Dashboard development and backend

Spectral library dashboard

Structural formula visualization

Figure: Spectral library dashboard showing the structural formula of a selected compound

Front-end logic

A custom, Vega-lite Kibana visualization retrieves a PNG image of a structural formula from picture.ntsportal.bafg.de and renders it. The correct structure is chosen based on the first document provided by the Kibana search context. The inchikey field is extracted from the document and used to build a URL which points to the correct structure. For example, Edetol is at https://picture.ntsportal.bafg.de/NSOXQYCFHDMMGV-UHFFFAOYSA-N.png.

Figure: Example structure retrieved from https://picture.ntsportal.bafg.de/NSOXQYCFHDMMGV-UHFFFAOYSA-N.png

Back-end infrastructure

The PNGs are written asynchronously by ntsportal::createAllStructures() to the picture server. The PNG files are first saved to a designated folder and from there synchronized automatically to the image server. createAllStructures() produces the structural formulas of all compounds in the CSL as PNGs. The PNGs must be updated with this function by the NTSPortal administrator when a new CSL version is used in NTSPortal.

createAllStructures consists of 4 steps:

1. A copy of the CSL at databasePath is created in a temporary directory.
2. The compound list is extracted from the SQlite .db file with the help of the RSQlite package.
3. The SMILES code of each compound is converted to a structural formula with the rcdk package (requires rJava).
4. The formulas are exported as .png files to the targetDir – best a folder synchronized with the picture server, from where they can be accessed by Kibana. The file names are the InChiKeys of the substances.

Figure: Generation of structural formulas from CSL compound list