ChEMBL Resources

Resources:
ChEMBL
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SureChEMBL
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ChEMBL-NTD
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ChEMBL-Malaria
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The SARfaris: GPCR, Kinase, ADME
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UniChem
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DrugEBIlity
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ECBD

Tuesday, 17 April 2018

Join the ChEMBL Team!



We are looking for talented individuals to help us maintain and develop the ChEMBL and SureChEMBL resources and currently have a number of open positions within the team. If you are looking for an exciting new role and would like to work with us on the beautiful Wellcome Genome Campus, here are details of the positions:

Data Integration Scientist


We are looking for a Scientist with a passion for data integration to manage the incorporation of drug discovery data into the ChEMBL database.

Responsibilities will include:
  • Responsibility for the handling, processing and integration of data into the ChEMBL database.
  • Facilitating the deposition of datasets directly into ChEMBL through working 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.

Essential requirements include:
  • A BSc (or equivalent) in a life-science subject (e.g. biological or biomedical sciences).
  • 3+ years of postgraduate experience in scientific application development, database development or text- & data-mining, with a demonstrable track record of achievement.
  • Proficient in at least one programming/scripting language (Python knowledge is highly desirable).
  • Good knowledge of relational databases, data modelling, SQL and PL/SQL, and RESTful web-services.
  • Experience in integrating diverse data sets.

For full details and to apply for the position, please visit the EMBL website:
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01173&newlang=1&loc%5B%5D=2


Software Engineer - Dev Ops


We are seeking a talented Software Engineer/Dev Ops Developer to work on SureChEMBL, one of the largest live resources of chemistry extracted from patent data.

Responsibilities will include:
  • Maintaining and improving the SureChEMBL system;
  • Building new monitoring tools and dashboards;
  • Developing new functionalities in collaboration with colleagues and collaborators;
  • Profiling and scaling the cloud-based IaaS patent processing pipeline;
  • Optimizing the application stack for maximum speed and scalability;

Essential requirements include:
  • A minimum of 3 years of professional development experience;
  • Strong core Java Enterprise Edition development skills and understanding of Java design principles;
  • Experience of defining and creating Continuous Integration and Development environments using technologies such as Jenkins, Maven, Artifactory;
  • A solid understanding of the Open Stack platform;
  • Experience with distributed queue messaging (e.g. Amazon SQS, RabbitMQ)
  • Experience with relational databases (mySQL, PostgreSQL);
  • A solid foundation in computer science, with strong competencies in concurrency, shell scripting, and software design;

For full details and to apply for the position, please visit the EMBL website:
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01163&newlang=1&loc%5B%5D=2


Software Engineer - Web Developer


We require a passionate Web Developer who can design and develop robust solutions that deliver ChEMBL data to our extensive user community.

Responsibilities will include:
  • Developing web-based solutions to better deliver ChEMBL resources to users
  • Maintaining and further developing the infrastructure that supports interfaces on chemogenomics data
  • Working with other members of the team, collaborators and users to develop and deliver new and innovative ways to analyse and visualise ChEMBL data
  • Integrating chemogenomics data with that from other relevant resources at the EBI and beyond
  • Keeping up-to-date with relevant developments in the field of web development

Essential requirements include:
  • A BSc (or equivalent) in a technical subject (e.g. life science, computing or mathematics)
  • 3+ years postgraduate experience in front-end software development with a demonstrable track record of delivery
  • Sound programming skills, including experience of Unix and Python
  • Experience in building and using web services and good knowledge of current web technologies;
  • Knowledge of search technologies e.g. Solr/Elastic
  • Knowledge of relational databases, SQL PL/SQL and NoSQL approaches
  • Evidence of good practice in software engineering to deliver clean, extensible and robust code through rapid development cycles with documentation and version control

For full details and to apply for the position, please visit the EMBL website:
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01174&newlang=1&loc%5B%5D=2

Wednesday, 28 March 2018

Have you heard of CORBEL?






Briefly, CORBEL is an initiative of thirteen biological and medical research infrastructures, which together create a platform for harmonised user access to biological and medical technologies, biological samples and data services required by cutting-edge biomedical research.

Do you know that ChEMBL, through ELIXIR, participates to the project and provides its expertise in, among other things, identification of existing bioactivities for compounds of interest, profiling of chemotypes, target identification, data storage and distribution? But of course, CORBEL gives you access to different services working in many different biomedical areas. You want to screen the compounds you have identified and then use Electron Microscopy to observe their effect on a cell type of your interest, there are services for you! This is just an example of how CORBEL can contribute to boost your research projects(s), don’t forget we are  37 partners!  

