Skip to main content

SureChEMBL - Chemical Structure Information in Patents


Today we have announced that we are taking over the running of the SureChem system from Digital Science. We have renamed this SureChEMBL to reflect the history and provenance of the technology and engineering, but also to align it with it's new home and future, we like the name, and hope you do. We are delighted that this has happened - Nicko and the team at Digital Science have been great, and the more we have dug in to how it works, the more we have appreciated the design and vision that they had.

If there is one consistent piece of feedback we get about ChEMBL it is in encouraging us to add patent data to what we do. So now we have, but because the data from patents is different in detail from that reported in the published literature, we will keep the databases separate, but closely integrated.

For those of you that are already SureChem users you will be familiar with the functionality and how it works; but for those that weren't SureChEMBL takes feeds of full text patents, identifies chemical objects from either the in-line text or from images and adds 2-D chemical structures. This is then loaded into a database and is searchable by chemical structure, so you can do substructure, similarity searching and so forth - all the good things you'd expect from a chemical database. This chemical search functionality is unavailable from the public, published patent documents, and is really essential for anyone seriously using the patent literature. Oh, and the system does this live, so as patents are published, they are processed and added to the system - the delay between publication and structures being available in SureChEMBL is about a day when converted from text, and a few days when converted from image sources.



SureChEMBL is hosted on the cloud - it's quite a complicated AWS solution, and it will take a few months for us to assume complete control of all the various parts, and, importantly keep things running smoothly behind the scenes, so the continuous access to fresh patent data is maintained.

SureChEMBL uses a number of third part software products in its operation, and arranging the licenses and permissions has been complex, and is still ongoing. The 3rd party software and data feeds used in SureChEMBL include:

Name to structureChemAxon, ACD/Labs, Perkin Elmer, OpenEye, OPSIN, NextMove
Chemical cartridge: ChemAxon
Image to structureKey Module
Patent data: FairView (IFI Claims) – processed patents, TwinDolphin – patent PDFs

These guys have all been a pleasure to work with so far, and SureChEMBL is a great showcase of their respective technologies and data:

We will host the system at the primary urls http://www.ebi.ac.uk/surechembl and also at http://www.surechembl.org - at the moment , these redirect to www.surechem.org, but as we switch things over they will point to servers provisioned by our team, so please start using these new urls for future access, although the original urls will continue to work into the future.

One of the more complicated things to transfer is the user accounts system - we can't simply transfer them over - and so have a plan to mail batches of users once a new sign-on system is in place in order to invite them to sign up to the new user account system. If you are not currently a registered user, please sign up with the current system, and we'll invite you to transfer over to our sign-on system once things are ready.

The EMBL-EBI has a broad range of life-science chemistry resources, and we integrate across chemistry related content using a chemical structure integration system call UniChem. In overview the EMBL-EBI chemistry resources include the following.



The future? - well the future is exciting, and we have lots of ideas to actively develop the SureChEMBL system. To be clear though, doing this will rely on us getting funding, and we're working hard on this. Some of the ideas we have for SureChEMBL include:
  • Put SureChEMBL chemical content into UniChem
  • Add sequence searching
  • Add disease term, animal model, etc. indexing
  • Development of community KNIME nodes
  • Add links to/from Europe PMC
  • Ligand Ensemble-based mapping of ChEMBL literature to patents
  • Refactor interface for EMBL look and feel
  • Extend image extraction retrospectively from 2006 using spot priced compute from AWS
  • Provide weekly/monthly feed of patent structures to PubChem
  • Add chemical structure tagging & search to full text content of Europe PMC
But one of the first things we plan to do is index genes and targets (in collaboration with local SME SciBite) and provide an RDF form of the data and REST web services as part of the IMI OpenPHACTS project.

