Activity Heat Map from ChEMBL ID webservice

JB 2015-05-08

PURPOSE:

Inspired by a a colleague who wanted to see activities of her compound in ChEMBL, and I tried to make a one page visualization. The original protocol does similarity search, but hie release doesn't (no webservice for similarity). I also wanted to use the webservice available so I have access to the latest ChEMBL data all the time, plus it is as quick as a query.

Please find the attached protocols that allows the users to draw a compound, do an exact search on ChEMBL, display activity heat map for this compounds per target/per organism, or per target only; give the possiblitiy to display article title and activity related to the cells in the heat map.

Most of the data displayed can't be linked back to ChEMBL via the assay description, or compound. The article is linked to the journal via an url retreived using the

http://www.ebi.ac.uk/citexplore/ SOAP webservice.

Please read the Help document to get more info

USAGE:

Import the protocol folder into your Pipeline Pilot 8.5 client (or 8.0). And then replace all the protocol links accordingly: see the red sticky notes.

The help file with installation and description is attached.

The following input is required to run the protocol:

Structure or ChEMBL_ID

The heat map protocol requires a ChEMBL_ID and is link to the Article. However it doesn't require the other two protocol to runs if you have already a system to get ChEMBL_ID.

Run

Once a compound is found heat maps are displayed if activities are found for your compound (Ki, IC50, EC50)

Then click on cell to display articles related to it (title, link, activity, reference of the compound in the paper, target name)

A Tab Bioactivities contains endpoints of the heat map, and any other recorded data. Three links are there: one to ChEMBL, one to display top 10 articles with most endpoints, and one to display top 10 articles with most targets where the activity is IC50, Ki, EC50...

REQUIREMENTS:

Pipeline Pilot 8.5 (or 8.0 may be)

Chemistry Collection

Reporting Collection

Possiblity to call ebi webservices, via url and SOAP call

DISCLAIMER: This custom protocol is compatible with 8.5.0. It is provided "as is" and is NOT supported by me nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.

You can play with the protocols, modify them, republish them here, or if you want more functionality feel free to ask: if I have time, I may do it.

ACKNOWLEGEMENT: Thanks to Craig Sheperd for the help on JSON, and to Malcom Baird to tell me that I couldn't link rows and columns of heat map (saved me time). And my colleagues in Dundee who tried it. (and Luke Fisher for the template to post this post).

Cheers,

Jérémy

PICTURES: