<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="metabolicmine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>


  <sources>
    <source name="ensembl-hgnc" type="ensembl-hgnc">
     <property name="src.data.dir" location="/shared/data/metabolic/ensembl-ids/current"/>
    </source> 
     <source name="ncbi-gene" type="ncbi-gene">
     <property name="src.data.dir" location="/shared/data/metabolic/ncbi/current/"/>
     <property name="organisms" value="9606"/>
    </source>
    <source name="ncbi-summaries" type="ncbi-summaries">
     <property name="src.data.dir" location="/shared/data/metabolic/gene-summaries/current/"/>
    </source>
   <source name="mgi-identifiers" type="mgi-identifiers">
      <property name="src.data.dir" location="/shared/data/mgi/current"/>
    </source>
   <source name="rgd-identifiers" type="rgd-identifiers">
      <property name="src.data.dir" location="/shared/data/metabolic/rgd-identifiers/current"/>
    </source>
    <source name="so" type="so">
      <property name="src.data.file" location="../../bio/sources/so/so.obo"/>
    </source> 
    <source name="protein-atlas" type="protein-atlas">
     <property name="src.data.dir" location="/shared/data/metabolic/protein-atlas/current"/>
    </source>
    <source name="ensembl-human" type="ensembl" dump="true">
     <property name="src.data.dir" location="/shared/data/ensembl/metabolic/human/current"/>
    </source>
    <source name="ensembl-gwas-db-human" type="ensembl-gwas-db">
     <property name="source.db.name" value="ensembl.9606.variation"/>
    </source>
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="9606 10090"/>
      <property name="createinterpro" value="true"/>
      <property name="src.data.dir" location="/shared/data/uniprot/current/split/"/>
    </source>
<!--    <source name="uniprot-fasta" type="fasta" dump="true">
      <property name="fasta.taxonId" value="9606 10090"/>
      <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="/shared/data/uniprot/2010_09/"/>
      <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="uniprot-keywords" type="uniprot-keywords">
      <property name="src.data.dir" location="/shared/data/uniprot/current"/>
      <property name="src.data.dir.includes" value="keywlist.xml"/>
    </source>
    <source name="interpro" type="interpro">
      <property name="src.data.dir" location="/shared/data/interpro/current"/>
    </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"/>
      <property name="src.data.dir" location="/shared/data/go-annotation/metabolic/"/>
      <property name="src.data.includes" value="**/gene_association*"/>
    </source>
    <source name="kegg-pathway" type="kegg-pathway">
      <property name="src.data.dir" location="/shared/data/metabolic/kegg/current"/>
      <property name="kegg.organisms" value="9606 10090"/>
    </source>
    <source name="reactome" type="biopax">
      <property name="src.data.dir" location="/shared/data/metabolic/biopax/reactome/current/not-curated"/>
      <property name="biopax.organisms" value="9606"/>
      <property name="biopax.datasourcename" value="Reactome"/>
      <property name="biopax.datasetname" value="Reactome data set"/>
      <property name="biopax.curated" value="false"/>
    </source>
    <source name="psi-intact" type="psi" dump="true">
      <property name="src.data.dir" location="/shared/data/psi/intact/current"/>
      <property name="intact.organisms" value="9606 10090"/>
    </source>
    <source name="biogrid" type="biogrid">
      <property name="src.data.dir" location="/shared/data/metabolic/biogrid"/>
      <property name="src.data.dir.includes" value="*psi25.xml"/>
      <property name="biogrid.organisms" value="9606 10090"/>
    </source>
    <source name="pubmed-gene" type="pubmed-gene" dump="true">
      <property name="src.data.dir" location="/shared/data/pubmed/current"/>
      <property name="pubmed.organisms" value="9606 10090"/>
      <property name="src.data.dir.includes" value="gene2pubmed"/>
      <property name="infoFile" location="/shared/data/pubmed/current/gene_info"/>
    </source>
    <source name="omim" type="omim">
      <property name="src.data.dir" location="/shared/data/metabolic/omim/test"/>
    </source>
    <source name="ensembl-mouse" type="ensembl" dump="true">
      <property name="src.data.dir" location="/shared/data/ensembl/metabolic/mouse/current"/>     
      <property name="src.data.dir.includes" value="10090.xml"/>
    </source>
    <source name="ensembl-human-chr-fasta" type="fasta">
      <property name="fasta.taxonId" value="9606"/>
      <property name="fasta.dataSetTitle" value="Ensembl human 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="/shared/data/ensembl/homo_sapiens/current_core/fasta"/>
    </source>
    <source name="ensembl-mouse-chr-fasta" type="fasta">
      <property name="fasta.taxonId" value="10090"/>
      <property name="fasta.dataSetTitle" value="Ensembl mouse 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="/shared/data/ensembl/mus_musculus/current_core/fasta"/>
    </source>
    <source name="treefam" type="treefam">
      <property name="src.data.dir" location="/shared/data/treefam/current"/>
      <property name="src.data.dir.includes" value="ortholog.txt.table"/>
      <property name="geneFile" value="/shared/data/treefam/current/genes.txt.table"/>
      <!-- will load all genes for human, rat and mouse -->
      <property name="treefam.organisms" value="9606 10090 10116"/>
      <!-- will only load gene if it is a homologue for human, rat or mouse -->
      <property name="treefam.homologues" value="9606 10090 10116"/>
    </source>
    <source name="ensembl-snp-db-human" type="ensembl-snp-db" dump="true">
     <property name="source.db.name" value="ensembl.9606.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"><commit_msg>add compara to metamine<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="metabolicmine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>


