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

  <sources>

    <source name="ensembl-snp-db-human" type="ensembl-snp-db" dump="true">
      <property name="source.db.name" value="ensembl.9606.variation" />
      <property name="organism" value="9606" />
      <property name="sources" value="dbSNP" />
    </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="ensembl-hgnc" type="ensembl-hgnc">
      <property name="src.data.dir" location="/micklem/data/ensembl-ids/current" />
    </source>
    <source name="ncbi-summaries" type="ncbi-summaries">
      <property name="src.data.dir" location="/micklem/data/metabolic/gene-summaries/current/" />
    </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>
    <source name="so" type="so">
      <property name="src.data.file" location="../../bio/sources/so/so.obo" />
    </source>

<!--
    <source name="arrayexpress-atlas-E-MEXP-2559" type="arrayexpress-atlas">
      <property name="src.data.dir" location="/micklem/data/metabolic/array-express/E-MEXP-2559/" />
    </source>

    <source name="arrayexpress-atlas" type="arrayexpress-atlas" dump="true">
      <property name="src.data.dir" location="/micklem/data/metabolic/array-express/E-MTAB-62/" />
    </source>
-->

    <source name="protein-atlas" type="protein-atlas">
      <property name="src.data.dir" location="/micklem/data/metabolic/protein-atlas/current" />
    </source>
    <source name="ensembl-human" type="ensembl-core" dump="true">
      <property name="src.data.dir" location="/micklem/data/ensembl/homo_sapiens/current_core" />
      <property name="src.data.dir.includes" value="9606.xml" />
    </source>
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="9606 10090" />
      <property name="createinterpro" value="true" />
      <property name="src.data.dir" location="/micklem/data/uniprot/current/" />
      <property name="loadtrembl" value="false"/>
    </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="/micklem/data/old_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="/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="psi-mi-ontology" type="psi-mi-ontology">
      <property name="src.data.file" location="/micklem/data/psi/ontology/current/psi-mi.obo" />
    </source>
    <source name="mgi-alleles" type="mgi-alleles">
      <property name="src.data.dir" location="/micklem/data/metabolic/mouse-pheno/current" />
    </source>
    <source name="mammalian-phenotype-ontology" type="mammalian-phenotype-ontology">
      <property name="src.data.file" location="/micklem/data/metabolic/mouse-pheno/current/MPheno_OBO.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" />
      <property name="src.data.dir" location="/micklem/data/go-annotation/metabolic" />
      <property name="src.data.includes" value="**/gene_association*" />
    </source>
    <source name="hpo" type="hpo">
      <property name="src.data.file" location="/micklem/data/hpo/hp.obo" />
    </source>
    <source name="psi-intact" type="psi" dump="true">
      <property name="src.data.dir" location="/micklem/data/psi/intact/current" />
      <property name="intact.organisms" value="9606 10090" />
    </source>
    <source name="biogrid" type="biogrid">
      <property name="src.data.dir" location="/micklem/data/biogrid/current" />
      <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="/micklem/data/pubmed/current" />
      <property name="pubmed.organisms" value="9606 10090" />
      <property name="src.data.dir.includes" value="gene2pubmed" />
    </source>
    <source name="omim" type="omim">
      <property name="src.data.dir" location="/micklem/data/metabolic/omim/current" />
    </source>
    <source name="ensembl-mouse" type="ensembl-core" dump="true">
      <property name="src.data.dir" location="/micklem/data/ensembl/mus_musculus/current_core" />
      <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="/micklem/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="/micklem/data/ensembl/mus_musculus/current_core/fasta" />
    </source>
    <source name="ensembl-compara" type="ensembl-compara" dump="true">
      <property name="src.data.dir" location="/micklem/data/ensembl-compara/current" />
      <property name="ensemblcompara.organisms" value="9606 10090 10116" />
    </source>

<!--
    <source name="ensembl-snp-db-mouse" type="ensembl-snp-db" dump="true">
        <property name="source.db.name" value="ensembl.10090.variation"/>
    </source>
-->

    <source name="kegg-pathway" type="kegg-pathway">
      <property name="src.data.dir" location="/micklem/data/metabolic/kegg/current" />
      <property name="kegg.organisms" value="9606 10090" />
    </source>
    <source name="reactome" type="biopax">
      <property name="src.data.dir" location="/micklem/data/reactome/current" />
      <property name="biopax.organisms" value="9606 10090" />
      <property name="biopax.datasourcename" value="Reactome" />
      <property name="biopax.datasetname" value="Reactome data set" />
      <property name="biopax.curated" value="false" />
    </source>
    <source name="huge-gwas" type="huge-gwas" dump="true">
      <property name="src.data.dir" location="/micklem/data/metabolic/huge/current" />
    </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" dump="true">
      <property name="src.data.file" location="build/organisms.xml" />
    </source>

<!--
    <source name="panther" type="panther">
          <property name="src.data.dir" location="/micklem/data/panther/current"/>
          <property name="panther.organisms" value="7227 6239 9606 10090 10116 7955"/>
    </source>

