ChEMBL_17 Released

We are pleased to announce the release of ChEMBL_17. This version of the database, prepared on 29th August 2013 contains:

1,519,640 compound records
1,324,941 compounds (of which 1,318,187 have mol files)
12,077,491 activities
734,201 assays
9,356 targets
51,277 documents

You can download the data from the ChEMBL FTP site. For more information please read the release notes.

Data changes since the last release:

Drug mechanism of action

For all FDA-approved drugs, information regarding the mechanism of action and associated efficacy targets has been curated from primary sources, such as literature and drug prescribing information. Targets have only been included for a drug if a) the drug is believed to interact directly with the target and b) there is evidence that this interaction contributes towards the efficacy of that drug in the indication(s) for which it is approved.

Metal-containing compounds

Structures for around 3200 metal-containing compounds have been removed from the database (though the bioactivity and other information for these compounds is retained). For more information, please see the previous blog posts: http://chembl.blogspot.co.uk/2013/08/removal-of-metal-containing-compounds.html

New data sets

Several new deposited/extracted data sets have also been included in the latest release: two deposited data sets from GlaxoSmithKine for Ghrelin receptor agonists and Motilin receptor agonists, a data set of the results of screening the MMV Malaria Box compound collection for activity against Schistosoma mansoni, two data sets screening the GSK PKIS compound collection for inhibition of luciferase activity, and finally pathology data from the Open TG-GATES project.

Interface changes since the last release:

Browse Drug Targets tab

A new tab has been created to show the new mechanism of action information for FDA approved drugs together with the references from which the information was obtained, and links to the relevant drug/target report card pages.

Document Report Card

A new table has been added to the document report card, showing other ChEMBL documents that are related to the current document. Pair-wise document similarity is assessed by two components. The first component is defined by whether a document cites or is referenced by the other. The second component is defined by the amount of overlap between the compounds and biological targets reported in the two respective documents. This overlap is quantified by the Tanimoto coefficient. Documents with the highest Tanimoto similarity scores to the query document are listed in this section. For example, the following page shows 5 additional ChEMBL documents that are deemed similar to the paper currently being viewed.

Database changes since the last release:

A number of new tables have been added to store the drug mechanism of action information (please see release notes and schema documentation for full details). In addition, a number of minor changes have been made to existing tables:

The PROTEIN_FAMILY_CLASSIFICATION table has been deprecated and replaced by a new hierarchical version: PROTEIN_CLASSIFICATION.

The MOLREGNO field has been removed from the ATC_CLASSIFICATION table and moved to a new mapping table: MOLECULE_ATC_CLASSIFICATION.

The MOLFORMULA field has been moved from the COMPOUND_STRUCTURES table to the COMPOUND_PROPERTIES table (and renamed).

The ChEMBL Team

Comments

Egon Willighagen said…

Can you make available the list CHEMBL ids of those 3200 metal-containing compounds?

17 September 2013 at 08:18

ChEMBL 34 is out!

We are delighted to announce the release of ChEMBL 34, which includes a full update to drug and clinical candidate drug data. This version of the database, prepared on 28/03/2024 contains: 2,431,025 compounds (of which 2,409,270 have mol files) 3,106,257 compound records (non-unique compounds) 20,772,701 activities 1,644,390 assays 15,598 targets 89,892 documents Data can be downloaded from the ChEMBL FTP site: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/ Please see ChEMBL_34 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/chembl_34_release_notes.txt New Data Sources European Medicines Agency (src_id = 66): European Medicines Agency's data correspond to EMA drugs prior to 20 January 2023 (excluding vaccines). 71 out of the 882 newly added EMA drugs are only authorised by EMA, rather than from other regulatory bodies e.g.

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

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

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

The ChEMBL-og

Search This Blog