The ChEMBL-og

                                     We recently did some KNIME training for ChEMBL at a workshop, and it was very popular. It made us think a little about just how much was available within Knime for ChEMBL, and we thought we'd ask if there was interest in us running a specific, detailed course on ChEMBL/KNIME next year. So here's a poll. We'll keep this open for a month (i.e. closes 18th November 2013) and then decide what to do (if anything). The stoopid free poll server I sued doesn't like the browser safari - so I'll transfer across to another system over the weekend, and try and transfer votes. Thank you to those that have voted so far. Would you be interested in Knime ChEMBL training? Yes - I'd like a two day course at the EBI next year Yes - I'd like webinars Yes - I'd like you to visit our lab (charge involved) Yes - but not from you guys. No - Knime, what'...

We posted earlier in the week about some behind the scenes changes we had made to our Web Services. Having read that post (if you missed the post and use our Web Services please take a look), you will know we setup a temporary base URL to allow users to test the new ChEMBL API powered services. The base URL is: https://www.ebi.ac.uk/chemblws2 We have made it straightforward for users to test the new services as all current methods are available using the new base URL. As well as maintaining existing functionality, we have also been able to add a couple of new features, the first of which is JSONP support. Those familiar with web application development will be familiar with the issue of requesting data from a domain different from that of the domain the web application is running. This type of data requested is prevented by the web browser, due to the enforcement of the same-origin policy. This is an important security concept, but there are times when it being able pull...

Over the last the year we have be doing a lot work designing and building an API layer to the ChEMBL database. The reason for adding this programmatic interface is to simplify many of the daily tasks we carry out on the database. From a technical perspective the API is actually a series Object Relational Mapper (ORM) classes built on top of the ChEMBL database using the Python Django web framework . For many of our daily programmatic tasks we use the ORM directly, but we also expose the ORM as a RESTful Interface using Tastypie . Some examples tools and processes currently using the new API include the ChEMBL twitter bot and the database migration process (creating PostgreSQL and MySQL versions of the ChEMBL Oracle database during the ChEMBL release cycle). We are now at the stage where we can start to think about updating some of the existing larger services to run off the new API and first of these to make the transition are the ChEMBL Web Services. So, what have we done? Ess...

Here's a little tip that may be of some use to you. The compound name search feature will also match substrings, so it is easy to type in a USAN/INN stem, and then retrieve all matching compounds - for example, "gliptin" will retrieve all DPP-IV inhibitors with non-proprietary (formal) names. This is pretty useful - of course the substring search functionality is not restricted to USANs/INNs. A list of the current USAN stems is here . Note, they were never designed to be orthogonal, so the low complexity ones will give a lot of false positives.....