Cistrome DB Toolkit Data

This wiki page contains information about the technical aspects of Toolkit for Cistrom Data Browser (hereafter, Toolkit, http://dbtoolkit.cistrome.org/), such as API endpoints and file types.

This Toolkit seems to deal with identical data compared with Cistrome Data Browser, but their data seems to be grouped by different attributes. Because of this, we may want to use Toolkit API as well in our Wrapper.

In Cistrome Data Browser, we can query using a certain 'transcription factors (TF)' to find samples that used the TF as a main experimental condition (TF => Samples). On the other hand, in Toolkit, we can query using a certain gene (or a genome interval) to find TFs (and related samples) that are known to target the gene(s) (Target Gene(s) => TFs/Samples).

One challenge is that, unlike Cistrome Data Browser, this site seems to show Citrome data directly in HTML files, without explicitly requesting for JSON format data.

List of Samples by Gene

The following URL query for samples by a gene name, i.e., GAPDH.

http://dbtoolkit.cistrome.org/?specie=hg38&keyword=GAPDH&factor=factor&distance=10k

This URL returns HTML file of the whole result page, and we can get table data in csv format from the following div element:

<div class="container" id="resultPanel" v-if="loadData({...}) ...></div>

Individual Sample Metadata

The URL to query for metadata of each sample shown in Inspector View is identical to that of Cistrome Data Browser.

http://dc2.cistrome.org/api/inspector?id={cid}

TODO

• A better way to get the query table, other than an HTML file?
• Can we get {cid} from the csv file?