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USEPA / ccdR

Predecessor to ctxR. Utilities for Interacting with the CTX APIs in R without prior API knowledge. All data is also available on the CompTox Chemical Dashboard (CCD) https://comptox.epa.gov/dashboard/
https://github.com/USEPA/ctxR
GNU General Public License v3.0
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Get exposure data mg/kg-day and get inchikeys #48

Open Jordi-Valls opened 5 months ago

Jordi-Valls commented 5 months ago

Dear all,

I recently used this R library and I missed some data that maybe I'm not able to find.

1- Using the API Exposure, I do not find information about the mg/kg-day information which is information of ExpoCast. For example, this information can be found in these two papers:

Wambaugh JF, Setzer RW, Reif DM, Gangwal S, Mitchell-Blackwood J, Arnot JA, Joliet O, Frame A, Rabinowitz J, Knudsen TB, Judson RS, Egeghy P, Vallero D, Cohen Hubal EA, 2013 High- Throughput Models for Exposure-Based Chemical Prioritization in the ExpoCast Project. Environ. Sci. Technol 130711145716006. 10.1021/es400482g

Wambaugh JF, Wang A, Dionisio KL, Frame A, Egeghy P, Judson R, Setzer RW, 2014 High Throughput Heuristics for Prioritizing Human Exposure to Environmental Chemicals. Environ. Sci. Technol 48, 12760–12767. 10.1021/es503583j [PubMed: 25343693]

Is there any way to retrieve this information from the Exposure API?

2- I want to mapp the DTXSIDS... To Inchikeys, In the API CHEMICAL I found one way to get the Inchikeys but if I execute by default do not work for me I receive the following error: Response Status: Unexpected token 'D', "DLFVBJFMPX"... is not valid JSON (CORS or Network Issue) Then, I do not receive any results.

3- How can I obtain a list of all Compounds from EPA? I need a mapping between your IDs DTXS and CASID or Inchikey, do you have any advice on how to proceed?

Thanks for your help,

Jordi

rachmaninoffpk commented 5 months ago

Hi Jordi,

Thank you for the questions.

  1. There are ongoing efforts to add endpoints to the Exposure APIs that will provide access to this and other exposure data. Additionally, we are developing out the functions to cover these endpoints so that data should be available in the future.

  2. Would you please provide a small reproducible example of the code you are using that generates this error, including the function call and input parameters? If there is a bug in the code causing this error, that would help us to find and address it.

  3. Accessing this amount of data would not be a good use case for the APIs, so the best way I can think of is downloading the most recent CCD chemical data. This data can be found at https://www.epa.gov/comptox-tools/downloadable-computational-toxicology-data#SCD. The files are large, but should provide a basis for the mapping you are trying to make. Additionally, if there are pieces of information missing from this but are accessible through the APIs, you might try batch searching on known identifiers from this download to augment the missing data.

Best,

Paul