Skip to main content

Table 2 Distinct drug-Health Outcome of Interest pairs by source

From: Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data

Source description

Drug and HOI mapping method

Distinct drug-HOI pairs in source

Distinct drug-HOI pairs in LAERTES (%)

Adverse drug reactions mined from US drug product labels using a validated natural language processing tool called SPLICER [29]

Drugs were coded using RxNorm and HOIs using MedDRA. The OMOP Standard Vocabulary was used to map MedDRA to SNOMED-CT.

272 436a

254 738 (93%)

Adverse drug events extracted from EU Summary of Product Characteristics by the PROTECT project

Drugs were mentioned by name and HOIs using MedDRA codes. Drug names were mapped to RxNorm using a combination of simple string matching and Bioportal ontology searches. Many combination products and some individual drugs were not mappable. All mappings were manually reviewed for accuracy.

26 989

24 537 (91%)

FDA Adverse Event Reporting System counts and Proportional Reporting Ratio from [45]

The OHDSI Usagi tool [46] was used to map drug and HOI mentions to RxNorm and MedDRA. The OMOP Standard Vocabulary was used to map MedDRA coded HOIs to SNOMED-CT. A paper describing the database and mapping method has been published [47].

3 766 382

2 753 078 (73%)

Abstracts from titles and abstracts indexed in MEDLINE that describe drug-HOI evidence according to MeSH indexing [48]

Drug and HOI concepts were both coded using MeSH. The OMOP Standard Vocabulary was used to map from MeSH drug concepts to RxNorm and MeSH HOI concepts to SNOMED-CT.

79 119b

77 395 (97.8%)

Sentence spans from titles and abstracts indexed in MEDLINE that describe drug-HOI evidence according to queries against the Semantic Medline database

Drug and HOI concepts were both coded using UMLS concept identifiers. The UMLS Metathesaurus MRCONSO table was used to map concepts to RxNorm, MeSH, MedDRA, and SNOMED-CT. The OMOP standard vocabulary was then used to map drug concepts only available as MeSH to RxNorm and HOI concepts only available as MedDRA or MeSH concepts to SNOMED-CT.

5 023b

2 813 (56%)

Chemical disease associations from the Comparative Toxicogenomics Database

Drug and HOI concepts were both coded using MeSH. The OMOP Standard Vocabulary was used to map from MeSH drug concepts to RxNorm and MeSH HOI concepts to SNOMED-CT.

503 835

432 850 (86%)

  1. aSPLICER drug-hoi pairs are at the clinical drug level. All other sources are at the ingredient level. bDoes not include drug-HOI evidence where the source refers to the drug by its MeSH pharmacologic group name. EU: European Union, FDA: Food and Drug Administration, HOI: Health outcome of Interest, OMOP: Observational Medical Outcomes Partnership, US: United States, MedDRA: Medical Dictionary for Regulatory Activities, MeSH: Medical Subject Headings
Back to article page

Journal of Biomedical Semantics

ISSN: 2041-1480