ChEMBL_19 Released - Now with Crop Protection Data!

We are pleased to announce the release of ChEMBL_19. This version of the database was prepared on 3rd July 2014 and contains:

1,637,862 compound records
1,411,786 compounds (of which 1,404,752 have molfiles)
12,843,338 bioactivities
1,106,285 bioassays
10,579 targets
57,156 abstracted documents

Data can be downloaded from the ChEMBL ftpsite. Please see ChEMBL_19 release notes for full details of the changes in this release.

New crop protection data

We have now expanded the content of ChEMBL to include data relevant to crop protection research. Bioactivity data covering insecticides, fungicides and herbicides were extracted from a number of different journals such as J. Agric. Food. Chem., J. Pesticide Sci., Crop Protection and Pest Manag. Sci. The addition of this dataset to ChEMBL was funded by Syngenta. In total, more than 40K compound records and 245K activities were added in this dataset. These data are included in the 'Scientific Literature' data source and can be retrieved from the ChEMBL interface using the taxonomy browser ('Browse Targets' -> 'Taxonomy') or through assay keyword searches (e.g., 'insecticidal', 'herbicidal').

Other changes since the last release

New neglected disease data sets

ChEMBL_19 includes the following data sets:

MMV malaria box Plasmodium falciparum screening data deposited by Eisai
MMV malaria box Onchocerca lienalis screening data deposited by Northwick Park Institute for Medical Research
MMV malaria box Cryptosporidium parvum screening data deposited by the University of Vermont
Trypanosoma cruzi fenarimol series screening data deposited by Drugs for Neglected Diseases Initiative (DNDi)
Plasmodium falciparum screening data from the Open Source Malaria project.

Hepatotoxicity data

Hepatotoxicity information for more than 1,200 compounds has been extracted from the following publication, relating to the 14th edition of the Drug hepatotoxicity bibliographic database:

Biour M, Ben Salem C, Chazouillères O, Grangé JD, Serfaty L and Poupon R. [Drug-induced liver injury; fourteenth updated edition of the bibliographic database of liver injuries and related drugs]. Gastroenterol. Clin. Biol., 2004, 28(8-9), 720-759.

New journal coverage
We are now pleased to be able to include MedChemComm in our list of journals for routine data extraction. ChEMBL_19 includes 120 articles from this excellent journal, published between 2013 and 2014. We are most grateful to the RSC for access to the source journal material. We will post more on this exciting new partnership in a future blog post!

Interface enhancements

New compound sketcher:
The ligand search now provides ChemAxon's Marvin JS sketcher as default for substructure/similarity searches.

Cochrane Collaboration reviews and British National Formulary (BNF) entries:
For drugs, the compound report card now provides links to any available Cochrane reviews and entries in the British National Formulary.

UniChem cross references:
UniChem now contains two additional sources: NMRShiftDB and the LINCS program. Cross references to these databases (where the compound occurs in the relevant source) are now provided on compound report card pages.

As usual, contact us at chembl-help@ebi.ac.uk for any questions/feedback.

The ChEMBL Team

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

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