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. 2021 Oct 24;11(11):1072.
doi: 10.3390/jpm11111072.

Mapping Compound Databases to Disease Maps-A MINERVA Plugin for CandActBase

Liza Vinhoven  1 , Malte Voskamp  1 , Manuel Manfred Nietert  1   2
Affiliations

Mapping Compound Databases to Disease Maps-A MINERVA Plugin for CandActBase

Liza Vinhoven et al. J Pers Med. .

Abstract

The MINERVA platform is currently the most widely used platform for visualizing and providing access to disease maps. Disease maps are systems biological maps of molecular interactions relevant in a certain disease context, where they can be used to support drug discovery. For this purpose, we extended MINERVA's own drug and chemical search using the MINERVA plugin starter kit. We developed a plugin to provide a linkage between disease maps in MINERVA and application-specific databases of candidate therapeutics. The plugin has three main functionalities; one shows all the targets of all the compounds in the database, the second is a compound-based search to highlight targets of specific compounds, and the third can be used to find compounds that affect a certain target. As a use case, we applied the plugin to link a disease map and compound database we previously established in the context of cystic fibrosis and, herein, point out possible issues and difficulties. The plugin is publicly available on GitLab; the use-case application to cystic fibrosis, connecting disease maps and the compound database CandActCFTR, is available online.

Keywords: data integration; disease maps; drug repurposing; drug targets; knowledge repository; systems medicine.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Concept and data flow of the plugin. Gene IDs and Chemical IDs are extracted from the disease map on MINERVA [3] (© Université du Luxembourg, 2021) and the CandActCFTR database, respectively. Using these unique identifiers, gene-chemical interactions are retrieved from the databases ChEMBL [6] (© EMBL-EBI 2018) and CTD [7] (© 2012–2021 NC State University) via the plugin. The results are then listed in the plugin and displayed in the disease map on MINERVA.
Figure 2
Figure 2
Screenshot from the MINERVA instance showing (a) a disease map and highlighted targets, and (b) a zoomed-in feature of the UI of the CandActBase plugin. The plugin interface allows the use of all functions from one window: 1. display results from compound query (ID, InChIKey, SMILES Code, chemical structure and synonyms), 2. reverse search by target from disease map, 3. button to highlight all targets of all database compounds in the disease map and 4. button to show targets of selected compound as list.
See this image and copyright information in PMC

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