    <source name="homologene" type="homologene">
          <property name="src.data.dir" location="/micklem/data/homologene/current"/>
          <property name="homologene.organisms" value="9606 10090"/>
    </source>
-->

  </sources>

  <post-processing>
    <post-process name="create-references" />
    <post-process name="transfer-sequences" dump="true" />

    <!-- this runs the postprocessing steps in all sources -->
    <post-process name="do-sources" />
    <post-process name="create-gene-flanking-features" />

    <post-process name="create-bioseg-location-index" />
    <post-process name="create-overlap-view" />

    <post-process name="summarise-objectstore" />
    <post-process name="create-autocomplete-index" />
    <post-process name="create-search-index" />
    <post-process name="create-attribute-indexes" />
  </post-processing>
</project>
<commit_msg>updated project.xml #291<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="humanmine.properties" />
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties" />

  <sources>

    <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="ensembl-hgnc" type="ensembl-hgnc">
      <property name="src.data.dir" location="/micklem/data/ensembl-ids/current" />
    </source>
    <source name="ncbi-summaries" type="ncbi-summaries">
      <property name="src.data.dir" location="/micklem/data/metabolic/gene-summaries/current/" />
    </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>
    <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="/micklem/data/metabolic/protein-atlas/current" />
    </source>
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="9606 10090" />
      <property name="createinterpro" value="true" />
      <property name="src.data.dir" location="/micklem/data/uniprot/current/" />
      <property name="loadtrembl" value="false"/>
    </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="psi-mi-ontology" type="psi-mi-ontology">
      <property name="src.data.file" location="/micklem/data/psi/ontology/current/psi-mi.obo" />
    </source>
    <source name="mgi-alleles" type="mgi-alleles">
      <property name="src.data.dir" location="/micklem/data/metabolic/mouse-pheno/current" />
    </source>
    <source name="mammalian-phenotype-ontology" type="mammalian-phenotype-ontology">
      <property name="src.data.file" location="/micklem/data/metabolic/mouse-pheno/current/MPheno_OBO.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" />
      <property name="src.data.dir" location="/micklem/data/go-annotation/metabolic" />
      <property name="src.data.includes" value="**/gene_association*" />
    </source>
    <source name="hpo" type="hpo">
      <property name="src.data.file" location="/micklem/data/hpo/hp.obo" />
    </source>
    <source name="psi-intact" type="psi" dump="true">
      <property name="src.data.dir" location="/micklem/data/psi/intact/current" />
      <property name="intact.organisms" value="9606 10090" />
    </source>
    <source name="biogrid" type="biogrid">
      <property name="src.data.dir" location="/micklem/data/biogrid/current" />
      <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="/micklem/data/pubmed/current" />
      <property name="pubmed.organisms" value="9606 10090" />
      <property name="src.data.dir.includes" value="gene2pubmed" />
    </source>
    <source name="omim" type="omim">
      <property name="src.data.dir" location="/micklem/data/metabolic/omim/current" />
    </source>
    <source name="kegg-pathway" type="kegg-pathway">
      <property name="src.data.dir" location="/micklem/data/metabolic/kegg/current" />
      <property name="kegg.organisms" value="9606 10090" />
    </source>
    <source name="reactome" type="biopax">
      <property name="src.data.dir" location="/micklem/data/reactome/current" />
      <property name="biopax.organisms" value="9606 10090" />
      <property name="biopax.datasourcename" value="Reactome" />
      <property name="biopax.datasetname" value="Reactome data set" />
      <property name="biopax.curated" value="false" />
    </source>
    <source name="huge-gwas" type="huge-gwas" dump="true">
      <property name="src.data.dir" location="/micklem/data/metabolic/huge/current" />
    </source>
    <source name="panther" type="panther">
          <property name="src.data.dir" location="/micklem/data/panther/current"/>
          <property name="panther.organisms" value="7227 6239 9606 10090 10116 7955"/>
    </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" dump="true">
      <property name="src.data.file" location="build/organisms.xml" />
    </source>
  </sources>

  <post-processing>
    <post-process name="create-references" />
    <post-process name="transfer-sequences" dump="true" />

    <!-- this runs the postprocessing steps in all sources -->
    <post-process name="do-sources" />
    <post-process name="create-gene-flanking-features" />

    <post-process name="create-bioseg-location-index" />
    <post-process name="create-overlap-view" />

    <post-process name="summarise-objectstore" />
    <post-process name="create-autocomplete-index" />
    <post-process name="create-search-index" />
    <post-process name="create-attribute-indexes" />
  </post-processing>
</project>

{'fraction_non_alphanumeric': 0.18217149907464528, 'fraction_numerical': 0.01579272054287477, 'mean_word_length': 3.7665392531608353, 'pattern_counts': {'":': 0, '<': 302, '<?xml version=': 0, '>': 302, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 11}, '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': '3179475', 'n_tokens_mistral': 5634, 'n_tokens_neox': 5325, 'n_words': 786}