Simple comparison between CTDquerier R package and CTDbase Batch Query web tool
4 May 2019
Package
CTDquerier 1.5.0
Contents
1 Introduction
1.1 The Comparative Toxicogenomics Database
The Comparative Toxicogenomics Database (CTDbase; http://ctdbase.org) is a public resource for toxicogenomic information manually curated from the peer-reviewed scientific literature, providing key information about the interactions of environmental chemicals with gene products and their effect on human disease [1][2].
1.2 CTDquerier R package
CTDquerier is an R package that allows to R users to download basic data from CTDbase about genes, chemicals and diseases. Once the user’s input is validated allows to query CTDbase to download the information of the given input from the other modules.
2 Quering The Comparative Toxicogenomics Database
CTDbase offers a public web-based interface that includes basic and advanced query options to access data for sequences, references, and toxic agents, and a platform for analysis sequences.
2.1 Keyword Search
In order to query CTDbase with a single term (aka. a gene, a chemical or a diseases) users can access to the web portal and use the keyword search.
The Comparative Toxicogenomics Database - Web Portal
Looking for the associations in CTDbase for the following set of then genes of interest implies to perform ten queries using this interface.
Follows the summary page of the results obtained after searching for the term XKR4:
The Comparative Toxicogenomics Database - Summary results for XKR4
2.2 Batch Query
The Batch Query tool (http://ctdbase.org/tools/batchQuery.go) is a provided by CTDbase and allows to download custom data associated with a set of chemicals, diseases and genes amount others.