As part of the WP4, Community Driven Cross-Infrastructure joint research – Bioscience, we were recently in Berlin to attend a Service Operator meeting and to meet the CORBEL users that requested our contribution to their project. That was a great opportunity to talk with them about their work and how ChEMBL could help them to achieve great things!

To keep it short, let’s just add that CORBEL has just launched a 2nd Open Call. To get an idea of what that might look like please have a look at the 1st Open Call selected projects. That might be the opportunity for you to submit your project and, if you request our help, for us to assist you in your work!




Tuesday, 6 March 2018

ChEMBL tissues: Increasing depth, breadth and accuracy of annotations



Our current tissue annotation efforts have been on increasing the breadth and depth of the tissue effort first started in ChEMBL 22. The figure above represents the increased depth and coverage from that initial point till now. 

We continue to use a suite of tissue ontologies namely: Uberon, Experimental Factor Ontology (http://www.ebi.ac.uk/ols/ontologies/efo), CALOHA (ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo) and Brenda Tissue Ontology ((http://www.ebi.ac.uk/ols/ontologies/bto)  to identify assays where the tissue is the assay system. We have increased the detail of information we capture to reflect the more granular tissues mentioned in the assays such as 'Popliteal lymph node' and 'Substantia nigra' pars compacta where previously the higher level term ‘lymph node’ and ‘Substantia nigra’ might have been captured.

Plasma based assays

We have recently focused annotation efforts on plasma based assays  in response to end user interest in this assays as well as acknowledging the general prevalence of plasma as an assay system for many functional/ADME assays.

Assays with multiple tissue types
We have also increased tissue curation of bioassays whose measurements are recorded across multiple tissues in a single assay e.g ‘Kidney/Liver’, ‘Heart/Liver’. In these cases, bespoke entries are created in the Tissue Dictionary, representing the tissue combination.
 
Ongoing improvements to tissue curation

·      These newly created tissue targets and assays annotated with these will be available in the next ChEMBL release (ChEMBL 24).
·      Our future web interface tissue search functionality will also make use of hierarchies inherent in the tissue ontologies to retrieve the more granular tissue terms on searching with a higher level term. An example would be that a tissue search for a high level term would include child terms of the higher level term e.g  A search for assays annotated with the tissue ‘compound eye’ UBERON:0000018 should also ideally retrieve assays annotated with direct children of this higher level term e.g ommatidium (UBERON:0000971).
·      The nature of ontological terms is such that species differences may not always be abundantly clear where single tissue term is used across different taxonomic groups to describe tissues that perform the same function in the different species but have clear anatomical differences. An example being the term eye which refers to the ‘compound eye’ UBERON:0000018 found in insects vs ‘camera type eye’ UBERON:0000019 as found in humans. We plan to use taxonomic constraint information to disambiguate cases like these and improve the correctness of mappings.
 
For queries and questions on tissue annotation-related matters please contact our help desk chembl-help@ebi.ac.uk

Tuesday, 23 January 2018

Targets in ChEMBL through the years

Evolution of targets over time


While ChEMBL was first released in 2009, the data on which it is built originate from publications extending back to 1975. Despite relatively sparse coverage from the early years in comparison to now, it is interesting to see how the publically available data for targets has grown over time. This interactive plot aims to present key data for each of ChEMBL’s targets over the years, in a style inspired by the late Hans Rosling’s TED talk on global development (if you haven't already seen it, I recommend that you watch it now!)

As shown above, dragging the slider at the bottom of the plot updates the year to reflect the data available up until that point.  The following values are shown:

  • Y-axis: The cumulative sum of compounds with a pChEMBL value for the target
  • X-axis: The maximum pChEMBL value or LLE (depending on radio button selection) achieved to date for target
  • Point Size: The maximum phase achieved for the target
  • Colour: Protein classification


Hovering the mouse over a datapoint will reveal the target's name, however as the number of points increases, it may become difficult to make sense of the data. In addition to the controls at the top of the plot, which allow you to zoom and pan the data, it is possible to filter the data by protein classification. For example, single clicking on "Enzyme" will toggle these points on and off, double clicking will turn all other points, allowing you to isolate the data for enzymes.

Use the plot to explore the target data in ChEMBL, feel free to share any interesting observations in the comments.

The plot was created using Dash and Plotly. You can view a larger version of the plot here, or download the source code here.