New Drug Warnings Browser

As mentioned in the announcement post of ChEMBL 29, a new Drug Warnings Browser has been created. This is an updated version of the entity browsers in ChEMBL (Compounds, Targets, Activities, etc). It contains new features that will be tried out with the Drug Warnings and will be applied to the other entities gradually. The new features of the Drug Warnings Browser are described below.

Improved visualization of the download process

When the user triggers a download, the visualization of the process of creating the final file has been improved.

Improved filtering capabilities

Many filtering capabilities have been improved with the Drug Warnings Browser. The histogram filters will now always show a bar for ‘null’ values, so the user can always know how many items in the dataset have a null value for the property being shown.

For the text-based properties, users can now search and filter for specific values in the dataset. In the following example, the user can search for terms that start with ‘Cardio’ in the values of the property Warning Class in the dataset:

The matching term can be used to filter out the data.

By clicking on the 3 dots button on the histograms, users can change the presentation of the histogram.

The filters for the number-based properties now allow users to filter by a range. The absolute minimum and maximum values are calculated automatically from the values found in the dataset for that current property.

Custom Filtering

Users can now apply custom filters to the dataset, apart from the ones provided by default. Users can filter the data in more complex ways than the default provided by the predefined filters. To use them, click on the ‘Custom Filtering’ button.

Clicking on the button will open a panel that indicates whether custom filters are being applied. To edit the custom filters, click on the 'Edit Button’.

The menu that opens has 2 main sections. The section to the left shows the custom filter being applied and allows to edit it. The section to the right provides a query builder that helps users to build queries for the dataset. The custom queries are query strings of Elasticsearch, here you can find more information about the query strings.

To help users understand the structure of the data, there is a dialog that shows the available properties in the dataset.

Also some examples are available for users to apply and see how the custom filters can be created.

The query builder section helps users to create custom filters by using a graphical interface. If auto-paste is activated, the query will be pasted to the editor at the same time as it is created.

When a custom filter is being applied, an icon will indicate it when the menu is closed.

Future Plans

The Drug Warnings Browser was created to improve these 'entity browser of pages in ChEMBL. The plan is to replace the other entity browsers with the new version gradually. If you have some feedback or want to report a bug, please contact us: chembl-help@ebi.ac.uk (See also this page for more information)

Comments

Release of ChEMBL 33

We are pleased to announce the release of ChEMBL 33! This fresh release comes with a few new data soures and also some new features: we added bioactivity data for understudied SLC targets from the RESOLUTE project and included a flag for Natural Products and for Chemical Probes. An annotation for the ACTION_TYPE of a measurement was included for approx. 270 K bioactivities. We also time-stamped every document in ChEMBL with their CREATION_DATE! Have fun playing around with ChEMBL 33 over the summer and please send feedback via chembl-help@ebi.ac.uk . ChEMBL database version ChEMBL 33 release notes ___________________________________________ # This version of the database, prepared on 31/05/2023 contains: 2,399,743 compounds (of which 2,372,674 have mol files) 3,051,613 compound records (non-unique compounds) 20,334,684 activities 1,610,596 assays 15,398 targets 88,630 documents BioAssay Data Sources: Number Assays: Number

This Python InChI Key resolver will blow your mind

This scientific clickbait title introduces our promised blog post about the integration of UniChem into our ChEMBL python client. UniChem is a very important resource, as it contains information about 134 million (and counting) unique compound structures and cross references between various chemistry resources. Since UniChem is developed in-house and provides its own web services , we thought it would make sense to integrate it with our python client library . Before we present a systematic translation between raw HTTP calls described in the UniChem API documentation and client calls, let us provide some preliminary information: In order to install the client, you should use pip : pip install -U chembl_webresource_client Once you have it installed, you can import the unichem module: from chembl_webresource_client.unichem import unichem_client as unichem OK, so how to resolve an InChI Key to InChI string? It's very simple: Of course in order to reso

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

Chemistry and Nature

As the Great Big Green Week (UK) draws to a close, so does EMBL-EBI’s own Sustainability week. The Wellcome Genome Campus held events in the areas of recycling, energy use, and biodiversity. The ChEMBL team was keen to get involved and we developed our own Nature Trail event highlighting some of the bioactive compounds from the flora and fauna found on-site, and elsewhere. Our favourite examples include the sensation of mint and chilli and the glorious smell of rain! The full Nature Trail can be made available for external Public Engagement events upon request . Databases, such as ChEMBL , are large stores of structured data, including genetic, biological, and chemistry data for life sciences research. Data on the natural world is often held by wildlife organisations; this can be used to research biodiversity and species decline. Various Citizen Science initiatives mean that everyone can get involved in submitting nature records. So why not join in with the Butterfly Conservation’s B

Drug warning update: withdrawn drugs and drugs that carry a black box warning

The drug warning information in ChEMBL has been updated for version 32. In particular, the withdrawn drug data has been fully reviewed and, to assist the manual curation process, our rules have been updated, clarified and formally written. In ChEMBL, a withdrawn drug is an approved drug (ie Phase 4) that has subsequently been withdrawn for toxicity reasons. For example, a drug is assigned as 'withdrawn' if: All doses are withdrawn (and not just the highest dose). The drug is withdrawn for all populations (and not just infants). The drugs is withdrawn for all indications. Any drug withdrawn for a lack of evidence of efficacy is not included. Any drug withdrawn for drug-drug interactions is included if it is a safety-related withdrawal. A regulatory body (e.g. EMA, FDA) is the preferred source of information for the withdrawn status. The withdrawn status is mapped to an individual drug form (e.g. a parent (salt-stripped) or salt drug form within a family of compound structures

The ChEMBL-og

Search This Blog