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Pathogen data in ChEMBL



Infectious disease is a leading cause of death globally and bioactivity data against pathogens (fungi, bacteria, viruses, and parasites) is an important category in ChEMBL, especially in light of the ongoing pandemic. In ChEMBL version 29, there are over 2 M bioactivity data points against fungal, bacterial or viral targets (for 460 K compounds) available for pathogen-related research.


How can I find pathogen data?


On the ChEMBL interface, the organism taxonomy is available as a filter that can be applied to bioactivity data. A sunburst visualisation of the organism taxonomy is also provided as an easy starting point to explore targets according to their taxonomy.



In the full database, the organism_classification table holds the underlying data and can be used in bespoke SQL queries. For example, queries may be performed to extract high level pathogen data such as all bioactivity data for small molecules screened against bacterial targets (example below) or more specific subsets focused on gram-positive pathogens or on a single bacterial species. The target type includes whole organisms as well as molecular targets (proteins, nucleic acids etc.) and additional filters can be applied to filter the target type as necessary.


What are the sources of pathogen data in ChEMBL?

We routinely extract bioactivity data from core medicinal chemistry journals and also accept deposited data (a full list can be found in the source table). In recent releases, data deposited by the Community for Open Antimicrobial Drug Discovery (CO-ADD, University of Queensland & Wellcome Trust) has enhanced our pathogen coverage. CO-ADD is an open-access, not-for-profit initiative whereby compounds provided by researchers and industry scientists are screened against a clinically relevant panel of bacteria and fungi. So far, 100 K activities (against ~ 24 K compounds) have been provided through CO-ADD. Since CO-ADD may re-screen hits against resistant bacterial strains or in cytotoxicity assays, more comprehensive data is available for some compounds. There are now 31 CO-ADD datasets in ChEMBL 29 (data source: src_ID 40) with more expected in upcoming releases.


ChEMBL also has a dedicated Neglected Tropical Disease repository (ChEMBL-NTD) for open-access primary screening and medicinal chemistry data directed at key parasites causing endemic tropical diseases. In addition, 22 datasets from screens of the ‘Malaria Box' (MMV) compound set are also provided through ChEMBL ensuring good coverage of key parasites. Currently, there are ~ 950 K activities for Plasmodium species alone.


Finally, ChEMBL version 27 was a special SARS-CoV-2 release focused on large-scale drug screening studies for anti-viral activity, in particular cell-based assays with well-characterised compounds. Rapid integration of SARS-CoV-2 activity data into ChEMBL provided a contribution towards the COVID-19 effort and several follow-up datasets have since been captured in subsequent releases.


Questions? Please get in touch on the Helpdesk or have a look through our training materials and FAQs.

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