ChEMBL_15 Released

We are pleased to announce the release of ChEMBL_15. This version of the database was prepared on 23rd January 2013 and contains:

1,434,432 compound records
1,254,575 compounds (of which 1,251,913 have mol files)
10,509,572 activities
679,259 assays
9,570 targets
48,735 documents
17 activity data sources

You can download the data from the ChEMBL ftpsite: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/

Please see chembl_15_release_notes.txt for full details of all changes in this release, including important schema changes!

Data changes since the last release:
We have made several major changes/additions to the data in ChEMBL_15:

Incorporation of data from the USP Dictionary of USAN and International Drug Names.
Incorporation of monoclonal antibody clinical candidates and sequences.
Creation of targets for protein complexes and protein families.
Standardisation of activity data and identification of potential issues.
Annotation of predicted compound binding domains for subset of activity data.

These data sets are described in more detail in the release notes and will also be the subject of future blog posts. In addition, we have incorporated new data from the following sources:

Open TG-GATEs
TP-search transporter database
MMV Malaria Box screening data
GSK Tuberculosis screening data
GSK deposited supplementary data
DNDi Trypanosoma brucei screening data
Harvard malaria screening data
WHO-TDR malaria screening data

Database changes since the last release:

This release of ChEMBL contains major changes to the schema and data model, particularly around the representation of protein targets.

Please see the release notes, ERD and schema documentation for more details of these changes. We will also run a series of webinars over the coming weeks, describing the new schema and the changes.

Interface changes since the last release:

New data tables have been introduced to display search results and bioactivity data. These tables allow users to customise the display and choose which columns they want to include. By default, a standard set of columns are included in the view, but additional columns can be added by clicking on the show/hide button above the table.

A BLAST search for biotherapeutic drugs has been included on the 'Ligand Search' tab (formerly 'compound search'), allowing retrieval of protein drugs by sequence similarity.

The 'Browse Drugs' tab now includes information for monoclonal antibody clinical candidates and compounds with USANs in addition to approved drugs. Additional fields have been added and drug icons have been divided into two sets representing structure-specific information (green) and product-specific information (blue) - the latter are shown only for approved drugs.

(btw the picture above is built from ChEMBL assay descriptions - thanks to George)

Comments

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

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

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

The ChEMBL-og

Search This Blog