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....

Comments

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 ?

27 November 2011 at 11:58

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.

27 November 2011 at 13:48

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!

4 December 2011 at 14:22

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.....

5 December 2011 at 06:00

New SureChEMBL announcement

(Generated with DALL-E 3 ∙ 30 October 2023 at 1:48 pm) We have some very exciting news to report: the new SureChEMBL is now available! Hooray! What is SureChEMBL, you may ask. Good question! In our portfolio of chemical biology services, alongside our established database of bioactivity data for drug-like molecules ChEMBL , our dictionary of annotated small molecule entities ChEBI , and our compound cross-referencing system UniChem , we also deliver a database of annotated patents! Almost 10 years ago , EMBL-EBI acquired the SureChem system of chemically annotated patents and made this freely accessible in the public domain as SureChEMBL. Since then, our team has continued to maintain and deliver SureChEMBL. However, this has become increasingly challenging due to the complexities of the underlying codebase. We were awarded a Wellcome Trust grant in 2021 to completely overhaul SureChEMBL, with a new UI, backend infrastructure, and new f

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

New Drug Approvals - Pt. XVII - Telavancin (Vibativ)

The latest new drug approval, on 11th September 2009 was Telavancin - which was approved for the treatment of adults with complicated skin and skin structure infections (cSSSI) caused by susceptible Gram-positive bacteria , including Staphylococcus aureus , both methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) strains. Telavancin is also active against Streptococcus pyogenes , Streptococcus agalactiae , Streptococcus anginosus group (includes S. anginosus, S. intermedius and S. constellatus ) and Enterococcus faecalis (vancomycin susceptible isolates only). Telavancin is a semisynthetic derivative of Vancomycin. Vancomycin itself is a natural product drug, isolated originally from soil samples in Borneo, and is produced by controlled fermentation of Amycolatopsis orientalis - a member of the Actinobacteria . Telavancin has a dual mechanism of action, firstly it inhibits bacterial cell wall synthesis by interfering with the polymerization and cross-linking of peptid

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

LSH-based similarity search in MongoDB is faster than postgres cartridge.

TL;DR: In his excellent blog post , Matt Swain described the implementation of compound similarity searches in MongoDB . Unfortunately, Matt's approach had suboptimal ( polynomial ) time complexity with respect to decreasing similarity thresholds, which renders unsuitable for production environments. In this article, we improve on the method by enhancing it with Locality Sensitive Hashing algorithm, which significantly reduces query time and outperforms RDKit PostgreSQL cartridge . myChEMBL 21 - NoSQL edition Given that NoSQL technologies applied to computational chemistry and cheminformatics are gaining traction and popularity, we decided to include a taster in future myChEMBL releases. Two especially appealing technologies are Neo4j and MongoDB . The former is a graph database and the latter is a BSON document storage. We would like to provide IPython notebook -based tutorials explaining how to use this software to deal with common cheminformatics p

The ChEMBL-og

Search This Blog