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Streamlining the Pesticide Mechanism of Action Classification

By Anonymous
Since ChEMBL 20, molecules in ChEMBL that are known pesticides have been linked to the mechanism of action classification assigned by the Fungicide Resistance Action Committee (FRAC: http://www.frac.info), Herbicide Resistance Action Committee (HRAC: http://www.hracglobal.com) or Insecticide Resistance Action Committee (IRAC: http://www.irac-online.org). These Committees provide information on the mechanism of action of key pesticides as part of ongoing efforts to combat pesticide resistant fungi, plants, and insects, and to prolong the use of existing pesticides. Supplementing ChEMBL with curated pesticide data from key organisations complements the wealth of compounds within ChEMBL explored for applications in human health, supporting a move towards a OneHealth approach. These classification schemes group pesticides both by their mode of action and chemical class. From ChEMBL 20 to ChEMBL 35 classifications were stored within ChEMBL in three tables, with three associated mapping tabl...
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New position: NLP Data Scientist/Scientific Data Engineer

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As part of a funded collaboration with Open Targets, there are two open positions as part of a team to develop a drug side effect resource: We are looking for two enthusiastic and talented NLP data scientists, cheminformaticians or bioinformaticians with experience in NLP and knowledge extraction to join the Open Targets Safety 2.0 project for a period of 3 years. You should enjoy delving into ways of addressing challenges in knowledge extraction and data standardisation, and want to contribute to open source code and resources.  The project will develop a new side effect resource for drug discovery based on the extraction of side effect data from a range of documents. Your role will focus on developing data extraction pipelines using NLP models and implementing modern NLP methods and technologies suitable to the extraction of safety data. The position provides a real opportunity to make a significant impact on a critical problem in drug discovery for the many users of the Open Ta...
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Open Position: Technical Lead Chemical Biology Services

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We are looking for a new Technical Lead to lead the technical maintenance and development of our group's services . This is an exciting opportunity for someone either from a scientific or informatics background to play a key role in our team which has a huge impact on the scientific communities that we serve. Applicants may be from anywhere in the world (visa support and relocation allowance); also note that the quoted salary is tax free and so is equivalent to the net salary from another job. If you have any questions about the role, feel free to reach out to me at oboyle@ebi.ac.uk. For more information, and to apply, click HERE !   About the Team We are looking for a Technical Lead to join the Chemical Biology Resources team at the European Bioinformatics Institute (EMBL-EBI). The Chemical Biology Resources team provides world-leading chemogenomics resources to the scientific community. ChEMBL is a database of quantitative small-molecule bioactivity data curated primarily from ...
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Adding Biomedical Annotation to SureChEMBL: Beyond the Chemical Space

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        Dear users,   Since its introduction in 2015, SureChEMBL has been a database focused on chemical annotations. We extract compound structures from patent texts, images, and Molfiles when available, and register them in our database . This chemistry-first approach is even reflected in our name.   However, we know that intellectual property documents capture far more than chemistry. This was illustrated by Stefan Senger in 2017 ( 10.1186/s13321-017-0214-2 ), who showed that compound–target interactions can appear years before being mentioned in the scientific literature.   Our first step into biomedical annotation A few years ago, we took a first step beyond chemistry by adding annotations for genes/proteins, diseases, and mechanisms of action in the SureChEMBL UI. These were generated by an in-house Natural Language Processing (NLP) model that performed reasonably well for an initial version.   Example of biomedical annotation in a pa...
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ChEBI 2.0 is here!

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ChEBI 2.0 is here! We’re excited to announce the release of ChEBI 2.0!  The next generation of the Chemical Entities of Biological Interest database. If you missed the background story and the details of the redevelopment, you can catch up in our earlier blog post here . What’s Changed: The new ChEBI web interface is live at https://www.ebi.ac.uk/chebi/   Legacy SOAP web services are deprecated — please migrate to our REST APIs  New ChEBI 2.0 data products (ontology, TSV, SDF, PostgreSQL dump) are available at https://ftp.ebi.ac.uk/pub/databases/chebi Submitter accounts have been migrated — you’ll need to reset your password before logging into the new submission portal Why ChEBI 2.0? The legacy ChEBI codebase had become increasingly difficult to maintain and update. ChEBI 2.0 has been rebuilt from the ground up with:  Simplified PostgreSQL schema  Faster search powered by Elasticsearch + RDKit  Refreshed public user interface modern infrastructure (Kuberne...
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ChEMBL Data Deposition Webinar

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     The Basics of ChEMBL Data Deposition Shortly, we are starting work on ChEMBL 37. Thus, we are running a 1 hour data depositor webinar , for anyone who is planning to deposit data to ChEMBL 37. If you are subscribed to the ChEMBL-depositors mailing list you will have heard about this already. If not, and you have an interest in depositing data to ChEMBL in future, we strongly reccommend you sign up to this  depositor mailing list . This will give you updates on the submission process and deadlines.   Webinar Info We are running on Friday 3 Oct , at 10:00 am , on Zoom . We will post the meeting link to the  ChEMBL-depositors  mailing list the day before.  Learning Objectives of the Webinar This webinar is designed to: Familiarise new depositors with the basic requirements for ChEMBL input data. Re-familiarise former depositors with the deposition process, and explain any new requirements.      A Reminder About ChEMBL 37 deadli...
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Drug Data in ChEMBL: a critical asset

By Anonymous
Breaking news  📢   We are excited to announce our new journal article that presents the comprehensive drug data in ChEMBL. The paper describes the state-of-the-art processes to curate and integrate the high-quality drug and clinical candidate drug data. The drug curation processes have been developed over more than 15 years and this is the first time that they have been published.  https://pubs.acs.org/doi/10.1021/acs.jmedchem.5c00920 Published as a 'Perspectives' article in the Journal of Medicinal Chemistry, the paper educates ChEMBL users, helping them to understand the nature of the drug and clinical candidate data and the rationale that underlies curation decisions. G iven the increasing reliance on high-quality data in computational drug discovery, AI and machine learning, the integrated nature of the drug data within the ChEMBL bioactivity resource is a critical asset. This is a bumper week for drug data in ChEMBL! On Monday, our latest ChEMBL 36 release included ...
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