In the new year, we will run a webinar on SureChEMBL (which we will announce here), but in the mean-time we're very happy to take questions on the SureChEMBL support email address surechembl-help (at) ebi.ac.uk.

jpo

Comments

Popular posts from this blog

A python client for accessing ChEMBL web services

Motivation The CheMBL Web Services provide simple reliable programmatic access to the data stored in ChEMBL database. RESTful API approaches are quite easy to master in most languages but still require writing a few lines of code. Additionally, it can be a challenging task to write a nontrivial application using REST without any examples. These factors were the motivation for us to write a small client library for accessing web services from Python. Why Python? We choose this language because Python has become extremely popular (and still growing in use) in scientific applications; there are several Open Source chemical toolkits available in this language, and so the wealth of ChEMBL resources and functionality of those toolkits can be easily combined. Moreover, Python is a very web-friendly language and we wanted to show how easy complex resource acquisition can be expressed in Python. Reinventing the wheel? There are already some libraries providing access to ChEMBL d

ChEMBL 29 Released

  We are pleased to announce the release of ChEMBL 29. This version of the database, prepared on 01/07/2021 contains: 2,703,543 compound records 2,105,464 compounds (of which 2,084,724 have mol files) 18,635,916 activities 1,383,553 assays 14,554 targets 81,544 documents Data can be downloaded from the ChEMBL FTP site:   https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29 .  Please see ChEMBL_29 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29/chembl_29_release_notes.txt New Deposited Datasets EUbOPEN Chemogenomic Library (src_id = 55, ChEMBL Document IDs CHEMBL4649982-CHEMBL4649998): The EUbOPEN consortium is an Innovative Medicines Initiative (IMI) funded project to enable and unlock biology in the open. The aims of the project are to assemble an open access chemogenomic library comprising about 5,000 well annotated compounds covering roughly 1,000 different proteins, to synthesiz

Identifying relevant compounds in patents

  As you may know, patents can be inherently noisy documents which can make it challenging to extract drug discovery information from them, such as the key targets or compounds being claimed. There are many reasons for this, ranging from deliberate obfuscation through to the long and detailed nature of the documents. For example, a typical small molecule patent may contain extensive background information relating to the target biology and disease area, chemical synthesis information, biological assay protocols and pharmacological measurements (which may refer to endogenous substances, existing therapies, reaction intermediates, reagents and reference compounds), in addition to description of the claimed compounds themselves.  The SureChEMBL system extracts this chemical information from patent documents through recognition of chemical names, conversion of images and extraction of attached files, and allows patents to be searched for chemical structures of interest. However, the curren

Julia meets RDKit

Julia is a young programming language that is getting some traction in the scientific community. It is a dynamically typed, memory safe and high performance JIT compiled language that was designed to replace languages such as Matlab, R and Python. We've been keeping an an eye on it for a while but we were missing something... yes, RDKit! Fortunately, Greg very recently added the MinimalLib CFFI interface to the RDKit repertoire. This is nothing else than a C API that makes it very easy to call RDKit from almost any programming language. More information about the MinimalLib is available directly from the source . The existence of this MinimalLib CFFI interface meant that we no longer had an excuse to not give it a go! First, we added a BinaryBuilder recipe for building RDKit's MinimalLib into Julia's Yggdrasil repository (thanks Mosè for reviewing!). The recipe builds and automatically uploads the library to Julia's general package registry. The build currently targe

New Drug Warnings Browser

As mentioned in the announcement post of  ChEMBL 29 , a new Drug Warnings Browser has been created. This is an updated version of the entity browsers in ChEMBL ( Compounds , Targets , Activities , etc). It contains new features that will be tried out with the Drug Warnings and will be applied to the other entities gradually. The new features of the Drug Warnings Browser are described below. More visible buttons to link to other entities This functionality is already available in the old entity browsers, but the button to use it is not easily recognised. In the new version, the buttons are more visible. By using those buttons, users can see the related activities, compounds, drugs, mechanisms of action and drug indications to the drug warnings selected. The page will take users to the corresponding entity browser with the items related to the ones selected, or to all the items in the dataset if the user didn’t select any. Additionally, the process of creating the join query is no