Is there a programmatically-accessible human pathogenicity database available?
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8.0 years ago
Dan D 7.3k

I'm working on a metagenomics project, and we'd like to be able to query the top species hits against some resource that would provide at least a True/False human pathogenicity association. Even better would be a scoring metric of some sort. I've seen a few web databases, but none of them fit the requirements of providing a programmatically-accessible pathogenicity value. PhiBase might be a good fit, but it's currently down.

Even if I need to download and run the database locally, or build something from one or more flat files, I'm totally fine with it. I'm just looking for some starting point at the moment.

pathogens database • 1.9k views
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8.0 years ago

see Database Of Host And Pathogen Pairs and @rdmpage 's blog ; http://iphylo.blogspot.com/2011/03/visualising-symbiome-hosts-parasites.html

"To illustrate the idea, below is the human "symbiome". This diagram shows all the taxa in GenBank arranged in a circle, with lines connecting those organisms that have DNA sequences where humans are recorded as their host. "

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That's funny, because I'm actually trying to add more context to the count tables that SURPI provides. As far as I know though, SURPI doesn't have any pathogenicity data in its reference set.

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