Estimated prevalence or incidence to diseases

General
1

Dear Team,

I am wondering are we able to generate estimated prevalence or incidence to diseases in Open Target platform?

Thanks.

Shicheng

2

Incidence/prevalence is a recurrent topic we haven’t able to crack. A few sources that I’m aware in which this information might be available in one form or another:

  • WHO - Has comprehensive data on the incidence of diseases per region/country
  • Orphanet has estimates on prevalence/incidence of rare diseases
  • Orphan drug designation - Can give us qualitative description of the indication incidence for the region of the regulatory agency.

@Shicheng_Guo did you have any particular methodology in mind?

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3

Approximate range for disease prevalence or incidence should be enough since everybody can understand the value will be quite different among different countries and races. Here are something we can try:

  1. National Health and Nutrition Examination Survey (NHANES)
  2. Surveillance, Epidemiology, and End Results (SEER) Program
  3. Global Burden of Disease Study (GBD)
  4. National Health Service (NHS) Digital
  5. European Disease Registries
  6. PubMed and Google Scholar
  7. ClinicalTrials.gov
  8. Centers for Disease Control and Prevention (CDC)
  9. World Bank Open Data
  10. Eurostat
4

Wikidata

I noticed Wikidata has a prevalence property (P1193) for diseases as well as an incidence property P2844.

Here’s a basic query (cannot figure out how to retain more metadata like the reference and population):

SELECT ?disease ?label ?prevalence
WHERE {
  ?disease wdt:P31 wd:Q12136.
  ?disease rdfs:label ?label.
  FILTER (LANG(?label) = "en")
  ?disease wdt:P1193 ?prevalence.
}
ORDER BY (?disease)
LIMIT 10
disease label prevalence
wd:Q127664 febrile seizure 0.04
wd:Q133823 migraine 0.126
wd:Q1338684 tension headache 0.891
wd:Q166907 cluster headache 0.001
wd:Q1935832 neurofibromatosis type II 0.000017806
wd:Q2067267 Niemann–Pick disease, type C 0.00000667
wd:Q219223 lactose intolerance 0.1
wd:Q219223 lactose intolerance 0.65

Ontologies

I wonder if a disease ontology like EFO or MONDO would be a good place to maintain these epidemiological metrics or whether that is out of scope of their purview?

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