OpenTox Data APIs

data management

At Douglas Connect we focus on improving data management and data access solutions for scientific, industry and regulatory use. A very important effort along these lines was the development of REST style APIs to enable real time access to three of the most widely used toxicological data sources: The EPA's in-vitro ToxCast/Tox21 database (https://www.epa.gov/chemical-research/toxicity-forecaster-toxcasttm-data), the EPA's in-vivo ToxRefDB database (https://www.epa.gov/chemical-research/toxcast-toxrefdb-data-release) and the NIBIOHN's toxicogenomics Open TG-Gates database (http://toxico.nibiohn.go.jp/english/).

In the past, access to any of these datasets included manual downloading, unzipping, and finally either parsing with custom code or extracting subsets via MS Excel. Needless to say, such an approach slows down research and introduces a lot of potential for errors along the way.

By exposing these databases as simple APIs using the widely understood JSON serialisation format, we made it much easier to access their data using a wide variety of tools, from R to Python to KNIME to Javascript running in the browser. OpenAPI/Swagger definitions are used to document the APIs and enable automated discovery services etc. in the future.

The ToxCast/Tox21 and ToxRefDB APIs are currently in public beta with the Open-TGGates expected to follow soon. You can find their documentation here:

* ToxCast/Tox21 (http://toxcast-api.cloud.douglasconnect.com/beta/ui/)

* ToxRefDB (http://toxrefdb-api.cloud.douglasconnect.com/beta/ui/)

To enable easy browsing of the data served by the APIs, we are currently developing a web based data explorer tool that uses the APIs to show a nice interface to the data, complete with rich filtering and search. With every user operation, the URL is updated that can be used to query for exactly the currently visible data set directly from our APIs. Additionally, we plan to enable users to download the visible data as a standard CSV file.

The OpenTox Data Explorer is in early development and currently only shows data of ToxRefDB, but you can already take a look at it here: https://opentox-data-explorer.cloud.douglasconnect.com/

We care deeply about open science and as such it is a priority for us to open source such work. By doing this, we enable the scientific community to verify the flow of the data, from the automated downloading of the official data release to the final JSON response served by our APIs. The ToxCast/Tox21 API is already open source and available at GitHub (including the code for both the API itself and the importer that parses the official upstream data release). The APIs for ToxRefDB and Open TG-Gates will be open sourced in the near future.

If you have ever used any of these data sources, please give our new APIs a try - and if you are interested in exposing your own data in a similar way, we'd be very happy to talk to you!

 

Daniel Bachler is a Senior Software Engineer at Douglas Connect

 

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Douglas Connect manages collaborative projects to achieve goals in scientific research, infrastructure development or service provision. Effective collaboration requires many elements including coordination, culture, communications, common understanding, decision-making and interoperability.

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