The ChEMBL-og

Easter is coming and for all those, who don't know what to do with their spare time and fancy entering a little competition, we've prepared a small challenge. Easter Egg? In software development, an Easter egg is funny (but harmless) and undocumented feature hidden from users in unusual places. Excel 97 has its Flight Simulator , FireFox about:robots address and Debian's apt-get has a moo command. The ChEMBL web services has now joined this list and we invite you to find its hidden feature and share with others. But why? We would like to encourage you to look at the source code of our web services.  Reading code is essential developer skill, as it helps in understanding how the code works. This can lead to the development of new software and/or improve an existing codebase. After skimming through the code, hopefully you will agree that it is well written and easy to extend. Let us know if you disagree, either by emailing us or creating a GitHub issue . We p...

  We have mentioned Beaker (a.k.a the ChEMBL cheminformatics utility web service), several times on the blog ( here , here and here ), but have not devoted an entire post to Beaker. Well, here it is. Beaker - what's this? It's a small utility, that makes chemistry software available securely over https . You no longer need to install a chemical toolkit in order to convert your molfile to SMILES or calculate descriptors. If you have an internet connection (if you can read this, chances are you do), you can use Beaker. We recommend you head over to the interactive online documentation ( https://www.ebi.ac.uk/chembl/api/utils/docs ), to see the full list of functionality it offers and try it with your own data. Which toolkits are used by Beaker? Under-the-hood Beaker is exposing the functionality of the RDKit cheminformatics library. Beaker's optical structure recognition methods use the OSRA library.   Do I need an API Key? As long as you are m...

When reviewing our old web services documentation ( https://www.ebi.ac.uk/chemblws/docs ), you will notice some methods can be accessed by both: GET and POST . One thing these methods have in common is that they all accept SMILES as search parameter. Why? Well, it turns out there are some SMILES, that can not be handled via GET, when using old web services. Take this SMILES as an example: [Na+].CO[C@@H](CCC#C\C=C/CCCC(C)CCCCC=C)C(=O)[O-] and you will see, that you can't construct a valid URL using ' https://www.ebi.ac.uk/chemblws/compounds/smiles/ ' as a base. To 'GET' around this issue, you will need to use POST. This is a bit sad, as it means you can not put a link to such a compound on your blog or ask about it on chemistry forum or send it to your friend via Skype :( What's more, if you would like to use POST for a non-SMILES method (e.g. get all assays by ChEMBL ID), you would also be out of luck. When reviewing the documentation of the new w...

As promised in our earlier post , here are some more details on making the most of the new ChEMBL web services. The best place to get started is to head over to the  documentation page: https://www.ebi.ac.uk/chembl/api/data/docs . There you will find the list of resources (e.g. Molecule, Target and Assay) that are available and their methods. More importantly you can also execute each method with your own or default parameters, and view the URL, the response content and response status code. This is definitely the quickest way to start familiarizing yourself with the new ChEMBL web services. Looking at the resources in more detail, you will find that each resource has three basic methods: 1. https://www.ebi.ac.uk/chembl/api/data/RESOURCE - will return all available objects of type RESOURCE from ChEMBL. An example could be https://www.ebi.ac.uk/chembl/api/data/molecule which returns all molecules (remember that data is paginated - more on this later). 2. https://www.ebi...