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Accessing SureChEMBL data in bulk




It is the peak of the summer (at least in this hemisphere) and many of our readers/users will be on holiday, perhaps on an island enjoying the sea. Luckily, for the rest of us there is still the 'sea' of SureChEMBL data that awaits to be enjoyed and explored for hidden 'treasures' (let me know if I pushed this analogy too far). See here and here for a reminder of SureChEMBL is and what it does. 

This wealth of (big) data can be accessed via the SureChEMBL interface, where users can submit quite sophisticated and granular queries by combining: i) Lucene fields against full-text and bibliographic metadata and ii) advanced structure query features against the annotated compound corpus. Examples of such queries will be the topic of a future post. Once the search results are back, users can browse through and export the chemistry from the patent(s) of interest. In addition to this functionality, we've been receiving user requests for local (behind the firewall), batch access of the SureChEMBL data almost since day one of releasing the interface last year. By such data, we mean not only the compound repository (which is available anyway) but also the comprehensive map of associations between compound and patents, i.e. which compound was extracted from which section of which patent, for all available compounds and patents. To address these requests, we currently provide two additional ways to access the SureChEMBL data:

1) The map file. This is a flat file including compound, patent and association information. The back file contains all associations for eligible patent documents published between 1960 and 2014. Since then, two more incremental update files have been available covering the first 2 quarters of 2015. More info on the structure of the file is found here and all files are available here. We will continue to add incremental updates quarterly. 

2) The data client. This is a script that firstly creates a relational database in the user's environment and then populates the database with SureChEMBL data it retrieves from our private ftp server on a nightly basis. In addition to the front file (the patent and compound info that arrives daily), the script can also fetch the back file for each past year and back-fill the database accordingly. In the end, the data client script effectively creates a local and live snapshot of the SureChEMBL database, which allows for further integration, querying, filtering, deployment, etc., on the users' side. More info on the details of the client can be found here and documentation on how to set the client up is available here. Note that the script will need credentials to access our private ftp server, which we are happy to provide if you ask. It is also worth mentioning that the data client provides more information in a more timely fashion than the map file (daily vs. quarterly) but it requires considerably more effort and resources to set it up, compared to reading a flat file. 

As usual, this is not all - there is soon going to be an additional way to batch-access the SureChEMBL data. As announced recently, an enhanced version of SureChEMBL data (chemical AND biological annotations from patents), will be semantically integrated in the OpenPHACTS system and will be part of the freely available OpenPHACTS API. This will be available later this year.


George

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