Add FDA Orange Book/open fda/ndfrt/rxnorm Information

[stuppie]

It would be really useful to add (at a bare minimum) the statement that a compound is FDA approved (for something) https://www.accessdata.fda.gov/scripts/cder/ob/

Example: https://www.accessdata.fda.gov/scripts/cder/ob/results_product.cfm?Appl_Type=N&Appl_No=021588

The Active Ingredient string matches the preferred name from UNII, and so we can match these up by UNII

[stuppie]

Some other things that we can add, that are potentially useful

Each entry in the OpenFDA data (may) contain:

• Mechanism of action
• Physiologic effect
• Pharmacologic class
• Chemical structure class

These are defined by NDF-RT. Documentation on OpenFDA: https://open.fda.gov/api/reference/ (under SPL) Documentation from SPL: https://www.fda.gov/ForIndustry/DataStandards/StructuredProductLabeling/ucm162549.htm All possible values for the 4 types of classes are listed here: https://ndclist.com/pharma-class/ or here: http://bioportal.bioontology.org/ontologies/NDFRT (example)

Example:

{'application_number': ['ANDA202603'],
 'brand_name': ['Methoxsalen'],
 'generic_name': ['METHOXSALEN'],
 'is_original_packager': [True],
 'manufacturer_name': ['Actavis Pharma, Inc.'],
 'nui': ['N0000175879',
  'N0000175984',
  'N0000007909',
  'N0000010217',
  'N0000009801'],
 'package_ndc': ['45963-325-50'],
 'pharm_class_cs': ['Psoralens [Chemical/Ingredient]'],
 'pharm_class_epc': ['Psoralen [EPC]',
  'Photoactivated Radical Generator [EPC]'],
 'pharm_class_moa': ['Photoabsorption [MoA]'],
 'pharm_class_pe': ['Photosensitizing Activity [PE]'],
 'product_ndc': ['45963-325'],
 'product_type': ['HUMAN PRESCRIPTION DRUG'],
 'route': ['ORAL'],
 'rxcui': ['197947'],
 'spl_id': ['8a918c03-b9b3-4234-b0b5-c511bb0e8d73'],
 'spl_set_id': ['c6432c42-e53d-4077-bf7b-f33349349de6'],
 'substance_name': ['METHOXSALEN'],
 'unii': ['U4VJ29L7BQ']}

[stuppie]

Documentation for NDF-RT: https://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT%20Documentation.pdf NDF-RT contains many other properties that are useful:

has_Ingredient: chemical ingredient of a generic ingredient preparation or drug CI_ChemClass: contraindicated structural chemical class of another generic if coadministered with the generic ingredient preparation or drug CI_MoA: contraindicated mechanism of action of another generic if co-administered CI_PE: contraindicated physiological effect of another generic if co-administered CI_with: therapeutic or co-morbid contraindication of a generic ingredient preparation or drug has_active_metabolites: chemically-active metabolic product of a generic ingredient preparation or drug metabolized_by: chemical or enzyme which metabolizes a generic ingredient preparation or drug has_MoA: molecular, subcellular, or cellular level functional activity of a generic ingredient preparation or drug with the generic ingredient preparation or drug has_PE: tissue, organ, or organ system level functional activity of a generic ingredient preparation or drug with the generic ingredient preparation or drug has_PK: absorption, distribution, and elimination of a generic ingredient preparation or drug site_of_metabolism: metabolic anatomic site of a generic ingredient preparation or drug may_treat: therapeutic use or indication of a generic ingredient preparation or drug may_prevent: preventative use or indication of a generic ingredient preparation or drug may_diagnose: diagnostic use or indication of a generic ingredient preparation or drug induces: therapeutic effect or state caused by a generic ingredient preparation or drug (e.g., abortifacient induces therapeutic abortion) effect_may_be_inhibited_by: preparation or drug which interferes with therapeutic effect of a generic ingredient preparation or drug

The may_treat edges were already added by Sebastian, but need to be updated.

An example: http://bioportal.bioontology.org/ontologies/NDFRT?p=classes&conceptid=N0000021984 http://purl.bioontology.org/ontology/NDFRT/N0000145802

[stuppie]

Counts of the number of edges that exist for each property, using only the ~10k NUI IDs where the RXCUI for it exists in Wikidata. Note: there are 37957 NDFRT entries. The ~30k that I'm not looking at are mostly dosage forms or packaging types (i.e. 'ALLANTOIN 0.2%/AMINACRINE 0.2%/SULFANILAMIDE 15% CREAM,VAG' and 'ALLANTOIN 0.5%/DIPHENHYDRAMINE HCL 2% CREAM,TOP')

    {'CI_ChemClass {NDFRT}': 91,
     'CI_MoA {NDFRT}': 72,
     'CI_PE {NDFRT}': 46,
     'CI_with {NDFRT}': 1106,
     'effect_may_be_inhibited_by {NDFRT}': 1,
     'has_Chemical_Structure {FDASPL}': 393,
     'has_Chemical_Structure {FMTSME}': 1,
     'has_DoseForm {NDFRT}': 4647,
     'has_Ingredient {NDFRT}': 2104,
     'has_MoA {FDASPL}': 669,
     'has_MoA {NDFRT}': 1468,
     'has_PE {FDASPL}': 202,
     'has_PE {NDFRT}': 1385,
     'has_PK {NDFRT}': 22,
     'has_active_metabolites {NDFRT}': 4,
     'induces {NDFRT}': 65,
     'may_diagnose {NDFRT}': 50,
     'may_prevent {NDFRT}': 397,
     'may_treat {NDFRT}': 1425,
     'site_of_metabolism {NDFRT}': 22}