The ChEMBL-og

As many of you know, SureChEMBL taps into the wealth of knowledge hidden in the patent documents. More specifically, SureChEMBL extracts and indexes chemistry from the full-text patent corpus (EPO, WIPO and USPTO; JPO titles and abstracts only) by means of automated text- and image-mining, on a daily basis. We have recently hosted a webinar about it which turned out to be very popular - for those who missed it, the video and slides are here . Besides the interface, SureChEMBL compound data can be accessed in various ways, such as UniChem and PubChem . The full compound dump is also available as a flat file download from our ftp server . Since the release of the SureChEMBL interface last September, we have received numerous requests for a way to access compound and patent data in a batch way. Typical use-cases would include retrieving all compounds for a list of patent IDs, or vice versa , retrieving all patents where one or more compounds have been extracted from. As a...

  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 many of you know, SureChEMBL is one of our most recent resources, which taps into the wealth of knowledge hidden in the patent documents. More specifically, SureChEMBL extracts and indexes chemistry from the full-text patent corpus (EPO, WIPO and USPTO) by means of automated text- and image-mining, tirelessly, on a daily basis. If you would like learn more about SureChEMBL, its applications and exciting recent developments and future plans, we'll be giving a free webinar on  Wednesday 11 March at 4pm GMT . Remember this is one of the times of year where daylight savings times may not be in sync, so check what time 4pm GMT is for your local timezone, for example, the time difference to Boston, MA at the moment is only 4 hours compared to the regular 5 hours. Please send us an email here to register your interest.  George

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...