Skip to main content

ChEMBL 21 web services update






Traditionally, along with the release of the new ChEMBL version, we have made a few updates to our RESTful API. Below you can find a short description of the most important changes:

 

Data API (https://www.ebi.ac.uk/chembl/api/data/docs):

1. New resources: Since ChEMBL 21 introduced a few new tables, we have made them available via the API. The new resources are:

Moreover, the target_component endpoint has been enhanced to provide a list of related GO terms.

2. Solr-based search: a very popular feature request was the ability to search resources by a keyword. A form of searching was already possible before, using filtering terms, such as [i]contains,[i]startswith and [i]endswtith filters. For example, in order to search molecules for 'metazide' in their preferred name, this filter can be used:


However, this approach has many drawbacks:
  • it's executed on the database level and can be very slow
  • in order to search in several attributes, you have to add the filter separately to each of them, which can result with a very long tail of filters
  • you can't search in one-to-many/many-to-many attributes (for example you cannot search molecule by its synonym because a molecule can have many synonyms)
The good news is that in order to solve this problem, we implemented a solr-based solution using django-haystack. Let's just jump straight into examples:

What if we want to search for some term in molecules, targets and assays at once? No problem, the chembl_id_lookup endpoint can be used for this, for example searching for 'morphine' will look like:


Looking at the results of the last request, it's very easy to tell (by examining the 'entity_type' attribute) that a large number of compounds and assays were returned.

Another important thing to note is that every result of search query has a 'score' attribute, indicating the relevancy of the given result. The results are sorted by the score descending (i.e. the most relevant are always first) and although you can add additional filters, for example:

you cannot change ordering by appending 'order_by=...' attribute.

You may ask, why do we only offer searching for 3 resources (well, 4 including the chembl_id_lookup)? This is because these resources are most popular and most important but we are planning to add more (such as searching in document abstracts, cell descriptions, activities) in the near future. If you have any suggestions about which resources should offer search functionality in the first place, please let us know in comments or write your suggestions to chembl-help@ebi.ac.uk. You can easily check which resources offer searching by looking at our live documentation, where all the searching methods are listed.

Furthermore, we would also appreciate your feedback about the quality of search results. If you believe that some results should have higher relevancy score than others and currently that's not the case, let us know so we can properly adjust boosts.

3. Compound images have transparent background by default. So now you can use them regardless of the color scheme used in your website:





 It's also possible to explicitly specify background color, by appending the 'bgColor=color_name' attribute for example in order to get a nice and warm orange background you have do:



The colour names are the standard names defined for HTML, you can check the full list here.

4. Datatables support: Datatables is one of the most popular jQuery plugins for rendering tabular data. In order for you to use it in a generic way (i.e. write the code in such a way it can use datatables to render data from any API endpoint), we have to be able to provide definitions of columns (e.g. how many columns we have for a given endpoint, are they searchable, sortable, what type of data they contain). This is possible using the schema API method (for example: https://www.ebi.ac.uk/chembl/api/data/molecule/schema.json), that describes every resource in a vary detailed way; however, the data provided by the schema has to be transformed to the format compatible with datatables. This is why we decided to provide another method, which is directly compatible with datatables: https://www.ebi.ac.uk/chembl/api/data/molecule/datatables.json.

Below is an example code snippet that renders a datatable from the target resource. Click on the 'Result' tab to see the table - you can sort by columns, change pages and set the number of rows displayed per page. Notice that if you change the name of the resource in the first line of code (from 'target' to 'source' or 'assay' for example), the columns and data will change as well.



Utils API (https://www.ebi.ac.uk/chembl/api/utils/docs):

There is a small update to the utilities (Beaker) part of the API. There is a new method called ctab2xyz, which converts a molfile to the xyz file format. You will notice the new method is now available in the live docs. Also the compound rendering code has been improved so it's now compatible with the latest versions of Pillow library.

Python client (https://github.com/chembl/chembl_webresource_client):

Our official Python client library has been updated as well in order to reflect recent changes. Just to remind you, in order to get the latest version of the client, you should install it via pip:

pip install -U chembl_webresource_client

Some examples of using recently added resources (drug indications, GO slim, drug metabolism):



Searching is exposed as well, examples below:



Another important change to the client is the integration with UniChem API. The latter deserves a separate blog post, so stay tuned.

Comments

Popular posts from this blog

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

ChEMBL 29 Released

  We are pleased to announce the release of ChEMBL 29. This version of the database, prepared on 01/07/2021 contains: 2,703,543 compound records 2,105,464 compounds (of which 2,084,724 have mol files) 18,635,916 activities 1,383,553 assays 14,554 targets 81,544 documents Data can be downloaded from the ChEMBL FTP site:   https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29 .  Please see ChEMBL_29 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29/chembl_29_release_notes.txt New Deposited Datasets EUbOPEN Chemogenomic Library (src_id = 55, ChEMBL Document IDs CHEMBL4649982-CHEMBL4649998): The EUbOPEN consortium is an Innovative Medicines Initiative (IMI) funded project to enable and unlock biology in the open. The aims of the project are to assemble an open access chemogenomic library comprising about 5,000 well annotated compounds covering roughly 1,000 different proteins, to synthesiz

Identifying relevant compounds in patents

  As you may know, patents can be inherently noisy documents which can make it challenging to extract drug discovery information from them, such as the key targets or compounds being claimed. There are many reasons for this, ranging from deliberate obfuscation through to the long and detailed nature of the documents. For example, a typical small molecule patent may contain extensive background information relating to the target biology and disease area, chemical synthesis information, biological assay protocols and pharmacological measurements (which may refer to endogenous substances, existing therapies, reaction intermediates, reagents and reference compounds), in addition to description of the claimed compounds themselves.  The SureChEMBL system extracts this chemical information from patent documents through recognition of chemical names, conversion of images and extraction of attached files, and allows patents to be searched for chemical structures of interest. However, the curren

Julia meets RDKit

Julia is a young programming language that is getting some traction in the scientific community. It is a dynamically typed, memory safe and high performance JIT compiled language that was designed to replace languages such as Matlab, R and Python. We've been keeping an an eye on it for a while but we were missing something... yes, RDKit! Fortunately, Greg very recently added the MinimalLib CFFI interface to the RDKit repertoire. This is nothing else than a C API that makes it very easy to call RDKit from almost any programming language. More information about the MinimalLib is available directly from the source . The existence of this MinimalLib CFFI interface meant that we no longer had an excuse to not give it a go! First, we added a BinaryBuilder recipe for building RDKit's MinimalLib into Julia's Yggdrasil repository (thanks Mosè for reviewing!). The recipe builds and automatically uploads the library to Julia's general package registry. The build currently targe

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. More visible buttons to link to other entities This functionality is already available in the old entity browsers, but the button to use it is not easily recognised. In the new version, the buttons are more visible. By using those buttons, users can see the related activities, compounds, drugs, mechanisms of action and drug indications to the drug warnings selected. The page will take users to the corresponding entity browser with the items related to the ones selected, or to all the items in the dataset if the user didn’t select any. Additionally, the process of creating the join query is no