Does anyone know of a dataset relating:

  • bacteria (not viruses or fungi)
  • infectiousness
  • symptoms

...or something of the sort?
I'm looking to classify infectiousness (ie. infectious/not infectious) via bacterial genomic sequencing/metadata. I have the capability to match names to genome fragments from other sets.

  • Post has been updated – Zach Eisner Feb 20 '17 at 3:29
  • This is not a binary distinction. Many bacteria can be present but have no disease. Additionally, some bacteria cause all manner of conditions. Strep, for example, can cause infections in every part of the body. The type of dataset you would need is highly dependent upon the questions you are trying to answer. There may be better ways to get at your answer if you can clarify the questions you are trying to ask. – Praxiteles Feb 21 '17 at 22:04
  • If you have NLP tools with bacteria names - you can parse eMedicine.com which will give you diagnoses and bacteria causing them. – Praxiteles Feb 21 '17 at 22:05
  • @Praxiteles Thank you! to clarify, the question is if the bacteria is known to elicit any symptoms in humans, and if so, what are they. – Zach Eisner Feb 22 '17 at 3:26
  • A single bacteria can elicit hundreds even thousands of different symptoms - and the overlap is immense. (i.e. staph or strep could cause the various symptoms associated with infections of the ear, skin (anywhere on the body), respiratory system, throat, wounds, post-surgical (internally), eyes, sinuses and more. New discoveries occur every week. The number of symptoms is almost incalculable. Additionally, many infections are multi-microbial. Lastly, many bacteria are just colonizers.) What are you trying to solve with having symptoms? It is possible your project may need a different approach. – Praxiteles Feb 23 '17 at 6:10

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