Skip to main content

ChEMBL 26 Released

By


We are pleased to announce the release of ChEMBL_26

This version of the database, prepared on 10/01/2020 contains:

  • 2,425,876 compound records
  • 1,950,765 compounds (of which 1,940,733 have mol files)
  • 15,996,368 activities
  • 1,221,311 assays
  • 13,377 targets
  • 76,076 documents
You can query the ChEMBL 26 data online via the ChEMBL Interface and you can also download the data from the ChEMBL FTP site. Please see ChEMBL_26 release notes for full details of all changes in this release.

Changes since the last release:

* Deposited Data Sets:

CO-ADD antimicrobial screening data:
Two new data sets have been included from the Community for Open Access Drug Discovery (CO-ADD). These data sets are screening of the NIH NCI Natural Product Set III in the CO-ADD assays (src_id = 40, Document ChEMBL_ID = CHEMBL4296183, DOI = 10.6019/CHEMBL4296183) and screening of the NIH NCI Diversity Set V in the CO-ADD assays (src_id = 40, Document ChEMBL_ID = CHEMBL4296182, DOI = 10.6019/CHEMBL4296182).

HESI - Evaluation of the utility of stem-cell derived cardiomyocytes for drug proarrhythmic potential (src_id = 49, Document ChEMBL_ID = CHEMBL4295262 , DOI = 10.6019/CHEMBL4295262). Summary assay results for this data set have been included in ChEMBL_26 and further supplementary data will be added in ChEMBL_27.

* Changes to structure-processing and compound properties:
We are now using RDKit for almost all of our compound-related processing. For the first time in ChEMBL_26, this will include compound standardization, salt-stripping, generation of canonical smiles, structural alerts, image depiction, substructure searches and similarity searches (via FPSim2: https://github.com/chembl/FPSim2). Therefore, all molecules have been reprocessed and you may notice some differences in molfiles, smiles and structure search results compared with previous releases. The ChEMBL structure curation pipeline has been released as an open source package: https://github.com/chembl/ChEMBL_Structure_Pipeline, and incorporated into our Beaker web services (see below). More information can be found here: http://chembl.blogspot.com/2020/02/chembl-compound-curation-pipeline.html.

We are also now using ChemAxon tools to calculate most acidic and basic pKa, logP and logD (pH 7.4) predictions, rather than ACDLabs software. These properties have therefore been recalculated and renamed in the database.

* Target Predictions:
Target predictions in ChEMBL are now generated by a new method, using conformal prediction (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0325-4). A docker image is available for those wishing to use the models locally: https://hub.docker.com/repository/docker/chembl/mcp (see https://chembl.blogspot.com/2020/01/new-chembl-ligand-based-target.html for more information). We also plan to provide a new target prediction web service in the future. The current target prediction web service (https://www.ebi.ac.uk/chembl/api/data/target_prediction/) has now been deprecated.

* Updated Data Sets:
Scientific Literature
Patent Bioactivity Data
Orange Book
USP Dictionary of USAN and International Drug Names
Clinical Candidates
WHO Anatomical Therapeutic Chemical Classification
British National Formulary
Manually Added Drugs

Database changes:

# Columns Added:

CELL_DICTIONARY
CELL_ONTOLOGY_ID VARCHAR2(10) ID for the corresponding cell type in the Cell Ontology

VARIANT_SEQUENCES
TAX_ID   NUMBER(11,0) NCBI Tax ID for the organism from which the sequence was obtained

COMPOUND_PROPERTIES
CX_MOST_APKA NUMBER(9,2) The most acidic pKa calculated using ChemAxon v17.29.0
CX_MOST_BPKA NUMBER(9,2) The most basic pKa calculated using ChemAxon v17.29.0
CX_LOGP NUMBER(9,2) The calculated octanol/water partition coefficient using ChemAxon v17.29.0
CX_LOGD NUMBER(9,2) The calculated octanol/water distribution coefficient at pH7.4 using ChemAxon v17.29.0

# Columns Removed:

COMPOUND_PROPERTIES
ACD_MOST_APKA Replaced by CX_MOST_APKA
ACD_MOST Replaced by CX_MOST_BPKA
ACD_LOGP Replaced by CX_LOGP
ACD_LOGD Replaced by CX_LOGD


Funding acknowledgements:

Work contributing to ChEMBL26 was funded by the Wellcome Trust, EMBL Member States, Open Targets, National Institutes of Health (NIH), EU Innovative Medicines Initiative 2 (IMI2) and EU Horizon 2020 programmes. Please see https://chembl.gitbook.io/chembl-interface-documentation/acknowledgments for more details.


If you require further information about ChEMBL, please contact us: chembl-help@ebi.ac.uk

# To receive updates when new versions of ChEMBL are available, please sign up to our mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/chembl-announce
# For general queries/feedback please email: chembl-help@ebi.ac.uk
# For details of upcoming webinars, please see: http://chembl.blogspot.com/search/label/Webinar
Labels:

Comments

Post a Comment

Popular posts from this blog

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

Legacy SureChEMBL retirement

By
Dear SureChEMBL users, About six months ago, we introduced the new version of SureChEMBL . It brought significant improvements in terms of performance and stability, and it also allows us to implement new functionalities. After the survey at the beginning of the year, we prioritised what should be delivered first. You should see the materialisation of our work in the coming months. As originally announced when the new SureChEMBL was introduced, the plan was to shut down the old system permanently to focus all our resources on the new SureChEMBL. This time has come, so expect www.surechembl-legacy.org to be unreachable in the coming days with no turning back! Consequently, and in parallel, the new SureChEMBL will lose its Beta status, and we will stop referring to it as the new version. This does not mean we are reducing our efforts to improve our system; on the contrary, this removes a distraction! If you have any feedback, you can contact us directly at surechembl-help@ebi.ac.uk . W
Post a Comment
Read more

ChEMBL & SureChEMBL anniversary symposium

By
  In 2024 we celebrate the 15th anniversary of the first public release of the ChEMBL database as well as the 10th anniversary of SureChEMBL. To recognise this important landmark we are organising a two-day symposium to celebrate the work achieved by ChEMBL and SureChEMBL, and look forward to its future.   Save the date for the ChEMBL 15 Year Symposium October 1-2, 2024     Day one will consist of four workshops, a basic ChEMBL drug design workshop; an advanced ChEMBL workshop (EUbOPEN community workshop); a ChEMBL data deposition workshop; and a SureChEMBL workshop. Day two will consist of a series of talks from invited speakers, a few poster flash talks, a local nature walk, as well as celebratory cake. During the breaks, the poster session will be a great opportunity to catch up with other users and collaborators of the ChEMBL resources and chat to colleagues, co-workers and others to find out more about how the database is being used. Lunch and refreshments will be pro
Post a Comment
Read more

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

A python client for accessing ChEMBL web services

By
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
1 comment
Read more