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Replace chemical spreadsheet with comp tox query script #90

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sgosline opened this issue Oct 15, 2024 · 1 comment
Open

Replace chemical spreadsheet with comp tox query script #90

sgosline opened this issue Oct 15, 2024 · 1 comment
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@sgosline
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sgosline commented Oct 15, 2024

Currently we are using a static file that is pulled regularly from comptox to get chemical metadata. These are no here:
https://github.com/PNNL-CompBio/srpAnalytics/blob/main/data/CCDBatch_2022-01-26_AND_2021_11_05.xlsx

They are referenced in the sample mapping script here:

chemMeta<-rio::import(comptoxfile)|>#,

And eventually merged with a manual mapping of chemical Ids to comptox ids here:

chemMeta <- chemMeta%>%

There are two issues with this:

  1. the comptox data can be queried automatically, via the API here. This can be fixed now, as there is a way to collect comp tox data directly from the website. Use the API to collect the data instead of doing a static query.
    https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis-about (we'll have to get an API key and add it to github secrets)
  2. The mapping is provided by the tanguay lab and we need a way to account for additional chemicals. Not sure how to fix this just yet.

For now we can focus on #1.

@sgosline sgosline self-assigned this Oct 15, 2024
@christinehc
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christinehc commented Nov 27, 2024

Fixed in bf9ac33.

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