ChEMBL Resources


Wednesday, 22 August 2018

Jobs in the ChEMBL Team

Looking for a change of job - come and join the ChEMBL team

We currently have three vacancies for scientists wanting to help us develop the ChEMBL resources.  The positions are based at EMBL-EBI on the Wellcome Genome Campus near Cambridge, UK.  More details of these positions and how to apply can be found on the EMBL-EBI website.

Scientific Data Engineer
You will contribute to the development of robust, production data pipelines as well as prototyping novel scientific solutions. You will have excellent communication skills, able to interact with technical experts as well as scientists seeking solutions to their "real world" problems.
Your role

The job responsibilities will include:

  • Responsibility for the handling, processing and integration of data into the ChEMBL database.
  • Facilitating the deposition of datasets directly into ChEMBL by working closely with external collaborators.
  • Applying text- & data-mining techniques for the development of effective large-scale curation strategies.
  • Developing methods for the application and maintenance of ontologies in ChEMBL.
  • Working with other teams to facilitate the integration of data between different EBI resources.

Biological Curator
You will be responsible for the curation of biological data in the ChEMBL database. You will have excellent attention to details, strong communication skills and be able to interact with technical experts as well as scientists seeking solutions to their "real world" problems.

 The job responsibilities will include:
  • To curate bioactivity data in the ChEMBL database ensuring the delivery of high quality data
  • To be responsible for mapping measured bioactivity data from the scientific literature to other biological entities (proteins, cell-lines etc) using a variety of bioinformatics resources and ontologies
  • To be responsible for identifying and validating the potential therapeutic targets of drug molecules and compounds in clinical development from a variety of sources
  • To work with data depositors to help them format and curate their data to the standards required for deposition into ChEMBL
  • To manually check and annotate data by reference to the original data sources such as the scientific literature, Pharma Company pipelines and prescribing information
  • To develop semi-automated processes for identifying and correcting erroneous data

Data Scientist/Text Miner
An exciting opportunity has been created for a talented data scientist/text miner to work on project on text mining methods for the identification and extraction of drug discovery relevant data. The position is funded by the Open Targets initiative which is a public-private initiative between EMBL-EBI, GlaxoSmithKline, Biogen. Takeda, Celgene and the Sanger Institute to generate and integrate evidence on the validity of biological targets for drug development. You will work with the Open Targets partners develop pipelines to identify and integrate relevant information into the Open Targets Platform.

The job responsibilities will include:
  • Developing text mining workflows for the identification of relevant scientific publications containing chemical probe and phenotypic assay data
  • Classifying and organising the phenotypic assay data in the ChEMBL database using relevant ontologies
  • Developing a text mining pipeline to identify and extract clinical trials outcomes from public data sources
  • Working with the Open Targets partners to assess, validate and refine the resulting methods
  • Working with Open Targets core team to integrate the data into the Open Targets Platform.

Thursday, 2 August 2018

New ChEMBL Interface

We are pleased to announce that we have a beta version of a new ChEMBL interface that we would like you to try out.  It can be found here 

There are also a lot of additional features in the new interface such as free text searching. You no longer need to specify that you want to search for a compound, target, document etc. Also as you type your search, there will be suggestions made for you.

You can also filter of results to see just the subset of data you are interested in using a number of different filtering options.

However, the new interface still retains some of the old features such as compound and target report cards.  More details on the new features can be found here and we have also updated our FAQs.  But most of all we hope it is intuitive to use.

It will replace the old interface soon but before we retire the old one we would like some feedback on the new one. We will continue to evolve it over the coming months so if you would like us to consider other features or enhancements please let us know and we will try to accommodate as many suggestions as possible.  Likewise if you spot anything you think isn’t working properly please let us know.  There are several ways you can make suggestions or report errors and they are described here.

We look forward to hearing your views.

The ChEMBL Team