<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/example-sources/"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="malariamine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>

  <sources>
    <source name="uniprot-malaria" type="uniprot">
      <property name="uniprot.organisms" value="36329"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/uniprot/"/>
    </source>
    <source name="malaria-gff" type="malaria-gff">
      <property name="gff3.taxonId" value="36329"/>
      <property name="gff3.seqDataSourceName" value="PlasmoDB"/>
      <property name="gff3.dataSourceName" value="PlasmoDB"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="PlasmoDB P. falciparum genome"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/genome/gff"/>
    </source>
    <source name="malaria-chromosome-fasta" type="fasta" dump="true">
      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="PlasmoDB"/>
      <property name="fasta.dataSetTitle" value="PlasmoDB chromosome sequence"/>
      <property name="fasta.taxonId" value="36329"/>
      <property name="fasta.includes" value="MAL*.fasta"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/genome/fasta"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="DATA_DIR/malaria/go/gene_ontology.obo"/>
    </source>
    <source name="go-annotation" type="go-annotation" dump="true">
      <property name="ontologyfile" location="DATA_DIR/malaria/go/gene_ontology.obo"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/go-annotation/"/>
    </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 interpro, don't create GO OntologyRelation objects.<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/example-sources/"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="malariamine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>

  <sources>
    <source name="uniprot-malaria" type="uniprot">
      <property name="uniprot.organisms" value="36329"/>
      <property name="createinterpro" value="true"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/uniprot/"/>
    </source>
    <source name="malaria-gff" type="malaria-gff">
      <property name="gff3.taxonId" value="36329"/>
      <property name="gff3.seqDataSourceName" value="PlasmoDB"/>
      <property name="gff3.dataSourceName" value="PlasmoDB"/>
      <property name="gff3.seqClsName" value="Chromosome"/>
      <property name="gff3.dataSetTitle" value="PlasmoDB P. falciparum genome"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/genome/gff"/>
    </source>
    <source name="malaria-chromosome-fasta" type="fasta" dump="true">
      <property name="fasta.className" value="org.intermine.model.bio.Chromosome"/>
      <property name="fasta.dataSourceName" value="PlasmoDB"/>
      <property name="fasta.dataSetTitle" value="PlasmoDB chromosome sequence"/>
      <property name="fasta.taxonId" value="36329"/>
      <property name="fasta.includes" value="MAL*.fasta"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/genome/fasta"/>
    </source>
    <source name="interpro" type="interpro">
      <property name="src.data.dir" location="DATA_DIR/malaria/interpro"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="DATA_DIR/malaria/go/gene_ontology.obo"/>
      <property name="createrelations" value="false"/>
    </source>
    <source name="go-annotation" type="go-annotation" dump="true">
      <property name="ontologyfile" location="DATA_DIR/malaria/go/gene_ontology.obo"/>
      <property name="src.data.dir" location="DATA_DIR/malaria/go-annotation/"/>
    </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': 0.1765741102854908, 'fraction_numerical': 0.007821666014861166, 'mean_word_length': 4.4357066950053134, 'pattern_counts': {'":': 0, '<': 96, '<?xml version=': 0, '>': 96, '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': '6702033', 'n_tokens_mistral': 1664, 'n_tokens_neox': 1602, 'n_words': 252}