<commit_before><project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="source.location" location="../bio/sources/"/>
  <property name="source.location" location="../bio/sources/experimental-sources/"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="plantmine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>

    <source name="plant-identifiers" type="plant-identifiers">
     <property name="src.data.dir" location="/micklem/data/users/rns/plant/genes-ids/"/>
     </source>
    <source name="ensembl-plant" type="ensembl" dump="true">
     <property name="src.data.dir" location="/micklem/data/ensembl/arabidopsis_thaliana/current_core"/>
      <property name="src.data.dir.includes" value="3702.xml"/>
    </source>
    <source name="uniprot" type="uniprot" dump="true">
      <property name="uniprot.organisms" value="3702"/>
      <property name="src.data.dir" location="/micklem/data/plantmine/uniprot"/>
      <property name="createinterpro" value="true"/>
      <property name="creatego" 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="interpro" type="interpro">
      <property name="src.data.dir" location="/micklem/data/interpro/current"/>
    </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"/>
      <property name="src.data.dir" location="/micklem/data/users/rns/plant/go-annotation/"/>
    </source>
    <source name="ensembl-plant-chr-fasta" type="fasta">
      <property name="fasta.taxonId" value="10090"/>
      <property name="fasta.dataSetTitle" value="Ensembl A. thaliana chromosome sequence"/>
      <property name="fasta.dataSourceName" value="Ensembl"/>
      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="*.fa"/>
      <property name="src.data.dir" location="/micklem/data/ensembl/arabidopsis_thaliana/current_core/fasta"/>
    </source>
    <source name="ensembl-snp-db-plant" type="ensembl-snp-db" dump="true">
     <property name="source.db.name" value="ensembl.3702.variation"/>
     <property name="organism" value="3702"/>
     <property name="sources" value="Ensembl"/>
    </source>
    <source name="update-publications" type="update-publications">
      <property name="src.data.file" location="build/publications.xml"/>
    </source>
    <source name="entrez-organism" type="entrez-organism">
      <property name="src.data.file" location="build/organisms.xml"/>
    </source>

  </sources>

  <post-processing>
    <post-process name="create-references" /><commit_msg>Add Ensembl GWAS.<commit_after><project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="source.location" location="../bio/sources/"/>
  <property name="source.location" location="../bio/sources/experimental-sources/"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="plantmine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>

    <source name="plant-identifiers" type="plant-identifiers">
     <property name="src.data.dir" location="/micklem/data/users/rns/plant/genes-ids/"/>
     </source>
    <source name="ensembl-plant" type="ensembl" dump="true">
     <property name="src.data.dir" location="/micklem/data/ensembl/arabidopsis_thaliana/current_core"/>
      <property name="src.data.dir.includes" value="3702.xml"/>
    </source>
    <source name="uniprot" type="uniprot" dump="true">
      <property name="uniprot.organisms" value="3702"/>
      <property name="src.data.dir" location="/micklem/data/plantmine/uniprot"/>
      <property name="createinterpro" value="true"/>
      <property name="creatego" 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="interpro" type="interpro">
      <property name="src.data.dir" location="/micklem/data/interpro/current"/>
    </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"/>
      <property name="src.data.dir" location="/micklem/data/users/rns/plant/go-annotation/"/>
    </source>
    <source name="ensembl-plant-chr-fasta" type="fasta">
      <property name="fasta.taxonId" value="10090"/>
      <property name="fasta.dataSetTitle" value="Ensembl A. thaliana chromosome sequence"/>
      <property name="fasta.dataSourceName" value="Ensembl"/>
      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="*.fa"/>
      <property name="src.data.dir" location="/micklem/data/ensembl/arabidopsis_thaliana/current_core/fasta"/>
    </source>
    <source name="ensembl-snp-db-plant" type="ensembl-snp-db" dump="true">
     <property name="source.db.name" value="ensembl.3702.variation"/>
     <property name="organism" value="3702"/>
     <property name="sources" value="Ensembl"/>
    </source>
    <source name="ensembl-gwas-db" type="ensembl-gwas-db"> 
      <property name="source.db.name" value="ensembl.3702.variation"/> 
    </source>
    <source name="update-publications" type="update-publications">
      <property name="src.data.file" location="build/publications.xml"/>
    </source>
    <source name="entrez-organism" type="entrez-organism">
      <property name="src.data.file" location="build/organisms.xml"/>
    </source>

  </sources>

  <post-processing>
    <post-process name="create-references" />
{'fraction_non_alphanumeric': 0.18188690656183854, 'fraction_numerical': 0.006954944058058663, 'mean_word_length': 4.270916334661354, 'pattern_counts': {'":': 0, '<': 122, '<?xml version=': 0, '>': 122, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 8}, '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': '1837932', 'n_tokens_mistral': 2149, 'n_tokens_neox': 2080, 'n_words': 313}