Dataset Open Access

Drug Indications Extracted from FAERS

Stupp, Gregory S; Su, Andrew I


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{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<p>This dataset contains drug indications extracted from the&nbsp;FDA Adverse Event Reporting System (<a href=\"https://www.fda.gov/drugs/guidancecomplianceregulatoryinformation/surveillance/adversedrugeffects/\">FAERS</a>).</p>\n\n<p>Source code here:&nbsp;<a href=\"https://github.com/stuppie/faers\">https://github.com/stuppie/faers</a></p>\n\n<p><strong>Method Outline</strong></p>\n\n<ul>\n\t<li>Data files are extracted from zip files, parsed from csvs, and imported into a MySQL database (see&nbsp;parser.py).</li>\n\t<li>Duplicate records are then de-duplicated by taking only the most recent version for each case ID (see&nbsp;dedupe.py).</li>\n\t<li>Indications are normalized by matching to UMLS terms by string matching. Cross-references to Human Phenotype Ontology are pulled from UMLS and xrefs to Monarch Disease Ontology (MONDO) are pulled from MONDO using the UMLS xrefs. (See&nbsp;normalize_indications.py)</li>\n\t<li>Drugs names are normalized first by applying a few simple string cleaning operations (strip, fix slashes and periods). Then they are attempted to be matched to rxnorm by exact string matching. Those that don&#39;t match are run against rxnorm&#39;s <a href=\"https://rxnav.nlm.nih.gov/RxNormAPIs.html#uLink=RxNorm_REST_getApproximateMatch\">approximate matching service</a>, and are accepted if the score is higher than&nbsp;67/100. The matched rxnorm CUIs are then mapped to the their Ingredient level rxnorm ID. (See&nbsp;normalize_drugs.py)</li>\n\t<li>Indications are then retrieved for each drug ingredient and filtered to require a minimum of 20 individual occurances. (See&nbsp;get_indications.py)</li>\n</ul>", 
  "license": "https://creativecommons.org/publicdomain/zero/1.0/legalcode", 
  "creator": [
    {
      "affiliation": "The Scripps Research Institute", 
      "@id": "https://orcid.org/0000-0002-0644-7212", 
      "@type": "Person", 
      "name": "Stupp, Gregory S"
    }, 
    {
      "affiliation": "The Scripps Research Institute", 
      "@id": "https://orcid.org/0000-0002-9859-4104", 
      "@type": "Person", 
      "name": "Su, Andrew I"
    }
  ], 
  "url": "https://zenodo.org/record/1436000", 
  "datePublished": "2018-09-28", 
  "version": "2018q2", 
  "keywords": [
    "faers, drug indications, fda, drugs"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/6eda3742-fb23-405b-96ec-7254bb83bf51/faers_indications.csv", 
      "encodingFormat": "csv", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.1436000", 
  "@id": "https://doi.org/10.5281/zenodo.1436000", 
  "@type": "Dataset", 
  "name": "Drug Indications Extracted from FAERS"
}
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