ChEMBL KNIME training?

                                    



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's that

jpo

free poll

ChEMBL Web Service Update 2: JSONP Support

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 data in from a trusted source enhances the functionality of the web application and makes the life of the developer much easier. Adding JSONP support to the ChEMBL Web Services allows users to now pull ChEMBL data into their web pages with minimal effort. So how do you add JSONP support? Simple, you add an extra argument to the to Web Service call which provides the name of a callback function, which is then used to wrap the regular JSON response.

Currently you can request a JSON response with the following URL:

https://www.ebi.ac.uk/chemblws2/compounds/CHEMBL941.json

To create a JSONP response you add the callback argument parameter (Note, you do not need to include .json and the callback argument can be any value):

https://www.ebi.ac.uk/chemblws2/compounds/CHEMBL941?callback=chembldata

We hope you find this useful and if you have any questions get in touch.

The ChEMBL Team

ChEMBL Web Service Update 1

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? Essentially we have rewritten the Web Services using the API (actually we use the ORM in this case) to interact with the ChEMBL data model. We have made this new set of Web Services available under the following base URL:

https://www.ebi.ac.uk/chemblws2

Those familiar with our current Web Services will notice we have added a ‘2’, to the end. An example call the current live service looks like:

https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1.json

and the same call to the new Web Services looks like:

https://www.ebi.ac.uk/chemblws2/compounds/CHEMBL1.json

To refresh yourself on all methods we currently make available please visit the Web Service Documentation page



The new Web Service base URL will provide you with all the same methods listed on page above and more importantly the format of the results returned by the Web Services will also be the same. Our plan going forward is to run both services for next 4-6 weeks and we ask users of the current ChEMBL Web Services to test the new versions (remember you just need to add a 2) and report back any issues encountered. Assuming we do not hit any major obstacles, after the 4-6 week period we will replace the current live services with the new ChEMBL API based services.



This first Web Service update is technology focused. We want to ensure the new services scale and perform well in the wild and that our end users do not notice a change (well we are hopefully expecting you to see a performance boost). Further down the line we will make some bigger changes to the Web Services, such as reviewing methods, attributes, naming conventions, introduce paging and more. We will obviously consult the community and allow for a period of transition before releasing any such changes. Now is the time to tell us if you have any must have new ws features.



Finally, it is not strictly true that the new Web Services are identical to the current live versions. There are a couple of new features we have built in, such as improved image rendering and JSONP responses. We will blog about these in new features in the next couple of days, but in the meantime please have a look at new ChEMBL Web Services and let us know how you get on.



The ChEMBL Team