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. 2019 Jan 8;47(D1):D930-D940.
doi: 10.1093/nar/gky1075.

ChEMBL: towards direct deposition of bioassay data

David Mendez  1 , Anna Gaulton  1 , A Patrícia Bento  1 , Jon Chambers  1 , Marleen De Veij  1 , Eloy Félix  1 , María Paula Magariños  1   2 , Juan F Mosquera  1 , Prudence Mutowo  1 , Michal Nowotka  1 , María Gordillo-Marañón  3 , Fiona Hunter  1 , Laura Junco  1 , Grace Mugumbate  1 , Milagros Rodriguez-Lopez  1 , Francis Atkinson  1 , Nicolas Bosc  1 , Chris J Radoux  1   2 , Aldo Segura-Cabrera  1 , Anne Hersey  1 , Andrew R Leach  1
Affiliations

ChEMBL: towards direct deposition of bioassay data

David Mendez et al. Nucleic Acids Res. .

Abstract

ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In the last two years, several important improvements have been made to the database and are described here. These include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.

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Figures

Figure 1.
Figure 1.
Autocomplete function of the search bar in the new web interface. Users can retrieve a list of entities matching a selected keyword (e.g. all Targets matching ‘BRD4’) or go directly to a Report Card for a selected entity (e.g. human BRD4: CHEMBL1163125).
Figure 2.
Figure 2.
Filtering search results on the new ChEMBL interface. A default set of filters are displayed for each entity type (e.g. compounds shown here), but further filters can be added using the settings icon at the top right of the ‘Filters’ panel. Multiple filters from the same or different categories can be selected by clicking on the bars.
Figure 3.
Figure 3.
Heatmap visualization. The Heatmap view can be invoked from a set of compound/target search results by selecting the ‘Heatmap’ icon from the top-left menu bar. This will produce a heatmap showing the selected compounds or targets plotted against the targets or compounds with which they have been shown (or tested) to interact. Clicking on a cell will allow retrieval of the bioactivity data supporting that compound/target interaction.
Figure 4.
Figure 4.
Sunburst visualization showing the ChEMBL protein family classification. (A) The classification is arranged in concentric circles with major families in the centre and smaller subfamilies around the edge. (B) To zoom in or expand a family, the user can click the relevant segment in the visualization and the resulting set of targets can be retrieved using a button below the plot.
Figure 5.
Figure 5.
Retrieval of bioactivity data from search results. The ‘Browse Activities’ link above the table of search results retrieves the set of activity measurements associated with the selected entities. From this view the user can further retrieve the distinct list of compounds/targets/assays/documents, again by selecting the link above the table.
See this image and copyright information in PMC

References

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