </source>
    <source name="uniprot" type="uniprot" dump="true">
      <property name="uniprot.organisms" value="7227 7237 6239 180454 7460 4932 9606 10090"/>
      <property name="src.data.dir" location="/shared/data/uniprot/current"/>
      <property name="createinterpro" value="true"/>
      <property name="use.split.files" value="true"/>
    </source>
    <source name="uniprot-keywords" type="uniprot-keywords">
      <property name="src.data.dir" location="/shared/data/uniprot/current"/>
      <property name="src.data.dir.includes" value="keydef.xml"/>
    </source>
    <source name="rnai" type="rnai">
      <property name="src.data.dir" location="/shared/data/wormRNAi/wormbase_rnai/current"/>
    </source>
    <source name="mage" type="mage">
      <property name="src.data.dir" location="/shared/data/mage/arbeitman"/>
      <property name="quantitationtypes" value="Signal med ratio"/>
    </source>
    <source name="bdgp-clone" type="bdgp-clone">
      <property name="src.data.dir" location="/shared/data/bdgp_clones"/>
      <property name="src.data.dir.includes" value="dgc2flybase.txt"/>
    </source>
    <source name="long_oligo" type="long_oligo">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="MRNA"/>
      <property name="gff3.seqDataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/long_oligo"/>
    </source>
    <source name="drosdel-gff" type="drosdel-gff">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.seqDataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/liftover/drosdel/combined"/>
    </source>
    <source name="ensembl-anopheles" type="ensembl" dump="true">
      <property name="organism" value="AGP"/>
    </source>
    <source name="ensembl-apis-mellifera" type="ensembl" dump="true">
      <property name="organism" value="AM"/>
    </source>
    <source name="flyreg" type="flyreg">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.seqDataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/REDfly/current/tfbs/"/>
    </source>   
    <source name="interpro" type="interpro">      
      <property name="src.data.dir" location="/shared/data/interpro/current"/>
    </source>
    <source name="homophila" type="homophila">
      <property name="src.data.dir" location="/shared/data/homophila/current"/>
      <property name="src.data.dir.includes" value="homophila_matches.txt"/>
      <property name="diseasefile" location="/shared/data/homophila/current/homophila_diseases.txt"/>
      <property name="proteingenefile" location="/shared/data/homophila/current/protein_gene.txt"/>
    </source>
    <source name="tiling_path" type="tiling_path" dump="true">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.seqDataSourceName" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/liftover/tiling_reordered/"/>
    </source>
    <source name="kegg-pathway" type="kegg-pathway">
      <property name="src.data.dir" location="/shared/data/kegg/current"/>
    </source>
    <source name="flyatlas" type="flyatlas">
      <property name="src.data.dir" location="/shared/data/flyatlas/current"/>
    </source>
    <source name="affy-probes" type="affy-probes">
      <property name="src.data.dir" location="/shared/data/affy-probes/current"/>
    </source>
    <source name="anoph-expr" type="anoph-expr">
      <property name="src.data.dir" location="/shared/data/anoph_expr"/>
      <property name="src.data.dir.includes" value="E-TABM-186-processed-data-1343527732.txt"/>
      <property name="genefile" value="/shared/data/anoph_expr/reporter_gene_mappingFile.txt"/>
    </source>
    <source name="tiffin" type="tiffin" dump="true">
      <property name="gff3.taxonId" value="7227"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.seqDataSourceName" value="Sanger"/>
      <property name="src.data.dir" location="/shared/data/tiffin/tiffin1.2"/>
    </source>
    <source name="tiffin-expression" type="tiffin-expression">
      <property name="src.data.dir" location="/shared/data/tiffin/"/>
      <property name="src.data.dir.includes" value="tiffin_ImaGo"/>
    </source>
    <source name="anoest" type="anoest">
      <property name="source.db.name" value="anoest"/>
    </source>
    <source name="protein_structure" type="protein_structure">
      <property name="src.data.dir" location="/shared/data/kenji/data/all/"/>
    </source>
    <source name="pdb" type="pdb">
      <property name="src.data.dir" location="/shared/data/pdb/current"/>
    </source>
    <source name="psi-intact" type="psi">
      <property name="src.data.dir" location="/shared/data/psi/intact/current"/>
      <property name="organisms" value="7227 6239 4932"/>
    </source>
    <source name="psi-mi-ontology" type="psi-mi-ontology">
      <property name="src.data.file" location="/shared/data/psi/ontology/current/psi-mi.obo"/>
    </source>
    <source name="go" type="go" dump="true">
      <property name="src.data.file" location="/shared/data/go-annotation/gene_ontology.obo"/>
    </source>
    <source name="go-annotation" type="go-annotation">
      <property name="ontologyfile" location="/shared/data/go-annotation/gene_ontology.obo"/>
{'fraction_non_alphanumeric': 0.178796830938633, 'fraction_numerical': 0.014233919699207735, 'mean_word_length': 4.00672268907563, 'pattern_counts': {'":': 0, '<': 275, '<?xml version=': 0, '>': 275, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, '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': '2086720', 'n_tokens_mistral': 5020, 'n_tokens_neox': 4768, 'n_words': 756}