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  1. NIF
  2. NIF-11892

DISCO: import data for CTG

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    • NIF

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      DISCO id: nif-0000-02683
      The current interop file is blank.

      Here's where to get the data:
      http://ctdbase.org/downloads/
      data is available as structured XML or flat files...not sure which is better. for now, i list the flat files. also, these tables seem to have both curated and inferred data, not sure if we want the inferred data or not (if we end up doing it ourselves). i think we should start with this, but we might consider actually requesting database dumps for the additional metadata.

      chemical-gene interactions:
      http://ctdbase.org/reports/CTD_chem_gene_ixns.tsv.gz

      chemical-disease reports:
      http://ctdbase.org/reports/CTD_chemicals_diseases.tsv.gz

      chemical-GO:
      http://ctdbase.org/reports/CTD_chem_go_enriched.tsv.gz

      chemical-pathway:
      http://ctdbase.org/reports/CTD_chem_pathways_enriched.tsv.gz

      gene disease:
      http://ctdbase.org/reports/CTD_genes_diseases.tsv.gz

      This site uses ontologies to describe a lot of the data, but their underlying data model is very rDB (http://ctdbase.org/tech/datamodels/pub/).

      Not sure if/how these interaction types need to be mapped to RO:
      http://ctdbase.org/reports/CTD_chem_gene_ixn_types.obo
      There's also a MESH/OMIM mapping file:
      http://ctdbase.org/reports/CTD_diseases.obo.gz
      And the exposure vocab:
      http://ctdbase.org/reports/CTD_exposure_ontology.obo
      These chemicals need to be mapped to chebi:
      http://ctdbase.org/reports/CTD_chemicals.tsv.gz

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              bandrow Anita Bandrowski (use this one!)
              nlw Nicole Washington
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