Skip to main content

ChEMBL_18 Released

By



We are pleased to announce the release of ChEMBL_18. This version of the database was prepared on 12th March 2014 and contains:
  • 1,566,466 compound records
  • 1,359,508 compounds (of which 1,352,681 have mol files)
  • 12,419,715 activities
  • 1,042,374 assays
  • 9,414 targets
  • 53,298 documents

The web front end at https://www.ebi.ac.uk/chembl is now connected to the ChEMBL 18 data, but you can also download the data from the ChEMBL ftpsite. Please see ChEMBL_18 release notes for full details of all changes in this release.

Changes since the last release

 

New data sets

 

The ChEMBL_18 release includes the following new datasets:
  • University of Vienna G-glycoprotein (pgp) screening data
  • UCSF MMV Malaria Box screening data
  • DNDi Trypanosoma cruzi screening data
  • DrugMatrix in vivo toxicology data
In addition, 43,335 new compound records from 2015 publications in the primary literature have been added to this release. Approved drug and usan data have also been updated, with 103 new structures added.

 

Updates to the protein family classification

 

A review and update of the ChEMBL protein family classification has been carried out. The main changes are listed below:

  • New ion channel/transporter classification, based on the BPS classification
  • New epigenetic protein classification, based on SGC/ChromoHub classification
  • Modification of kinase classification, to follow Human Kinome classification

 

Assay classification and ontology mapping

 

The following annotations and classifications have been added to the ChEMBL assay data:
  • Classification of assay format (e.g., biochemical, cell-based, organism-based) using BioAssay Ontology
  • Classification of endpoints (e.g., IC50, AUC, Ki) using BioAssay Ontology
  • Addition of Physicochemical and Toxicity assay type classification
  • Mapping of assay cell-lines to CLO, EFO and Cellosaurus
  • Mapping of standard units to Unit Ontology and QUDT

 

 

Capture of assay parameters

 

A new table in the database (assay_parameters), is used to capture additional properties of assays such as dose, administration route, time points. These additional parameters are displayed on the Assay Report Card.

 

Target predictions

 

Bioactivity data for single protein targets in ChEMBL have been used to train and validate two Naive Bayesian multi-label classifier models (at <= 1uM and <= 10uM bioactivity cutoffs respectively). These models have been subsequently employed to predict biological targets for a set of approved drugs, which are displayed on in the new Target Predictions section of the Compound Report Card, where applicable. Since some of the predictions correspond to compound/target pairs that were included in the training set for the models, these are shown in white, to distinguish them from genuine predictions (coloured light yellow). Only predictions scoring >= 0.2 are included in the result tables. The models were built with open source tools such as RDKit and scikit-learn and are available upon request.



We would appreciate any feedback on this feature, and any further ideas you may have on including predicted data on top of ChEMBL experimental data.

 

UniChem connectivity mapping

 

In addition to the standard UniChem cross-references shown on the report card (based on exact InChI Key matching), a new link is included to an expanded view of UniChem cross-references, generated based on InChI connectivity layer matching (e.g.,

https://www.ebi.ac.uk/chembl/compound/unichem_connectivity/GJJFMKBJSRMPLA-DZGCQCFKSA-N). 

This expanded view shows any compounds in UniChem that share the same connectivity as the query structure, even if they have stereochemical, isotopic or protonation state differences. The differences between the query and retrieved structures are shown by their position in the table: the first column shows compounds that match in all InChI layers, while the subsequent columns show those structures that differ in stereochemistry (s column), isotope (i column), protonation state (p column), or various combinations of these layers (final four columns). A button at the top of the table gives the additional option to retrieve compounds that match individual components of a mixture or salt. Where the query structure consists of multiple components, matches to each of these components will be coloured different colours (e.g., black, blue, red). 

 

ChEMBL RDF Update

 

The ChEMBL RDF data model has been enhanced and now includes the following information:
  • Drug mechanism of action and binding site information
  • Molecule hierarchy
  • Target relationships
  • Assay format
  • Cell-line information
More information (documentation, SPARQL endpoint and example queries), about the RDF version of the ChEMBL database can be found on the EBI-RDF Platform and you can download the RDF files from the ChEMBL ftpsite.

 

Web Service Update

 

Three new Web Service calls focused on approved drugs, mechanism of action and compound forms are now available. Example calls to these methods can be seen below and also please visit the ChEMBL Web Service page for more details.


http://www.ebi.ac.uk/chemblws/targets/CHEMBL1824/approvedDrug.json
http://www.ebi.ac.uk/chemblws/compounds/CHEMBL1642/drugMechanism.json
http://www.ebi.ac.uk/chemblws/compounds/CHEMBL278020/form.json


As always, we greatly appreciate to reporting of any omissions or errors.

The ChEMBL Team
Labels:

Comments

Unknown said…
Nice work on the predictions. But how exactly are they done? I'm curious as to which features are used, and what are the performance statistics at various posterior probability cutoffs.
3 April 2014 at 10:05
Unknown said…
Hi David,
For more info see http://chembl.blogspot.co.uk/2014/04/ligand-based-target-predictions-in.html
3 April 2014 at 14:42
Post a Comment

Popular posts from this blog

ChEMBL 34 is out!

By
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.
Post a Comment
Read more

New SureChEMBL announcement

By
(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
Post a Comment
Read more

Accessing SureChEMBL data in bulk

By
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
Post a Comment
Read more

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

By jpo
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
Post a Comment
Read more

Mapping lists of IDs in ChEMBL

By
In order to facilitate the mapping of identifiers in ChEMBL, we have developed a new type of search in the ChEMBL Interface. Now, it is possible to enter a list of ChEMBL IDs and see a list of the corresponding entities. Here is an example: 1. Open the ChEMBL Interface , on the main search bar, click on 'Advanced Search': 2. Click on the 'Search by IDs' tab: 3. Select the source entity of the IDs and the destination entity that you want to map to: 4. Enter the identifiers, you can either paste them, or select a file to upload. When you paste IDs, by default it tries to detect the separator. You can also select from a list of separators to force a specific one: Alternatively, you can upload a file, the file can be compressed in GZIP and ZIP formats, this makes the transfer of the file to the ChEMBL servers faster. Examples of the files that can be uploaded to the search by IDs can be found  here . 5. Click on the search button: 6. You will be redirected to a search resul
Post a Comment
Read more