Skip to main content

Interest in Links to Patents From Structures in ChEMBL

We are exploring establishing links from the ChEMBL compounds to patents. The implementation can have two basic routes....

  • Links from the interface to patents (simple and quick to do now we have UniChem).
  • Patent uri's in the database itself (more complex, and more difficult to keep up to date, but arguably more useful).

So to help our planning for next year, comments, wishes are most welcome....


Bio to Chem said…
This sounds useful but that would depend on how and what links are going to be made. What would be the source of patent-extracted structures you would match against ?
jpo said…
Well, ChEMBL is not, and cannot become, a patent database; but there is value in providing links between compounds that are in ChEMBL and the patent literature. The integration would be at the level of proving a link from a ChEMBLid to the underlying patents claiming that compound, simply as a link to the patent document. Initially for compounds, but maybe, depending on how things work out, to targets too.

As to the source of the patent structures. There are a number of initiatives underway at the moment to text-mine chemical structures from patents. We're currently not free to say what some of these sources are, but one source could be the feed from the EPO team.

These structures would be loaded into UniChem (qv) and all the lookups done there.
Bio to Chem said…
An EPO patent structure feed would link nicely to the EBI patent abstracts and the ChEMBL/UniChem links already in CiteExplore for the papers. The tricky bit is locating the exemplar in the document. The millions of Complex Work Unit-derived structures just surfaced in SCRIPDB might also be might be worth considering but are USPTO-only. For the record you already have indirect patent document links in ChEMBL because the ChemSpider entries have an InChI look-up link to SureChem. You can only open three document links (for free) but some are first-filings. I think I know what one of the other feed options might be but we will see if/when this appears!
jpo said…
Thanks for the comments. At the moment, we have no funding or resource for any of these, so our aspirations are modest :) Just links to patents from Chemblids.

A big problem with other ways of chemical patent data are shown by your other comments - indirect access through semi-open resources, with significant onus on the user to ensure they don't violate any explicit or ambiguous usage constraints/licenses.

One of the ideas of patent filings is explicitly to make things easy to find so researchers don't waste time recreating other peoples IP, and also can build on top of this. Current systems do not really allow this.....

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: .  Please see ChEMBL_29 release notes for full details of all changes in this release: 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