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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)
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.
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:
srpAnalytics/sampleChemMapping/mapSamplesToChems.R
Line 217 in a810f2a
And eventually merged with a manual mapping of chemical Ids to comptox ids here:
srpAnalytics/sampleChemMapping/mapSamplesToChems.R
Line 234 in a810f2a
There are two issues with this:
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)
For now we can focus on #1.
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