  <sources>
    <source name="ensembl-hgnc" type="ensembl-hgnc">
     <property name="src.data.dir" location="/shared/data/metabolic/ensembl-ids/current"/>
    </source> 
     <source name="ncbi-gene" type="ncbi-gene">
     <property name="src.data.dir" location="/shared/data/metabolic/ncbi/current/"/>
     <property name="organisms" value="9606"/>
    </source>
    <source name="ncbi-summaries" type="ncbi-summaries">
     <property name="src.data.dir" location="/shared/data/metabolic/gene-summaries/current/"/>
    </source>
   <source name="mgi-identifiers" type="mgi-identifiers">
      <property name="src.data.dir" location="/shared/data/mgi/current"/>
    </source>
   <source name="rgd-identifiers" type="rgd-identifiers">
      <property name="src.data.dir" location="/shared/data/metabolic/rgd-identifiers/current"/>
    </source>
    <source name="so" type="so">
      <property name="src.data.file" location="../../bio/sources/so/so.obo"/>
    </source> 
    <source name="protein-atlas" type="protein-atlas">
     <property name="src.data.dir" location="/shared/data/metabolic/protein-atlas/current"/>
    </source>
    <source name="ensembl-human" type="ensembl" dump="true">
     <property name="src.data.dir" location="/shared/data/ensembl/metabolic/human/current"/>
    </source>
    <source name="ensembl-gwas-db-human" type="ensembl-gwas-db">
     <property name="source.db.name" value="ensembl.9606.variation"/>
    </source>
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="9606 10090"/>
      <property name="createinterpro" value="true"/>
      <property name="src.data.dir" location="/shared/data/uniprot/current/split/"/>
    </source>
<!--    <source name="uniprot-fasta" type="fasta" dump="true">
      <property name="fasta.taxonId" value="9606 10090"/>
      <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="/shared/data/uniprot/2010_09/"/>
      <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="uniprot-keywords" type="uniprot-keywords">
      <property name="src.data.dir" location="/shared/data/uniprot/current"/>
      <property name="src.data.dir.includes" value="keywlist.xml"/>
    </source>
    <source name="interpro" type="interpro">
      <property name="src.data.dir" location="/shared/data/interpro/current"/>
    </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"/>
      <property name="src.data.dir" location="/shared/data/go-annotation/metabolic/"/>
      <property name="src.data.includes" value="**/gene_association*"/>
    </source>
    <source name="kegg-pathway" type="kegg-pathway">
      <property name="src.data.dir" location="/shared/data/metabolic/kegg/current"/>
      <property name="kegg.organisms" value="9606 10090"/>
    </source>
    <source name="reactome" type="biopax">
      <property name="src.data.dir" location="/shared/data/metabolic/biopax/reactome/current/not-curated"/>
      <property name="biopax.organisms" value="9606"/>
      <property name="biopax.datasourcename" value="Reactome"/>
      <property name="biopax.datasetname" value="Reactome data set"/>
      <property name="biopax.curated" value="false"/>
    </source>
    <source name="psi-intact" type="psi" dump="true">
      <property name="src.data.dir" location="/shared/data/psi/intact/current"/>
      <property name="intact.organisms" value="9606 10090"/>
    </source>
    <source name="biogrid" type="biogrid">
      <property name="src.data.dir" location="/shared/data/metabolic/biogrid"/>
      <property name="src.data.dir.includes" value="*psi25.xml"/>
      <property name="biogrid.organisms" value="9606 10090"/>
    </source>
    <source name="pubmed-gene" type="pubmed-gene" dump="true">
      <property name="src.data.dir" location="/shared/data/pubmed/current"/>
      <property name="pubmed.organisms" value="9606 10090"/>
      <property name="src.data.dir.includes" value="gene2pubmed"/>
      <property name="infoFile" location="/shared/data/pubmed/current/gene_info"/>
    </source>
    <source name="omim" type="omim">
      <property name="src.data.dir" location="/shared/data/metabolic/omim/test"/>
    </source>
    <source name="ensembl-mouse" type="ensembl" dump="true">
      <property name="src.data.dir" location="/shared/data/ensembl/metabolic/mouse/current"/>     
      <property name="src.data.dir.includes" value="10090.xml"/>
    </source>
    <source name="ensembl-human-chr-fasta" type="fasta">
      <property name="fasta.taxonId" value="9606"/>
      <property name="fasta.dataSetTitle" value="Ensembl human 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="/shared/data/ensembl/homo_sapiens/current_core/fasta"/>
    </source>
    <source name="ensembl-mouse-chr-fasta" type="fasta">
      <property name="fasta.taxonId" value="10090"/>
      <property name="fasta.dataSetTitle" value="Ensembl mouse 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="/shared/data/ensembl/mus_musculus/current_core/fasta"/>
    </source>
    <source name="treefam" type="treefam">
      <property name="src.data.dir" location="/shared/data/treefam/current"/>
      <property name="src.data.dir.includes" value="ortholog.txt.table"/>
      <property name="geneFile" value="/shared/data/treefam/current/genes.txt.table"/>
      <property name="treefam.organisms" value="9606 10090 10116"/>
    </source>
    <source name="ensembl-compara" type="ensembl-compara">
      <property name="src.data.dir" location="/shared/data/metabolic/ensembl-compara"/>
      <property name="ensemblcompara.organisms" value="9606 10090 10116"/>
    </source>

    <source name="ensembl-snp-db-human" type="ensembl-snp-db" dump="true">
     <property name="source.db.name" value="ensembl.9606.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">
{'fraction_non_alphanumeric': 0.18146447250924863, 'fraction_numerical': 0.015435642301313944, 'mean_word_length': 4.025320512820513, 'pattern_counts': {'":': 0, '<': 278, '<?xml version=': 0, '>': 278, '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': '4118888', 'n_tokens_mistral': 5262, 'n_tokens_neox': 4969, 'n_words': 772}