ChEMBL Resources


Thursday, 6 October 2016

ChEMBL 22 release - technical notes

The ChEMBL 22 release brings lots of new data. But we also released some new software so if you are interested in technical details please read on.

1. First of all, please note that ChEMBL 22 is the last release where we provide Oracle 9i dumps.
Oracle 9i has been out of support now for at nearly a decade and shouldn't be in use anymore but please let us know if this is a problem. On the other hand, we will do our best to provide Oracle 12c dumps for the next release.

2. If you are using the python API client please upgrade it by running:

[sudo] pip install -U chembl_webresource_client

This will upgrade the client to the latest version which solves some minor bugs and adds an ability to search in document abstracts. It will also create a new cache so you will see new chembl data immediately. Otherwise, you will need to clear your cache manually.

3. New version (2.4.9) of the ChEMBL API has been released as well. This version includes:
 - new endpoints: tissue and target_relation
 - mechanism endpoint contains references now
 - solr index has been added to documents so their abstracts can be searched for example searching  for 'cytocine': api/data/document/search.json?q=cytokine
 - the outdated chemical cartridge used by API (Biovia Direct) has been updated from 6.3 to 2016 Direct. The result is better handling of SMILES string, for example this API call:[O--].[Fe++].OCC1OC(OC2C(CO)OC(OC3C(O)C(CO)OC(OCC4OC(OCC5OC(O)C(O)C(OC6OC(CO)C(O)C(OC7OC(COC8OC(COC9OC(CO)C(O)C(O)C9O)C(O)C(O)C8O)C(O)C(OC8OC(CO)C(O)C(OC9OC(CO)C(O)C(OC%2510OC(COC%2511OC(COC%2512OC(COC%2513OC(COC%2514OC(COC%2515OC(CO)C(O)C(O)C%2515O)C(O)C(OC%2515OC(CO)C(O)C%2515O)C%2514O)C(O)C(O)C%2513O)C(O)C(O)C%2512O)C(O)C(O)C%2511O)C(O)C(OC%2511OC(CO)C(O)C(O)C%2511O)C%2510O)C9O)C8O)C7O)C6O)C5O)C(O)C(O)C4O)C3O)C2O)C(O)C1O/70
works fine now.
 - status endpoint provides API software version as well as ChEMBL release version.
 - there are many smaller bug fixes and improvements.

4. Since our API is maturing we started preparing collection of embedable widgets written in JS/CSS/HTML that you can use on your website/blog/webapplication. This will be a base for our new ChEMBL website. An example widget providing some besic information about a ChEMBL compound can be found below, the code used to embed it is:

<object data="" width="800px" height="350px"></object>

Another example is an assay co-occurance matrix for compounds extracted from a single document. Again the code to embed is:

<object data="" width="800px" height="800px"></object>